Mercurial > repos > tduigou > cloning_simulation
comparison output.json @ 0:dc450979fcd4 draft
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
| author | tduigou |
|---|---|
| date | Fri, 16 May 2025 09:39:03 +0000 |
| parents | |
| children | 044d36066cb3 |
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| -1:000000000000 | 0:dc450979fcd4 |
|---|---|
| 1 { | |
| 2 "summary": { | |
| 3 "num_errors": 0, | |
| 4 "num_failures": 0, | |
| 5 "num_skips": 0, | |
| 6 "num_tests": 6 | |
| 7 }, | |
| 8 "tests": [ | |
| 9 { | |
| 10 "data": { | |
| 11 "inputs": { | |
| 12 "adv|use_file_names_as_ids": true, | |
| 13 "assembly_csv": { | |
| 14 "id": "a2e8f3fd1611e7f5", | |
| 15 "src": "hda" | |
| 16 }, | |
| 17 "assembly_plan_name": "Type2sRestrictionAssembly", | |
| 18 "genbank_files": { | |
| 19 "id": "1d1943aa60deb628", | |
| 20 "src": "hdca" | |
| 21 }, | |
| 22 "topology": "circular" | |
| 23 }, | |
| 24 "job": { | |
| 25 "command_line": "mkdir 'outdir_zip' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmps36anksu/files/6/a/4/dataset_6a407f29-14a2-4358-8781-97a5a60006bf.dat,/tmp/tmps36anksu/files/9/c/0/dataset_9c05120b-2a93-4298-a718-2db482dec9e0.dat,/tmp/tmps36anksu/files/e/9/d/dataset_e9dd6c4a-5d1c-48d6-b072-bb67929590f5.dat,/tmp/tmps36anksu/files/c/2/a/dataset_c2a67b9c-bd0d-483b-b229-1f396bc8c275.dat,/tmp/tmps36anksu/files/5/3/d/dataset_53dc6b3e-3d2b-4fb7-b279-8b7204ae8d00.dat,/tmp/tmps36anksu/files/4/0/f/dataset_40fa89b4-5e49-467e-aa6a-d4b8c9b8a8b0.dat,/tmp/tmps36anksu/files/1/4/b/dataset_14b815cb-038e-4836-bb4e-3f049395271c.dat,/tmp/tmps36anksu/files/3/2/7/dataset_32719970-8009-4818-a623-ba980af84d70.dat,/tmp/tmps36anksu/files/6/8/e/dataset_68e30a2d-a44d-40e6-a619-efa1e8cd6e4b.dat,/tmp/tmps36anksu/files/2/3/c/dataset_23c06fae-96cc-4ff8-9e23-111139ce1a92.dat,/tmp/tmps36anksu/files/d/2/9/dataset_d29c16a7-2470-418e-a8f1-1da7c5372dde.dat,/tmp/tmps36anksu/files/2/9/0/dataset_290bfdf4-f595-42f1-a2f0-0f9a9d8e71df.dat' --domesticated_seq '' --assembly_csv '/tmp/tmps36anksu/files/4/2/0/dataset_420c4b07-ea17-4e63-9f48-4cc364e28432.dat' --assembly_plan_name 'Type2sRestrictionAssembly' --file_name_mapping '/tmp/tmps36anksu/files/6/a/4/dataset_6a407f29-14a2-4358-8781-97a5a60006bf.dat:part_A.gb,/tmp/tmps36anksu/files/9/c/0/dataset_9c05120b-2a93-4298-a718-2db482dec9e0.dat:part_B.gb,/tmp/tmps36anksu/files/e/9/d/dataset_e9dd6c4a-5d1c-48d6-b072-bb67929590f5.dat:part_C.gb,/tmp/tmps36anksu/files/c/2/a/dataset_c2a67b9c-bd0d-483b-b229-1f396bc8c275.dat:part_D.gb,/tmp/tmps36anksu/files/5/3/d/dataset_53dc6b3e-3d2b-4fb7-b279-8b7204ae8d00.dat:part_E.gb,/tmp/tmps36anksu/files/4/0/f/dataset_40fa89b4-5e49-467e-aa6a-d4b8c9b8a8b0.dat:part_F.gb,/tmp/tmps36anksu/files/1/4/b/dataset_14b815cb-038e-4836-bb4e-3f049395271c.dat:part_G.gb,/tmp/tmps36anksu/files/3/2/7/dataset_32719970-8009-4818-a623-ba980af84d70.dat:part_H.gb,/tmp/tmps36anksu/files/6/8/e/dataset_68e30a2d-a44d-40e6-a619-efa1e8cd6e4b.dat:part_I.gb,/tmp/tmps36anksu/files/2/3/c/dataset_23c06fae-96cc-4ff8-9e23-111139ce1a92.dat:part_J.gb,/tmp/tmps36anksu/files/d/2/9/dataset_d29c16a7-2470-418e-a8f1-1da7c5372dde.dat:part_K.gb,/tmp/tmps36anksu/files/2/9/0/dataset_290bfdf4-f595-42f1-a2f0-0f9a9d8e71df.dat:part_L.gb' --file_name_mapping_dom '' --use_file_names_as_id 'true' --outdir_simulation 'outdir_zip' --output_simulation 'output_zip.zip' --enzyme 'auto' --topology 'circular'&& cp 'output_zip.zip' '/tmp/tmps36anksu/job_working_directory/000/14/outputs/dataset_19827d46-96d8-48c8-b434-17f9e4732aec.dat'", | |
| 26 "command_version": "", | |
| 27 "copied_from_job_id": null, | |
| 28 "create_time": "2025-05-16T08:54:45.629427", | |
| 29 "dependencies": [], | |
| 30 "exit_code": 0, | |
| 31 "external_id": "69472", | |
| 32 "galaxy_version": "24.2", | |
| 33 "handler": null, | |
| 34 "history_id": "1d1943aa60deb628", | |
| 35 "id": "306d449b91ecb0a3", | |
| 36 "inputs": { | |
| 37 "assembly_csv": { | |
| 38 "id": "a2e8f3fd1611e7f5", | |
| 39 "src": "hda", | |
| 40 "uuid": "420c4b07-ea17-4e63-9f48-4cc364e28432" | |
| 41 }, | |
| 42 "genbank_files1": { | |
| 43 "id": "1d1943aa60deb628", | |
| 44 "src": "hda", | |
| 45 "uuid": "6a407f29-14a2-4358-8781-97a5a60006bf" | |
| 46 }, | |
| 47 "genbank_files10": { | |
| 48 "id": "b55875807068e59e", | |
| 49 "src": "hda", | |
| 50 "uuid": "23c06fae-96cc-4ff8-9e23-111139ce1a92" | |
| 51 }, | |
| 52 "genbank_files11": { | |
| 53 "id": "4b64a67f616af776", | |
| 54 "src": "hda", | |
| 55 "uuid": "d29c16a7-2470-418e-a8f1-1da7c5372dde" | |
| 56 }, | |
| 57 "genbank_files12": { | |
| 58 "id": "1fda217ac9617c88", | |
| 59 "src": "hda", | |
| 60 "uuid": "290bfdf4-f595-42f1-a2f0-0f9a9d8e71df" | |
| 61 }, | |
| 62 "genbank_files2": { | |
| 63 "id": "13a3899f03fff34a", | |
| 64 "src": "hda", | |
| 65 "uuid": "9c05120b-2a93-4298-a718-2db482dec9e0" | |
| 66 }, | |
| 67 "genbank_files3": { | |
| 68 "id": "6872e1ad22eb2e5d", | |
| 69 "src": "hda", | |
| 70 "uuid": "e9dd6c4a-5d1c-48d6-b072-bb67929590f5" | |
| 71 }, | |
| 72 "genbank_files4": { | |
| 73 "id": "248d7f69d2402068", | |
| 74 "src": "hda", | |
| 75 "uuid": "c2a67b9c-bd0d-483b-b229-1f396bc8c275" | |
| 76 }, | |
| 77 "genbank_files5": { | |
| 78 "id": "a363c57bce5ddac4", | |
| 79 "src": "hda", | |
| 80 "uuid": "53dc6b3e-3d2b-4fb7-b279-8b7204ae8d00" | |
| 81 }, | |
| 82 "genbank_files6": { | |
| 83 "id": "8ab843ac4a5890da", | |
| 84 "src": "hda", | |
| 85 "uuid": "40fa89b4-5e49-467e-aa6a-d4b8c9b8a8b0" | |
| 86 }, | |
| 87 "genbank_files7": { | |
| 88 "id": "6206f91299006d13", | |
| 89 "src": "hda", | |
| 90 "uuid": "14b815cb-038e-4836-bb4e-3f049395271c" | |
| 91 }, | |
| 92 "genbank_files8": { | |
| 93 "id": "278f145ab0478700", | |
| 94 "src": "hda", | |
| 95 "uuid": "32719970-8009-4818-a623-ba980af84d70" | |
| 96 }, | |
| 97 "genbank_files9": { | |
| 98 "id": "84aedadb70ef205b", | |
| 99 "src": "hda", | |
| 100 "uuid": "68e30a2d-a44d-40e6-a619-efa1e8cd6e4b" | |
| 101 } | |
| 102 }, | |
| 103 "job_messages": [], | |
| 104 "job_metrics": [], | |
| 105 "job_runner_name": null, | |
| 106 "job_stderr": "", | |
| 107 "job_stdout": "", | |
| 108 "model_class": "Job", | |
| 109 "output_collections": {}, | |
| 110 "outputs": { | |
| 111 "output_zip": { | |
| 112 "id": "306d449b91ecb0a3", | |
| 113 "src": "hda", | |
| 114 "uuid": "19827d46-96d8-48c8-b434-17f9e4732aec" | |
| 115 } | |
| 116 }, | |
| 117 "params": { | |
| 118 "__input_ext": "\"input\"", | |
| 119 "adv": "{\"enzyme\": \"auto\", \"use_file_names_as_ids\": true}", | |
| 120 "assembly_plan_name": "\"Type2sRestrictionAssembly\"", | |
| 121 "chromInfo": "\"/tmp/tmps36anksu/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", | |
| 122 "dbkey": "\"?\"", | |
| 123 "domesticated_input": null, | |
| 124 "genbank_files": "{\"values\": [{\"id\": 1, \"src\": \"hdca\"}]}", | |
| 125 "topology": "\"circular\"" | |
| 126 }, | |
| 127 "state": "ok", | |
| 128 "stderr": "\rassembly: 0%| | 0/4 [00:00<?, ?it/s, now=None]\r \r\rassembly: 0%| | 0/4 [00:00<?, ?it/s, now=None]\rassembly: 50%|\u2588\u2588\u2588\u2588\u2588 | 2/4 [00:00<00:00, 2.38it/s, now=None]\rassembly: 75%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u258c | 3/4 [00:01<00:00, 2.15it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 4/4 [00:02<00:00, 1.76it/s, now=None]\r \r", | |
| 129 "stdout": "Simulating assembly plan assambly...\n{'cancelled_assemblies': 0, 'errored_assemblies': 0, 'valid_assemblies': 4}\nGenerating assemblies reports...\nFiles in the zip archive:\nassambly_simulation/assambly_all_required_parts.txt\nassambly_simulation/assambly_constructs_level_2.csv\nassambly_simulation/assambly_simulation_stats.csv\nassambly_simulation/assambly_constructs_level_1.csv\nassambly_simulation/Report.pdf\nassambly_simulation/assembly_plan_graph.pdf\nassambly_simulation/assambly_summary.csv\nassambly_simulation/construct_3/construct_3_type2s_mix_parts_graph.pdf\nassambly_simulation/construct_3/construct_3_summary.csv\nassambly_simulation/construct_3/construct_3_type2s_mix_connections_graph.pdf\nassambly_simulation/construct_3/construct_3.gb\nassambly_simulation/construct_3/construct_3.pdf\nassambly_simulation/construct_3/provided_parts_records/part_L.gb\nassambly_simulation/construct_3/provided_parts_records/part_K.gb\nassambly_simulation/construct_3/provided_parts_records/part_J.gb\nassambly_simulation/construct_3/provided_parts_records/construct_1.gb\nassambly_simulation/all_construct_records/construct_2.gb\nassambly_simulation/all_construct_records/construct_3.gb\nassambly_simulation/all_construct_records/construct_4.gb\nassambly_simulation/all_construct_records/construct_1.gb\nassambly_simulation/construct_1/construct_1_type2s_mix_connections_graph.pdf\nassambly_simulation/construct_1/construct_1_summary.csv\nassambly_simulation/construct_1/construct_1_type2s_mix_parts_graph.pdf\nassambly_simulation/construct_1/construct_1.pdf\nassambly_simulation/construct_1/construct_1.gb\nassambly_simulation/construct_1/provided_parts_records/part_F.gb\nassambly_simulation/construct_1/provided_parts_records/part_B.gb\nassambly_simulation/construct_1/provided_parts_records/part_D.gb\nassambly_simulation/construct_1/provided_parts_records/part_A.gb\nassambly_simulation/construct_1/provided_parts_records/part_C.gb\nassambly_simulation/construct_1/provided_parts_records/part_E.gb\nassambly_simulation/part_records/part_L.gb\nassambly_simulation/part_records/part_F.gb\nassambly_simulation/part_records/part_B.gb\nassambly_simulation/part_records/part_K.gb\nassambly_simulation/part_records/part_D.gb\nassambly_simulation/part_records/part_A.gb\nassambly_simulation/part_records/part_C.gb\nassambly_simulation/part_records/part_G.gb\nassambly_simulation/part_records/part_I.gb\nassambly_simulation/part_records/part_E.gb\nassambly_simulation/part_records/part_J.gb\nassambly_simulation/part_records/part_H.gb\nassambly_simulation/construct_2/construct_2_type2s_mix_parts_graph.pdf\nassambly_simulation/construct_2/construct_2.pdf\nassambly_simulation/construct_2/construct_2.gb\nassambly_simulation/construct_2/construct_2_summary.csv\nassambly_simulation/construct_2/construct_2_type2s_mix_connections_graph.pdf\nassambly_simulation/construct_2/provided_parts_records/part_F.gb\nassambly_simulation/construct_2/provided_parts_records/part_A.gb\nassambly_simulation/construct_2/provided_parts_records/part_G.gb\nassambly_simulation/construct_2/provided_parts_records/part_I.gb\nassambly_simulation/construct_2/provided_parts_records/part_H.gb\nassambly_simulation/construct_4/construct_4_type2s_mix_parts_graph.pdf\nassambly_simulation/construct_4/construct_4.pdf\nassambly_simulation/construct_4/construct_4.gb\nassambly_simulation/construct_4/construct_4_summary.csv\nassambly_simulation/construct_4/construct_4_type2s_mix_connections_graph.pdf\nassambly_simulation/construct_4/provided_parts_records/part_L.gb\nassambly_simulation/construct_4/provided_parts_records/part_K.gb\nassambly_simulation/construct_4/provided_parts_records/construct_2.gb\nassambly_simulation/construct_4/provided_parts_records/part_J.gb\n", | |
| 130 "tool_id": "cloning_simulation", | |
| 131 "tool_stderr": "\rassembly: 0%| | 0/4 [00:00<?, ?it/s, now=None]\r \r\rassembly: 0%| | 0/4 [00:00<?, ?it/s, now=None]\rassembly: 50%|\u2588\u2588\u2588\u2588\u2588 | 2/4 [00:00<00:00, 2.38it/s, now=None]\rassembly: 75%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u258c | 3/4 [00:01<00:00, 2.15it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 4/4 [00:02<00:00, 1.76it/s, now=None]\r \r", | |
| 132 "tool_stdout": "Simulating assembly plan assambly...\n{'cancelled_assemblies': 0, 'errored_assemblies': 0, 'valid_assemblies': 4}\nGenerating assemblies reports...\nFiles in the zip archive:\nassambly_simulation/assambly_all_required_parts.txt\nassambly_simulation/assambly_constructs_level_2.csv\nassambly_simulation/assambly_simulation_stats.csv\nassambly_simulation/assambly_constructs_level_1.csv\nassambly_simulation/Report.pdf\nassambly_simulation/assembly_plan_graph.pdf\nassambly_simulation/assambly_summary.csv\nassambly_simulation/construct_3/construct_3_type2s_mix_parts_graph.pdf\nassambly_simulation/construct_3/construct_3_summary.csv\nassambly_simulation/construct_3/construct_3_type2s_mix_connections_graph.pdf\nassambly_simulation/construct_3/construct_3.gb\nassambly_simulation/construct_3/construct_3.pdf\nassambly_simulation/construct_3/provided_parts_records/part_L.gb\nassambly_simulation/construct_3/provided_parts_records/part_K.gb\nassambly_simulation/construct_3/provided_parts_records/part_J.gb\nassambly_simulation/construct_3/provided_parts_records/construct_1.gb\nassambly_simulation/all_construct_records/construct_2.gb\nassambly_simulation/all_construct_records/construct_3.gb\nassambly_simulation/all_construct_records/construct_4.gb\nassambly_simulation/all_construct_records/construct_1.gb\nassambly_simulation/construct_1/construct_1_type2s_mix_connections_graph.pdf\nassambly_simulation/construct_1/construct_1_summary.csv\nassambly_simulation/construct_1/construct_1_type2s_mix_parts_graph.pdf\nassambly_simulation/construct_1/construct_1.pdf\nassambly_simulation/construct_1/construct_1.gb\nassambly_simulation/construct_1/provided_parts_records/part_F.gb\nassambly_simulation/construct_1/provided_parts_records/part_B.gb\nassambly_simulation/construct_1/provided_parts_records/part_D.gb\nassambly_simulation/construct_1/provided_parts_records/part_A.gb\nassambly_simulation/construct_1/provided_parts_records/part_C.gb\nassambly_simulation/construct_1/provided_parts_records/part_E.gb\nassambly_simulation/part_records/part_L.gb\nassambly_simulation/part_records/part_F.gb\nassambly_simulation/part_records/part_B.gb\nassambly_simulation/part_records/part_K.gb\nassambly_simulation/part_records/part_D.gb\nassambly_simulation/part_records/part_A.gb\nassambly_simulation/part_records/part_C.gb\nassambly_simulation/part_records/part_G.gb\nassambly_simulation/part_records/part_I.gb\nassambly_simulation/part_records/part_E.gb\nassambly_simulation/part_records/part_J.gb\nassambly_simulation/part_records/part_H.gb\nassambly_simulation/construct_2/construct_2_type2s_mix_parts_graph.pdf\nassambly_simulation/construct_2/construct_2.pdf\nassambly_simulation/construct_2/construct_2.gb\nassambly_simulation/construct_2/construct_2_summary.csv\nassambly_simulation/construct_2/construct_2_type2s_mix_connections_graph.pdf\nassambly_simulation/construct_2/provided_parts_records/part_F.gb\nassambly_simulation/construct_2/provided_parts_records/part_A.gb\nassambly_simulation/construct_2/provided_parts_records/part_G.gb\nassambly_simulation/construct_2/provided_parts_records/part_I.gb\nassambly_simulation/construct_2/provided_parts_records/part_H.gb\nassambly_simulation/construct_4/construct_4_type2s_mix_parts_graph.pdf\nassambly_simulation/construct_4/construct_4.pdf\nassambly_simulation/construct_4/construct_4.gb\nassambly_simulation/construct_4/construct_4_summary.csv\nassambly_simulation/construct_4/construct_4_type2s_mix_connections_graph.pdf\nassambly_simulation/construct_4/provided_parts_records/part_L.gb\nassambly_simulation/construct_4/provided_parts_records/part_K.gb\nassambly_simulation/construct_4/provided_parts_records/construct_2.gb\nassambly_simulation/construct_4/provided_parts_records/part_J.gb\n", | |
| 133 "update_time": "2025-05-16T08:54:59.050276", | |
| 134 "user_email": "planemo@galaxyproject.org", | |
| 135 "user_id": "1d1943aa60deb628" | |
| 136 }, | |
| 137 "status": "success", | |
| 138 "test_index": 0, | |
| 139 "time_seconds": 53.80709099769592, | |
| 140 "tool_id": "cloning_simulation", | |
| 141 "tool_version": "0.1.0+galaxy0" | |
| 142 }, | |
| 143 "has_data": true, | |
| 144 "id": "cloning_simulation-0" | |
| 145 }, | |
| 146 { | |
| 147 "data": { | |
| 148 "inputs": { | |
| 149 "adv|use_file_names_as_ids": true, | |
| 150 "assembly_csv": { | |
| 151 "id": "343611dad2e145e6", | |
| 152 "src": "hda" | |
| 153 }, | |
| 154 "assembly_plan_name": "GibsonAssembly", | |
| 155 "genbank_files": { | |
| 156 "id": "13a3899f03fff34a", | |
| 157 "src": "hdca" | |
| 158 }, | |
| 159 "topology": "circular" | |
| 160 }, | |
| 161 "job": { | |
| 162 "command_line": "mkdir 'outdir_zip' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmps36anksu/files/5/c/2/dataset_5c2150b5-537a-4971-98ef-959bb4141fac.dat' --domesticated_seq '' --assembly_csv '/tmp/tmps36anksu/files/7/a/0/dataset_7a09a16a-a7f7-44ce-8e1d-5f6baf385c44.dat' --assembly_plan_name 'GibsonAssembly' --file_name_mapping '/tmp/tmps36anksu/files/5/c/2/dataset_5c2150b5-537a-4971-98ef-959bb4141fac.dat:gibson_sequences.fa' --file_name_mapping_dom '' --use_file_names_as_id 'true' --outdir_simulation 'outdir_zip' --output_simulation 'output_zip.zip' --enzyme 'auto' --topology 'circular'&& cp 'output_zip.zip' '/tmp/tmps36anksu/job_working_directory/000/17/outputs/dataset_4c70b3f9-9fb4-4e1c-942c-47fd78a5a348.dat'", | |
| 163 "command_version": "", | |
| 164 "copied_from_job_id": null, | |
| 165 "create_time": "2025-05-16T08:55:10.522461", | |
| 166 "dependencies": [ | |
| 167 { | |
| 168 "cacheable": false, | |
| 169 "dependency_resolver": { | |
| 170 "auto_init": true, | |
| 171 "auto_install": true, | |
| 172 "can_uninstall_dependencies": true, | |
| 173 "ensure_channels": "conda-forge,bioconda", | |
| 174 "model_class": "CondaDependencyResolver", | |
| 175 "prefix": "/home/rkhaled/miniconda3", | |
| 176 "read_only": false, | |
| 177 "resolver_type": "conda", | |
| 178 "resolves_simple_dependencies": true, | |
| 179 "use_local": false, | |
| 180 "versionless": false | |
| 181 }, | |
| 182 "dependency_type": "conda", | |
| 183 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-414e7261396ae5d11be85675e1e19db222325018468f2829061591addd560be0", | |
| 184 "exact": true, | |
| 185 "model_class": "MergedCondaDependency", | |
| 186 "name": "flametree", | |
| 187 "version": "0.1.11" | |
| 188 }, | |
| 189 { | |
| 190 "cacheable": false, | |
| 191 "dependency_resolver": { | |
| 192 "auto_init": true, | |
| 193 "auto_install": true, | |
| 194 "can_uninstall_dependencies": true, | |
| 195 "ensure_channels": "conda-forge,bioconda", | |
| 196 "model_class": "CondaDependencyResolver", | |
| 197 "prefix": "/home/rkhaled/miniconda3", | |
| 198 "read_only": false, | |
| 199 "resolver_type": "conda", | |
| 200 "resolves_simple_dependencies": true, | |
| 201 "use_local": false, | |
| 202 "versionless": false | |
| 203 }, | |
| 204 "dependency_type": "conda", | |
| 205 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-414e7261396ae5d11be85675e1e19db222325018468f2829061591addd560be0", | |
| 206 "exact": true, | |
| 207 "model_class": "MergedCondaDependency", | |
| 208 "name": "biopython", | |
| 209 "version": "1.85" | |
| 210 }, | |
| 211 { | |
| 212 "cacheable": false, | |
| 213 "dependency_resolver": { | |
| 214 "auto_init": true, | |
| 215 "auto_install": true, | |
| 216 "can_uninstall_dependencies": true, | |
| 217 "ensure_channels": "conda-forge,bioconda", | |
| 218 "model_class": "CondaDependencyResolver", | |
| 219 "prefix": "/home/rkhaled/miniconda3", | |
| 220 "read_only": false, | |
| 221 "resolver_type": "conda", | |
| 222 "resolves_simple_dependencies": true, | |
| 223 "use_local": false, | |
| 224 "versionless": false | |
| 225 }, | |
| 226 "dependency_type": "conda", | |
| 227 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-414e7261396ae5d11be85675e1e19db222325018468f2829061591addd560be0", | |
| 228 "exact": true, | |
| 229 "model_class": "MergedCondaDependency", | |
| 230 "name": "proglog", | |
| 231 "version": "0.1.10" | |
| 232 }, | |
| 233 { | |
| 234 "cacheable": false, | |
| 235 "dependency_resolver": { | |
| 236 "auto_init": true, | |
| 237 "auto_install": true, | |
| 238 "can_uninstall_dependencies": true, | |
| 239 "ensure_channels": "conda-forge,bioconda", | |
| 240 "model_class": "CondaDependencyResolver", | |
| 241 "prefix": "/home/rkhaled/miniconda3", | |
| 242 "read_only": false, | |
| 243 "resolver_type": "conda", | |
| 244 "resolves_simple_dependencies": true, | |
| 245 "use_local": false, | |
| 246 "versionless": false | |
| 247 }, | |
| 248 "dependency_type": "conda", | |
| 249 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-414e7261396ae5d11be85675e1e19db222325018468f2829061591addd560be0", | |
| 250 "exact": true, | |
| 251 "model_class": "MergedCondaDependency", | |
| 252 "name": "pandas", | |
| 253 "version": "2.2.3" | |
| 254 }, | |
| 255 { | |
| 256 "cacheable": false, | |
| 257 "dependency_resolver": { | |
| 258 "auto_init": true, | |
| 259 "auto_install": true, | |
| 260 "can_uninstall_dependencies": true, | |
| 261 "ensure_channels": "conda-forge,bioconda", | |
| 262 "model_class": "CondaDependencyResolver", | |
| 263 "prefix": "/home/rkhaled/miniconda3", | |
| 264 "read_only": false, | |
| 265 "resolver_type": "conda", | |
| 266 "resolves_simple_dependencies": true, | |
| 267 "use_local": false, | |
| 268 "versionless": false | |
| 269 }, | |
| 270 "dependency_type": "conda", | |
| 271 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-414e7261396ae5d11be85675e1e19db222325018468f2829061591addd560be0", | |
| 272 "exact": true, | |
| 273 "model_class": "MergedCondaDependency", | |
| 274 "name": "dnacauldron", | |
| 275 "version": "2.0.12" | |
| 276 }, | |
| 277 { | |
| 278 "cacheable": false, | |
| 279 "dependency_resolver": { | |
| 280 "auto_init": true, | |
| 281 "auto_install": true, | |
| 282 "can_uninstall_dependencies": true, | |
| 283 "ensure_channels": "conda-forge,bioconda", | |
| 284 "model_class": "CondaDependencyResolver", | |
| 285 "prefix": "/home/rkhaled/miniconda3", | |
| 286 "read_only": false, | |
| 287 "resolver_type": "conda", | |
| 288 "resolves_simple_dependencies": true, | |
| 289 "use_local": false, | |
| 290 "versionless": false | |
| 291 }, | |
| 292 "dependency_type": "conda", | |
| 293 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-414e7261396ae5d11be85675e1e19db222325018468f2829061591addd560be0", | |
| 294 "exact": true, | |
| 295 "model_class": "MergedCondaDependency", | |
| 296 "name": "pdf-reports", | |
| 297 "version": "0.3.9" | |
| 298 }, | |
| 299 { | |
| 300 "cacheable": false, | |
| 301 "dependency_resolver": { | |
| 302 "auto_init": true, | |
| 303 "auto_install": true, | |
| 304 "can_uninstall_dependencies": true, | |
| 305 "ensure_channels": "conda-forge,bioconda", | |
| 306 "model_class": "CondaDependencyResolver", | |
| 307 "prefix": "/home/rkhaled/miniconda3", | |
| 308 "read_only": false, | |
| 309 "resolver_type": "conda", | |
| 310 "resolves_simple_dependencies": true, | |
| 311 "use_local": false, | |
| 312 "versionless": false | |
| 313 }, | |
| 314 "dependency_type": "conda", | |
| 315 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-414e7261396ae5d11be85675e1e19db222325018468f2829061591addd560be0", | |
| 316 "exact": true, | |
| 317 "model_class": "MergedCondaDependency", | |
| 318 "name": "sequenticon", | |
| 319 "version": "0.1.8" | |
| 320 }, | |
| 321 { | |
| 322 "cacheable": false, | |
| 323 "dependency_resolver": { | |
| 324 "auto_init": true, | |
| 325 "auto_install": true, | |
| 326 "can_uninstall_dependencies": true, | |
| 327 "ensure_channels": "conda-forge,bioconda", | |
| 328 "model_class": "CondaDependencyResolver", | |
| 329 "prefix": "/home/rkhaled/miniconda3", | |
| 330 "read_only": false, | |
| 331 "resolver_type": "conda", | |
| 332 "resolves_simple_dependencies": true, | |
| 333 "use_local": false, | |
| 334 "versionless": false | |
| 335 }, | |
| 336 "dependency_type": "conda", | |
| 337 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-414e7261396ae5d11be85675e1e19db222325018468f2829061591addd560be0", | |
| 338 "exact": true, | |
| 339 "model_class": "MergedCondaDependency", | |
| 340 "name": "dna_features_viewer", | |
| 341 "version": "3.1.4" | |
| 342 } | |
| 343 ], | |
| 344 "exit_code": 0, | |
| 345 "external_id": "69816", | |
| 346 "galaxy_version": "24.2", | |
| 347 "handler": null, | |
| 348 "history_id": "13a3899f03fff34a", | |
| 349 "id": "6fff2cd3fd6e4947", | |
| 350 "inputs": { | |
| 351 "assembly_csv": { | |
| 352 "id": "343611dad2e145e6", | |
| 353 "src": "hda", | |
| 354 "uuid": "7a09a16a-a7f7-44ce-8e1d-5f6baf385c44" | |
| 355 }, | |
| 356 "genbank_files1": { | |
| 357 "id": "03c59a54410e4ccf", | |
| 358 "src": "hda", | |
| 359 "uuid": "5c2150b5-537a-4971-98ef-959bb4141fac" | |
| 360 } | |
| 361 }, | |
| 362 "job_messages": [], | |
| 363 "job_metrics": [], | |
| 364 "job_runner_name": null, | |
| 365 "job_stderr": "", | |
| 366 "job_stdout": "", | |
| 367 "model_class": "Job", | |
| 368 "output_collections": {}, | |
| 369 "outputs": { | |
| 370 "output_zip": { | |
| 371 "id": "6fff2cd3fd6e4947", | |
| 372 "src": "hda", | |
| 373 "uuid": "4c70b3f9-9fb4-4e1c-942c-47fd78a5a348" | |
| 374 } | |
| 375 }, | |
| 376 "params": { | |
| 377 "__input_ext": "\"input\"", | |
| 378 "adv": "{\"enzyme\": \"auto\", \"use_file_names_as_ids\": true}", | |
| 379 "assembly_plan_name": "\"GibsonAssembly\"", | |
| 380 "chromInfo": "\"/tmp/tmps36anksu/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", | |
| 381 "dbkey": "\"?\"", | |
| 382 "domesticated_input": null, | |
| 383 "genbank_files": "{\"values\": [{\"id\": 2, \"src\": \"hdca\"}]}", | |
| 384 "topology": "\"circular\"" | |
| 385 }, | |
| 386 "state": "ok", | |
| 387 "stderr": "\rassembly: 0%| | 0/5 [00:00<?, ?it/s, now=None]\r \r\rassembly: 0%| | 0/5 [00:00<?, ?it/s, now=None]\rassembly: 40%|\u2588\u2588\u2588\u2588 | 2/5 [00:00<00:00, 4.10it/s, now=None]\rassembly: 60%|\u2588\u2588\u2588\u2588\u2588\u2588 | 3/5 [00:00<00:00, 4.10it/s, now=None]\rassembly: 80%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588 | 4/5 [00:00<00:00, 4.09it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 5/5 [00:01<00:00, 3.38it/s, now=None]\r \r", | |
| 388 "stdout": "Simulating assembly plan assambly...\n{'cancelled_assemblies': 0, 'errored_assemblies': 2, 'valid_assemblies': 3}\nGenerating assemblies reports...\nFiles in the zip archive:\nassambly_simulation/assambly_all_required_parts.txt\nassambly_simulation/assambly_assembly_plan.csv\nassambly_simulation/assambly_simulation_stats.csv\nassambly_simulation/Report.pdf\nassambly_simulation/assambly_warnings.csv\nassambly_simulation/assambly_errors.csv\nassambly_simulation/assambly_summary.csv\nassambly_simulation/construct_3/construct_3_summary.csv\nassambly_simulation/construct_3/construct_3.gb\nassambly_simulation/construct_3/construct_3.pdf\nassambly_simulation/construct_3/construct_3_connections_graph.pdf\nassambly_simulation/construct_3/provided_parts_records/Frag_5b.gb\nassambly_simulation/construct_3/provided_parts_records/Frag_4c.gb\nassambly_simulation/construct_3/provided_parts_records/Frag_3.gb\nassambly_simulation/construct_3/provided_parts_records/Frag_1.gb\nassambly_simulation/construct_3/provided_parts_records/Frag_2.gb\nassambly_simulation/all_construct_records/construct_2.gb\nassambly_simulation/all_construct_records/construct_3.gb\nassambly_simulation/all_construct_records/construct_1.gb\nassambly_simulation/construct_1/construct_1_summary.csv\nassambly_simulation/construct_1/construct_1.pdf\nassambly_simulation/construct_1/construct_1_connections_graph.pdf\nassambly_simulation/construct_1/construct_1.gb\nassambly_simulation/construct_1/provided_parts_records/Frag_5.gb\nassambly_simulation/construct_1/provided_parts_records/Frag_4.gb\nassambly_simulation/construct_1/provided_parts_records/Frag_3.gb\nassambly_simulation/construct_1/provided_parts_records/Frag_1.gb\nassambly_simulation/construct_1/provided_parts_records/Frag_2.gb\nassambly_simulation/part_records/Frag_5.gb\nassambly_simulation/part_records/Frag_5b.gb\nassambly_simulation/part_records/Frag_4.gb\nassambly_simulation/part_records/Frag_4c.gb\nassambly_simulation/part_records/Frag_4b.gb\nassambly_simulation/part_records/Frag_3.gb\nassambly_simulation/part_records/Frag_1.gb\nassambly_simulation/part_records/Frag_2.gb\nassambly_simulation/construct_2/construct_2.pdf\nassambly_simulation/construct_2/construct_2_connections_graph.pdf\nassambly_simulation/construct_2/construct_2.gb\nassambly_simulation/construct_2/construct_2_summary.csv\nassambly_simulation/construct_2/provided_parts_records/Frag_5.gb\nassambly_simulation/construct_2/provided_parts_records/Frag_4b.gb\nassambly_simulation/construct_2/provided_parts_records/Frag_3.gb\nassambly_simulation/construct_2/provided_parts_records/Frag_1.gb\nassambly_simulation/construct_2/provided_parts_records/Frag_2.gb\nassambly_simulation/construct_5/error.csv\nassambly_simulation/construct_5/construct_5_connections_graph.pdf\nassambly_simulation/construct_5/warnings.csv\nassambly_simulation/construct_5/fragments_in_construct_5_homology_mix/Frag_1_01.pdf\nassambly_simulation/construct_5/fragments_in_construct_5_homology_mix/Frag_2_01.pdf\nassambly_simulation/construct_5/fragments_in_construct_5_homology_mix/Frag_3_01.pdf\nassambly_simulation/construct_5/fragments_in_construct_5_homology_mix/Frag_4_01.pdf\nassambly_simulation/construct_5/fragments_in_construct_5_homology_mix/Frag_4b_01.pdf\nassambly_simulation/construct_5/provided_parts_plots/Frag_4b.pdf\nassambly_simulation/construct_5/provided_parts_plots/Frag_4.pdf\nassambly_simulation/construct_5/provided_parts_plots/Frag_3.pdf\nassambly_simulation/construct_5/provided_parts_plots/Frag_2.pdf\nassambly_simulation/construct_5/provided_parts_plots/Frag_1.pdf\nassambly_simulation/construct_5/provided_parts_records/Frag_4.gb\nassambly_simulation/construct_5/provided_parts_records/Frag_4b.gb\nassambly_simulation/construct_5/provided_parts_records/Frag_3.gb\nassambly_simulation/construct_5/provided_parts_records/Frag_1.gb\nassambly_simulation/construct_5/provided_parts_records/Frag_2.gb\nassambly_simulation/construct_4/construct_4_connections_graph.pdf\nassambly_simulation/construct_4/error.csv\nassambly_simulation/construct_4/warnings.csv\nassambly_simulation/construct_4/provided_parts_plots/Frag_4.pdf\nassambly_simulation/construct_4/provided_parts_plots/Frag_3.pdf\nassambly_simulation/construct_4/provided_parts_plots/Frag_2.pdf\nassambly_simulation/construct_4/provided_parts_plots/Frag_1.pdf\nassambly_simulation/construct_4/provided_parts_records/Frag_4.gb\nassambly_simulation/construct_4/provided_parts_records/Frag_3.gb\nassambly_simulation/construct_4/provided_parts_records/Frag_1.gb\nassambly_simulation/construct_4/provided_parts_records/Frag_2.gb\nassambly_simulation/construct_4/fragments_in_construct_4_homology_mix/Frag_1_01.pdf\nassambly_simulation/construct_4/fragments_in_construct_4_homology_mix/Frag_2_01.pdf\nassambly_simulation/construct_4/fragments_in_construct_4_homology_mix/Frag_3_01.pdf\nassambly_simulation/construct_4/fragments_in_construct_4_homology_mix/Frag_4_01.pdf\n", | |
| 389 "tool_id": "cloning_simulation", | |
| 390 "tool_stderr": "\rassembly: 0%| | 0/5 [00:00<?, ?it/s, now=None]\r \r\rassembly: 0%| | 0/5 [00:00<?, ?it/s, now=None]\rassembly: 40%|\u2588\u2588\u2588\u2588 | 2/5 [00:00<00:00, 4.10it/s, now=None]\rassembly: 60%|\u2588\u2588\u2588\u2588\u2588\u2588 | 3/5 [00:00<00:00, 4.10it/s, now=None]\rassembly: 80%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588 | 4/5 [00:00<00:00, 4.09it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 5/5 [00:01<00:00, 3.38it/s, now=None]\r \r", | |
| 391 "tool_stdout": "Simulating assembly plan assambly...\n{'cancelled_assemblies': 0, 'errored_assemblies': 2, 'valid_assemblies': 3}\nGenerating assemblies reports...\nFiles in the zip archive:\nassambly_simulation/assambly_all_required_parts.txt\nassambly_simulation/assambly_assembly_plan.csv\nassambly_simulation/assambly_simulation_stats.csv\nassambly_simulation/Report.pdf\nassambly_simulation/assambly_warnings.csv\nassambly_simulation/assambly_errors.csv\nassambly_simulation/assambly_summary.csv\nassambly_simulation/construct_3/construct_3_summary.csv\nassambly_simulation/construct_3/construct_3.gb\nassambly_simulation/construct_3/construct_3.pdf\nassambly_simulation/construct_3/construct_3_connections_graph.pdf\nassambly_simulation/construct_3/provided_parts_records/Frag_5b.gb\nassambly_simulation/construct_3/provided_parts_records/Frag_4c.gb\nassambly_simulation/construct_3/provided_parts_records/Frag_3.gb\nassambly_simulation/construct_3/provided_parts_records/Frag_1.gb\nassambly_simulation/construct_3/provided_parts_records/Frag_2.gb\nassambly_simulation/all_construct_records/construct_2.gb\nassambly_simulation/all_construct_records/construct_3.gb\nassambly_simulation/all_construct_records/construct_1.gb\nassambly_simulation/construct_1/construct_1_summary.csv\nassambly_simulation/construct_1/construct_1.pdf\nassambly_simulation/construct_1/construct_1_connections_graph.pdf\nassambly_simulation/construct_1/construct_1.gb\nassambly_simulation/construct_1/provided_parts_records/Frag_5.gb\nassambly_simulation/construct_1/provided_parts_records/Frag_4.gb\nassambly_simulation/construct_1/provided_parts_records/Frag_3.gb\nassambly_simulation/construct_1/provided_parts_records/Frag_1.gb\nassambly_simulation/construct_1/provided_parts_records/Frag_2.gb\nassambly_simulation/part_records/Frag_5.gb\nassambly_simulation/part_records/Frag_5b.gb\nassambly_simulation/part_records/Frag_4.gb\nassambly_simulation/part_records/Frag_4c.gb\nassambly_simulation/part_records/Frag_4b.gb\nassambly_simulation/part_records/Frag_3.gb\nassambly_simulation/part_records/Frag_1.gb\nassambly_simulation/part_records/Frag_2.gb\nassambly_simulation/construct_2/construct_2.pdf\nassambly_simulation/construct_2/construct_2_connections_graph.pdf\nassambly_simulation/construct_2/construct_2.gb\nassambly_simulation/construct_2/construct_2_summary.csv\nassambly_simulation/construct_2/provided_parts_records/Frag_5.gb\nassambly_simulation/construct_2/provided_parts_records/Frag_4b.gb\nassambly_simulation/construct_2/provided_parts_records/Frag_3.gb\nassambly_simulation/construct_2/provided_parts_records/Frag_1.gb\nassambly_simulation/construct_2/provided_parts_records/Frag_2.gb\nassambly_simulation/construct_5/error.csv\nassambly_simulation/construct_5/construct_5_connections_graph.pdf\nassambly_simulation/construct_5/warnings.csv\nassambly_simulation/construct_5/fragments_in_construct_5_homology_mix/Frag_1_01.pdf\nassambly_simulation/construct_5/fragments_in_construct_5_homology_mix/Frag_2_01.pdf\nassambly_simulation/construct_5/fragments_in_construct_5_homology_mix/Frag_3_01.pdf\nassambly_simulation/construct_5/fragments_in_construct_5_homology_mix/Frag_4_01.pdf\nassambly_simulation/construct_5/fragments_in_construct_5_homology_mix/Frag_4b_01.pdf\nassambly_simulation/construct_5/provided_parts_plots/Frag_4b.pdf\nassambly_simulation/construct_5/provided_parts_plots/Frag_4.pdf\nassambly_simulation/construct_5/provided_parts_plots/Frag_3.pdf\nassambly_simulation/construct_5/provided_parts_plots/Frag_2.pdf\nassambly_simulation/construct_5/provided_parts_plots/Frag_1.pdf\nassambly_simulation/construct_5/provided_parts_records/Frag_4.gb\nassambly_simulation/construct_5/provided_parts_records/Frag_4b.gb\nassambly_simulation/construct_5/provided_parts_records/Frag_3.gb\nassambly_simulation/construct_5/provided_parts_records/Frag_1.gb\nassambly_simulation/construct_5/provided_parts_records/Frag_2.gb\nassambly_simulation/construct_4/construct_4_connections_graph.pdf\nassambly_simulation/construct_4/error.csv\nassambly_simulation/construct_4/warnings.csv\nassambly_simulation/construct_4/provided_parts_plots/Frag_4.pdf\nassambly_simulation/construct_4/provided_parts_plots/Frag_3.pdf\nassambly_simulation/construct_4/provided_parts_plots/Frag_2.pdf\nassambly_simulation/construct_4/provided_parts_plots/Frag_1.pdf\nassambly_simulation/construct_4/provided_parts_records/Frag_4.gb\nassambly_simulation/construct_4/provided_parts_records/Frag_3.gb\nassambly_simulation/construct_4/provided_parts_records/Frag_1.gb\nassambly_simulation/construct_4/provided_parts_records/Frag_2.gb\nassambly_simulation/construct_4/fragments_in_construct_4_homology_mix/Frag_1_01.pdf\nassambly_simulation/construct_4/fragments_in_construct_4_homology_mix/Frag_2_01.pdf\nassambly_simulation/construct_4/fragments_in_construct_4_homology_mix/Frag_3_01.pdf\nassambly_simulation/construct_4/fragments_in_construct_4_homology_mix/Frag_4_01.pdf\n", | |
| 392 "update_time": "2025-05-16T08:55:23.301357", | |
| 393 "user_email": "planemo@galaxyproject.org", | |
| 394 "user_id": "1d1943aa60deb628" | |
| 395 }, | |
| 396 "status": "success", | |
| 397 "test_index": 1, | |
| 398 "time_seconds": 24.055506706237793, | |
| 399 "tool_id": "cloning_simulation", | |
| 400 "tool_version": "0.1.0+galaxy0" | |
| 401 }, | |
| 402 "has_data": true, | |
| 403 "id": "cloning_simulation-1" | |
| 404 }, | |
| 405 { | |
| 406 "data": { | |
| 407 "inputs": { | |
| 408 "adv|use_file_names_as_ids": true, | |
| 409 "assembly_csv": { | |
| 410 "id": "eae50b1e0ba0bca8", | |
| 411 "src": "hda" | |
| 412 }, | |
| 413 "assembly_plan_name": "LigaseCyclingReactionAssembly", | |
| 414 "genbank_files": { | |
| 415 "id": "6872e1ad22eb2e5d", | |
| 416 "src": "hdca" | |
| 417 }, | |
| 418 "topology": "circular" | |
| 419 }, | |
| 420 "job": { | |
| 421 "command_line": "mkdir 'outdir_zip' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmps36anksu/files/a/a/0/dataset_aa035ce9-b3ee-4c4d-a5c1-e2451c4297c2.dat,/tmp/tmps36anksu/files/4/b/b/dataset_4bb2bf6a-b351-4a80-ab47-d4d56aefa38c.dat' --domesticated_seq '' --assembly_csv '/tmp/tmps36anksu/files/5/a/f/dataset_5af89b00-757d-4606-b6c8-d00d3f0ca39e.dat' --assembly_plan_name 'LigaseCyclingReactionAssembly' --file_name_mapping '/tmp/tmps36anksu/files/a/a/0/dataset_aa035ce9-b3ee-4c4d-a5c1-e2451c4297c2.dat:RFP_GFP_plasmid_BOs.fa,/tmp/tmps36anksu/files/4/b/b/dataset_4bb2bf6a-b351-4a80-ab47-d4d56aefa38c.dat:RFP_GFP_plasmid_parts.fa' --file_name_mapping_dom '' --use_file_names_as_id 'true' --outdir_simulation 'outdir_zip' --output_simulation 'output_zip.zip' --enzyme 'auto' --topology 'circular'&& cp 'output_zip.zip' '/tmp/tmps36anksu/job_working_directory/000/21/outputs/dataset_bd5c88b9-1efd-4507-b875-13dfebff9d6a.dat'", | |
| 422 "command_version": "", | |
| 423 "copied_from_job_id": null, | |
| 424 "create_time": "2025-05-16T08:55:35.420052", | |
| 425 "dependencies": [ | |
| 426 { | |
| 427 "cacheable": false, | |
| 428 "dependency_resolver": { | |
| 429 "auto_init": true, | |
| 430 "auto_install": true, | |
| 431 "can_uninstall_dependencies": true, | |
| 432 "ensure_channels": "conda-forge,bioconda", | |
| 433 "model_class": "CondaDependencyResolver", | |
| 434 "prefix": "/home/rkhaled/miniconda3", | |
| 435 "read_only": false, | |
| 436 "resolver_type": "conda", | |
| 437 "resolves_simple_dependencies": true, | |
| 438 "use_local": false, | |
| 439 "versionless": false | |
| 440 }, | |
| 441 "dependency_type": "conda", | |
| 442 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-414e7261396ae5d11be85675e1e19db222325018468f2829061591addd560be0", | |
| 443 "exact": true, | |
| 444 "model_class": "MergedCondaDependency", | |
| 445 "name": "flametree", | |
| 446 "version": "0.1.11" | |
| 447 }, | |
| 448 { | |
| 449 "cacheable": false, | |
| 450 "dependency_resolver": { | |
| 451 "auto_init": true, | |
| 452 "auto_install": true, | |
| 453 "can_uninstall_dependencies": true, | |
| 454 "ensure_channels": "conda-forge,bioconda", | |
| 455 "model_class": "CondaDependencyResolver", | |
| 456 "prefix": "/home/rkhaled/miniconda3", | |
| 457 "read_only": false, | |
| 458 "resolver_type": "conda", | |
| 459 "resolves_simple_dependencies": true, | |
| 460 "use_local": false, | |
| 461 "versionless": false | |
| 462 }, | |
| 463 "dependency_type": "conda", | |
| 464 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-414e7261396ae5d11be85675e1e19db222325018468f2829061591addd560be0", | |
| 465 "exact": true, | |
| 466 "model_class": "MergedCondaDependency", | |
| 467 "name": "biopython", | |
| 468 "version": "1.85" | |
| 469 }, | |
| 470 { | |
| 471 "cacheable": false, | |
| 472 "dependency_resolver": { | |
| 473 "auto_init": true, | |
| 474 "auto_install": true, | |
| 475 "can_uninstall_dependencies": true, | |
| 476 "ensure_channels": "conda-forge,bioconda", | |
| 477 "model_class": "CondaDependencyResolver", | |
| 478 "prefix": "/home/rkhaled/miniconda3", | |
| 479 "read_only": false, | |
| 480 "resolver_type": "conda", | |
| 481 "resolves_simple_dependencies": true, | |
| 482 "use_local": false, | |
| 483 "versionless": false | |
| 484 }, | |
| 485 "dependency_type": "conda", | |
| 486 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-414e7261396ae5d11be85675e1e19db222325018468f2829061591addd560be0", | |
| 487 "exact": true, | |
| 488 "model_class": "MergedCondaDependency", | |
| 489 "name": "proglog", | |
| 490 "version": "0.1.10" | |
| 491 }, | |
| 492 { | |
| 493 "cacheable": false, | |
| 494 "dependency_resolver": { | |
| 495 "auto_init": true, | |
| 496 "auto_install": true, | |
| 497 "can_uninstall_dependencies": true, | |
| 498 "ensure_channels": "conda-forge,bioconda", | |
| 499 "model_class": "CondaDependencyResolver", | |
| 500 "prefix": "/home/rkhaled/miniconda3", | |
| 501 "read_only": false, | |
| 502 "resolver_type": "conda", | |
| 503 "resolves_simple_dependencies": true, | |
| 504 "use_local": false, | |
| 505 "versionless": false | |
| 506 }, | |
| 507 "dependency_type": "conda", | |
| 508 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-414e7261396ae5d11be85675e1e19db222325018468f2829061591addd560be0", | |
| 509 "exact": true, | |
| 510 "model_class": "MergedCondaDependency", | |
| 511 "name": "pandas", | |
| 512 "version": "2.2.3" | |
| 513 }, | |
| 514 { | |
| 515 "cacheable": false, | |
| 516 "dependency_resolver": { | |
| 517 "auto_init": true, | |
| 518 "auto_install": true, | |
| 519 "can_uninstall_dependencies": true, | |
| 520 "ensure_channels": "conda-forge,bioconda", | |
| 521 "model_class": "CondaDependencyResolver", | |
| 522 "prefix": "/home/rkhaled/miniconda3", | |
| 523 "read_only": false, | |
| 524 "resolver_type": "conda", | |
| 525 "resolves_simple_dependencies": true, | |
| 526 "use_local": false, | |
| 527 "versionless": false | |
| 528 }, | |
| 529 "dependency_type": "conda", | |
| 530 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-414e7261396ae5d11be85675e1e19db222325018468f2829061591addd560be0", | |
| 531 "exact": true, | |
| 532 "model_class": "MergedCondaDependency", | |
| 533 "name": "dnacauldron", | |
| 534 "version": "2.0.12" | |
| 535 }, | |
| 536 { | |
| 537 "cacheable": false, | |
| 538 "dependency_resolver": { | |
| 539 "auto_init": true, | |
| 540 "auto_install": true, | |
| 541 "can_uninstall_dependencies": true, | |
| 542 "ensure_channels": "conda-forge,bioconda", | |
| 543 "model_class": "CondaDependencyResolver", | |
| 544 "prefix": "/home/rkhaled/miniconda3", | |
| 545 "read_only": false, | |
| 546 "resolver_type": "conda", | |
| 547 "resolves_simple_dependencies": true, | |
| 548 "use_local": false, | |
| 549 "versionless": false | |
| 550 }, | |
| 551 "dependency_type": "conda", | |
| 552 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-414e7261396ae5d11be85675e1e19db222325018468f2829061591addd560be0", | |
| 553 "exact": true, | |
| 554 "model_class": "MergedCondaDependency", | |
| 555 "name": "pdf-reports", | |
| 556 "version": "0.3.9" | |
| 557 }, | |
| 558 { | |
| 559 "cacheable": false, | |
| 560 "dependency_resolver": { | |
| 561 "auto_init": true, | |
| 562 "auto_install": true, | |
| 563 "can_uninstall_dependencies": true, | |
| 564 "ensure_channels": "conda-forge,bioconda", | |
| 565 "model_class": "CondaDependencyResolver", | |
| 566 "prefix": "/home/rkhaled/miniconda3", | |
| 567 "read_only": false, | |
| 568 "resolver_type": "conda", | |
| 569 "resolves_simple_dependencies": true, | |
| 570 "use_local": false, | |
| 571 "versionless": false | |
| 572 }, | |
| 573 "dependency_type": "conda", | |
| 574 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-414e7261396ae5d11be85675e1e19db222325018468f2829061591addd560be0", | |
| 575 "exact": true, | |
| 576 "model_class": "MergedCondaDependency", | |
| 577 "name": "sequenticon", | |
| 578 "version": "0.1.8" | |
| 579 }, | |
| 580 { | |
| 581 "cacheable": false, | |
| 582 "dependency_resolver": { | |
| 583 "auto_init": true, | |
| 584 "auto_install": true, | |
| 585 "can_uninstall_dependencies": true, | |
| 586 "ensure_channels": "conda-forge,bioconda", | |
| 587 "model_class": "CondaDependencyResolver", | |
| 588 "prefix": "/home/rkhaled/miniconda3", | |
| 589 "read_only": false, | |
| 590 "resolver_type": "conda", | |
| 591 "resolves_simple_dependencies": true, | |
| 592 "use_local": false, | |
| 593 "versionless": false | |
| 594 }, | |
| 595 "dependency_type": "conda", | |
| 596 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-414e7261396ae5d11be85675e1e19db222325018468f2829061591addd560be0", | |
| 597 "exact": true, | |
| 598 "model_class": "MergedCondaDependency", | |
| 599 "name": "dna_features_viewer", | |
| 600 "version": "3.1.4" | |
| 601 } | |
| 602 ], | |
| 603 "exit_code": 0, | |
| 604 "external_id": "70205", | |
| 605 "galaxy_version": "24.2", | |
| 606 "handler": null, | |
| 607 "history_id": "6872e1ad22eb2e5d", | |
| 608 "id": "8205956dbdec438f", | |
| 609 "inputs": { | |
| 610 "assembly_csv": { | |
| 611 "id": "eae50b1e0ba0bca8", | |
| 612 "src": "hda", | |
| 613 "uuid": "5af89b00-757d-4606-b6c8-d00d3f0ca39e" | |
| 614 }, | |
| 615 "genbank_files1": { | |
| 616 "id": "e685210c6961cf21", | |
| 617 "src": "hda", | |
| 618 "uuid": "aa035ce9-b3ee-4c4d-a5c1-e2451c4297c2" | |
| 619 }, | |
| 620 "genbank_files2": { | |
| 621 "id": "fb0119a6d133c713", | |
| 622 "src": "hda", | |
| 623 "uuid": "4bb2bf6a-b351-4a80-ab47-d4d56aefa38c" | |
| 624 } | |
| 625 }, | |
| 626 "job_messages": [], | |
| 627 "job_metrics": [], | |
| 628 "job_runner_name": null, | |
| 629 "job_stderr": "", | |
| 630 "job_stdout": "", | |
| 631 "model_class": "Job", | |
| 632 "output_collections": {}, | |
| 633 "outputs": { | |
| 634 "output_zip": { | |
| 635 "id": "8205956dbdec438f", | |
| 636 "src": "hda", | |
| 637 "uuid": "bd5c88b9-1efd-4507-b875-13dfebff9d6a" | |
| 638 } | |
| 639 }, | |
| 640 "params": { | |
| 641 "__input_ext": "\"input\"", | |
| 642 "adv": "{\"enzyme\": \"auto\", \"use_file_names_as_ids\": true}", | |
| 643 "assembly_plan_name": "\"LigaseCyclingReactionAssembly\"", | |
| 644 "chromInfo": "\"/tmp/tmps36anksu/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", | |
| 645 "dbkey": "\"?\"", | |
| 646 "domesticated_input": null, | |
| 647 "genbank_files": "{\"values\": [{\"id\": 3, \"src\": \"hdca\"}]}", | |
| 648 "topology": "\"circular\"" | |
| 649 }, | |
| 650 "state": "ok", | |
| 651 "stderr": "\rassembly: 0%| | 0/2 [00:00<?, ?it/s, now=None]\r \r\rassembly: 0%| | 0/2 [00:00<?, ?it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 2/2 [00:00<00:00, 2.34it/s, now=None]\r \r", | |
| 652 "stdout": "Simulating assembly plan assambly...\n{'cancelled_assemblies': 0, 'errored_assemblies': 2, 'valid_assemblies': 0}\nGenerating assemblies reports...\nFiles in the zip archive:\nassambly_simulation/assambly_all_required_parts.txt\nassambly_simulation/assambly_simulation_stats.csv\nassambly_simulation/Report.pdf\nassambly_simulation/assambly_warnings.csv\nassambly_simulation/assambly_errors.csv\nassambly_simulation/assambly_summary.csv\nassambly_simulation/Construct2_flawed/Construct2_flawed_connections_graph.pdf\nassambly_simulation/Construct2_flawed/error.csv\nassambly_simulation/Construct2_flawed/fragments_in_Construct2_flawed_homology_mix/RFP_GFP_BO_10268_01.pdf\nassambly_simulation/Construct2_flawed/fragments_in_Construct2_flawed_homology_mix/RFP_GFP_BO_10244_01.pdf\nassambly_simulation/Construct2_flawed/fragments_in_Construct2_flawed_homology_mix/RFP_GFP_BO_10281_01.pdf\nassambly_simulation/Construct2_flawed/fragments_in_Construct2_flawed_homology_mix/p1_mRFP1-part1_01.pdf\nassambly_simulation/Construct2_flawed/fragments_in_Construct2_flawed_homology_mix/p3_mRFP1-part3_01.pdf\nassambly_simulation/Construct2_flawed/fragments_in_Construct2_flawed_homology_mix/p7_backbone_01.pdf\nassambly_simulation/Construct2_flawed/fragments_in_Construct2_flawed_homology_mix/RFP_GFP_BO_10232_01.pdf\nassambly_simulation/Construct2_flawed/fragments_in_Construct2_flawed_homology_mix/p4_sfGFP-part1_01.pdf\nassambly_simulation/Construct2_flawed/fragments_in_Construct2_flawed_homology_mix/p5_sfGFP-part2_01.pdf\nassambly_simulation/Construct2_flawed/fragments_in_Construct2_flawed_homology_mix/RFP_GFP_BO_10233_01.pdf\nassambly_simulation/Construct2_flawed/fragments_in_Construct2_flawed_homology_mix/p2_mRFP1-part2_01.pdf\nassambly_simulation/Construct2_flawed/fragments_in_Construct2_flawed_homology_mix/p6_sfGFP-part3_01.pdf\nassambly_simulation/Construct2_flawed/provided_parts_plots/p4_sfGFP-part1.pdf\nassambly_simulation/Construct2_flawed/provided_parts_plots/RFP_GFP_BO_10233.pdf\nassambly_simulation/Construct2_flawed/provided_parts_plots/RFP_GFP_BO_10232.pdf\nassambly_simulation/Construct2_flawed/provided_parts_plots/p6_sfGFP-part3.pdf\nassambly_simulation/Construct2_flawed/provided_parts_plots/p1_mRFP1-part1.pdf\nassambly_simulation/Construct2_flawed/provided_parts_plots/p3_mRFP1-part3.pdf\nassambly_simulation/Construct2_flawed/provided_parts_plots/p2_mRFP1-part2.pdf\nassambly_simulation/Construct2_flawed/provided_parts_plots/RFP_GFP_BO_10244.pdf\nassambly_simulation/Construct2_flawed/provided_parts_plots/RFP_GFP_BO_10268.pdf\nassambly_simulation/Construct2_flawed/provided_parts_plots/RFP_GFP_BO_10281.pdf\nassambly_simulation/Construct2_flawed/provided_parts_plots/p5_sfGFP-part2.pdf\nassambly_simulation/Construct2_flawed/provided_parts_plots/p7_backbone.pdf\nassambly_simulation/Construct2_flawed/provided_parts_records/p5_sfGFP-part2.gb\nassambly_simulation/Construct2_flawed/provided_parts_records/RFP_GFP_BO_10233.gb\nassambly_simulation/Construct2_flawed/provided_parts_records/p6_sfGFP-part3.gb\nassambly_simulation/Construct2_flawed/provided_parts_records/RFP_GFP_BO_10232.gb\nassambly_simulation/Construct2_flawed/provided_parts_records/p2_mRFP1-part2.gb\nassambly_simulation/Construct2_flawed/provided_parts_records/RFP_GFP_BO_10268.gb\nassambly_simulation/Construct2_flawed/provided_parts_records/p1_mRFP1-part1.gb\nassambly_simulation/Construct2_flawed/provided_parts_records/p7_backbone.gb\nassambly_simulation/Construct2_flawed/provided_parts_records/RFP_GFP_BO_10281.gb\nassambly_simulation/Construct2_flawed/provided_parts_records/RFP_GFP_BO_10244.gb\nassambly_simulation/Construct2_flawed/provided_parts_records/p3_mRFP1-part3.gb\nassambly_simulation/Construct2_flawed/provided_parts_records/p4_sfGFP-part1.gb\nassambly_simulation/Construct1/error.csv\nassambly_simulation/Construct1/Construct1_connections_graph.pdf\nassambly_simulation/Construct1/warnings.csv\nassambly_simulation/Construct1/provided_parts_plots/p4_sfGFP-part1.pdf\nassambly_simulation/Construct1/provided_parts_plots/p6_sfGFP-part3.pdf\nassambly_simulation/Construct1/provided_parts_plots/p1_mRFP1-part1.pdf\nassambly_simulation/Construct1/provided_parts_plots/p3_mRFP1-part3.pdf\nassambly_simulation/Construct1/provided_parts_plots/p2_mRFP1-part2.pdf\nassambly_simulation/Construct1/provided_parts_plots/p5_sfGFP-part2.pdf\nassambly_simulation/Construct1/provided_parts_plots/p7_backbone.pdf\nassambly_simulation/Construct1/fragments_in_Construct1_homology_mix/p1_mRFP1-part1_01.pdf\nassambly_simulation/Construct1/fragments_in_Construct1_homology_mix/p3_mRFP1-part3_01.pdf\nassambly_simulation/Construct1/fragments_in_Construct1_homology_mix/p7_backbone_01.pdf\nassambly_simulation/Construct1/fragments_in_Construct1_homology_mix/p4_sfGFP-part1_01.pdf\nassambly_simulation/Construct1/fragments_in_Construct1_homology_mix/p5_sfGFP-part2_01.pdf\nassambly_simulation/Construct1/fragments_in_Construct1_homology_mix/p2_mRFP1-part2_01.pdf\nassambly_simulation/Construct1/fragments_in_Construct1_homology_mix/p6_sfGFP-part3_01.pdf\nassambly_simulation/Construct1/provided_parts_records/p5_sfGFP-part2.gb\nassambly_simulation/Construct1/provided_parts_records/p6_sfGFP-part3.gb\nassambly_simulation/Construct1/provided_parts_records/p2_mRFP1-part2.gb\nassambly_simulation/Construct1/provided_parts_records/p1_mRFP1-part1.gb\nassambly_simulation/Construct1/provided_parts_records/p7_backbone.gb\nassambly_simulation/Construct1/provided_parts_records/p3_mRFP1-part3.gb\nassambly_simulation/Construct1/provided_parts_records/p4_sfGFP-part1.gb\n", | |
| 653 "tool_id": "cloning_simulation", | |
| 654 "tool_stderr": "\rassembly: 0%| | 0/2 [00:00<?, ?it/s, now=None]\r \r\rassembly: 0%| | 0/2 [00:00<?, ?it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 2/2 [00:00<00:00, 2.34it/s, now=None]\r \r", | |
| 655 "tool_stdout": "Simulating assembly plan assambly...\n{'cancelled_assemblies': 0, 'errored_assemblies': 2, 'valid_assemblies': 0}\nGenerating assemblies reports...\nFiles in the zip archive:\nassambly_simulation/assambly_all_required_parts.txt\nassambly_simulation/assambly_simulation_stats.csv\nassambly_simulation/Report.pdf\nassambly_simulation/assambly_warnings.csv\nassambly_simulation/assambly_errors.csv\nassambly_simulation/assambly_summary.csv\nassambly_simulation/Construct2_flawed/Construct2_flawed_connections_graph.pdf\nassambly_simulation/Construct2_flawed/error.csv\nassambly_simulation/Construct2_flawed/fragments_in_Construct2_flawed_homology_mix/RFP_GFP_BO_10268_01.pdf\nassambly_simulation/Construct2_flawed/fragments_in_Construct2_flawed_homology_mix/RFP_GFP_BO_10244_01.pdf\nassambly_simulation/Construct2_flawed/fragments_in_Construct2_flawed_homology_mix/RFP_GFP_BO_10281_01.pdf\nassambly_simulation/Construct2_flawed/fragments_in_Construct2_flawed_homology_mix/p1_mRFP1-part1_01.pdf\nassambly_simulation/Construct2_flawed/fragments_in_Construct2_flawed_homology_mix/p3_mRFP1-part3_01.pdf\nassambly_simulation/Construct2_flawed/fragments_in_Construct2_flawed_homology_mix/p7_backbone_01.pdf\nassambly_simulation/Construct2_flawed/fragments_in_Construct2_flawed_homology_mix/RFP_GFP_BO_10232_01.pdf\nassambly_simulation/Construct2_flawed/fragments_in_Construct2_flawed_homology_mix/p4_sfGFP-part1_01.pdf\nassambly_simulation/Construct2_flawed/fragments_in_Construct2_flawed_homology_mix/p5_sfGFP-part2_01.pdf\nassambly_simulation/Construct2_flawed/fragments_in_Construct2_flawed_homology_mix/RFP_GFP_BO_10233_01.pdf\nassambly_simulation/Construct2_flawed/fragments_in_Construct2_flawed_homology_mix/p2_mRFP1-part2_01.pdf\nassambly_simulation/Construct2_flawed/fragments_in_Construct2_flawed_homology_mix/p6_sfGFP-part3_01.pdf\nassambly_simulation/Construct2_flawed/provided_parts_plots/p4_sfGFP-part1.pdf\nassambly_simulation/Construct2_flawed/provided_parts_plots/RFP_GFP_BO_10233.pdf\nassambly_simulation/Construct2_flawed/provided_parts_plots/RFP_GFP_BO_10232.pdf\nassambly_simulation/Construct2_flawed/provided_parts_plots/p6_sfGFP-part3.pdf\nassambly_simulation/Construct2_flawed/provided_parts_plots/p1_mRFP1-part1.pdf\nassambly_simulation/Construct2_flawed/provided_parts_plots/p3_mRFP1-part3.pdf\nassambly_simulation/Construct2_flawed/provided_parts_plots/p2_mRFP1-part2.pdf\nassambly_simulation/Construct2_flawed/provided_parts_plots/RFP_GFP_BO_10244.pdf\nassambly_simulation/Construct2_flawed/provided_parts_plots/RFP_GFP_BO_10268.pdf\nassambly_simulation/Construct2_flawed/provided_parts_plots/RFP_GFP_BO_10281.pdf\nassambly_simulation/Construct2_flawed/provided_parts_plots/p5_sfGFP-part2.pdf\nassambly_simulation/Construct2_flawed/provided_parts_plots/p7_backbone.pdf\nassambly_simulation/Construct2_flawed/provided_parts_records/p5_sfGFP-part2.gb\nassambly_simulation/Construct2_flawed/provided_parts_records/RFP_GFP_BO_10233.gb\nassambly_simulation/Construct2_flawed/provided_parts_records/p6_sfGFP-part3.gb\nassambly_simulation/Construct2_flawed/provided_parts_records/RFP_GFP_BO_10232.gb\nassambly_simulation/Construct2_flawed/provided_parts_records/p2_mRFP1-part2.gb\nassambly_simulation/Construct2_flawed/provided_parts_records/RFP_GFP_BO_10268.gb\nassambly_simulation/Construct2_flawed/provided_parts_records/p1_mRFP1-part1.gb\nassambly_simulation/Construct2_flawed/provided_parts_records/p7_backbone.gb\nassambly_simulation/Construct2_flawed/provided_parts_records/RFP_GFP_BO_10281.gb\nassambly_simulation/Construct2_flawed/provided_parts_records/RFP_GFP_BO_10244.gb\nassambly_simulation/Construct2_flawed/provided_parts_records/p3_mRFP1-part3.gb\nassambly_simulation/Construct2_flawed/provided_parts_records/p4_sfGFP-part1.gb\nassambly_simulation/Construct1/error.csv\nassambly_simulation/Construct1/Construct1_connections_graph.pdf\nassambly_simulation/Construct1/warnings.csv\nassambly_simulation/Construct1/provided_parts_plots/p4_sfGFP-part1.pdf\nassambly_simulation/Construct1/provided_parts_plots/p6_sfGFP-part3.pdf\nassambly_simulation/Construct1/provided_parts_plots/p1_mRFP1-part1.pdf\nassambly_simulation/Construct1/provided_parts_plots/p3_mRFP1-part3.pdf\nassambly_simulation/Construct1/provided_parts_plots/p2_mRFP1-part2.pdf\nassambly_simulation/Construct1/provided_parts_plots/p5_sfGFP-part2.pdf\nassambly_simulation/Construct1/provided_parts_plots/p7_backbone.pdf\nassambly_simulation/Construct1/fragments_in_Construct1_homology_mix/p1_mRFP1-part1_01.pdf\nassambly_simulation/Construct1/fragments_in_Construct1_homology_mix/p3_mRFP1-part3_01.pdf\nassambly_simulation/Construct1/fragments_in_Construct1_homology_mix/p7_backbone_01.pdf\nassambly_simulation/Construct1/fragments_in_Construct1_homology_mix/p4_sfGFP-part1_01.pdf\nassambly_simulation/Construct1/fragments_in_Construct1_homology_mix/p5_sfGFP-part2_01.pdf\nassambly_simulation/Construct1/fragments_in_Construct1_homology_mix/p2_mRFP1-part2_01.pdf\nassambly_simulation/Construct1/fragments_in_Construct1_homology_mix/p6_sfGFP-part3_01.pdf\nassambly_simulation/Construct1/provided_parts_records/p5_sfGFP-part2.gb\nassambly_simulation/Construct1/provided_parts_records/p6_sfGFP-part3.gb\nassambly_simulation/Construct1/provided_parts_records/p2_mRFP1-part2.gb\nassambly_simulation/Construct1/provided_parts_records/p1_mRFP1-part1.gb\nassambly_simulation/Construct1/provided_parts_records/p7_backbone.gb\nassambly_simulation/Construct1/provided_parts_records/p3_mRFP1-part3.gb\nassambly_simulation/Construct1/provided_parts_records/p4_sfGFP-part1.gb\n", | |
| 656 "update_time": "2025-05-16T08:55:47.617074", | |
| 657 "user_email": "planemo@galaxyproject.org", | |
| 658 "user_id": "1d1943aa60deb628" | |
| 659 }, | |
| 660 "status": "success", | |
| 661 "test_index": 2, | |
| 662 "time_seconds": 24.352636098861694, | |
| 663 "tool_id": "cloning_simulation", | |
| 664 "tool_version": "0.1.0+galaxy0" | |
| 665 }, | |
| 666 "has_data": true, | |
| 667 "id": "cloning_simulation-2" | |
| 668 }, | |
| 669 { | |
| 670 "data": { | |
| 671 "inputs": { | |
| 672 "adv|use_file_names_as_ids": true, | |
| 673 "assembly_csv": { | |
| 674 "id": "c4d206bede85e5c1", | |
| 675 "src": "hda" | |
| 676 }, | |
| 677 "assembly_plan_name": "BASICAssembly", | |
| 678 "genbank_files": { | |
| 679 "id": "248d7f69d2402068", | |
| 680 "src": "hdca" | |
| 681 }, | |
| 682 "topology": "circular" | |
| 683 }, | |
| 684 "job": { | |
| 685 "command_line": "mkdir 'outdir_zip' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmps36anksu/files/0/9/d/dataset_09dd12f1-a528-4e2a-a1d3-b9b57e7a02a2.dat,/tmp/tmps36anksu/files/b/e/6/dataset_be63c5f6-6c15-43c9-a467-0f00c3395bcf.dat,/tmp/tmps36anksu/files/2/e/0/dataset_2e03930b-3e9f-45be-9750-42560f39cf14.dat,/tmp/tmps36anksu/files/5/b/d/dataset_5bdbe27f-640f-4db1-bc7b-fcedf4b2737a.dat,/tmp/tmps36anksu/files/c/d/5/dataset_cd53d85a-7ced-4da5-bc73-eb4b74a200e3.dat' --domesticated_seq '' --assembly_csv '/tmp/tmps36anksu/files/e/d/3/dataset_ed3f4797-0002-46e3-a245-70ec97e59118.dat' --assembly_plan_name 'BASICAssembly' --file_name_mapping '/tmp/tmps36anksu/files/0/9/d/dataset_09dd12f1-a528-4e2a-a1d3-b9b57e7a02a2.dat:GFP.gb,/tmp/tmps36anksu/files/b/e/6/dataset_be63c5f6-6c15-43c9-a467-0f00c3395bcf.dat:p15A_kan.gb,/tmp/tmps36anksu/files/2/e/0/dataset_2e03930b-3e9f-45be-9750-42560f39cf14.dat:promoter.gb,/tmp/tmps36anksu/files/5/b/d/dataset_5bdbe27f-640f-4db1-bc7b-fcedf4b2737a.dat:RFP.gb,/tmp/tmps36anksu/files/c/d/5/dataset_cd53d85a-7ced-4da5-bc73-eb4b74a200e3.dat:oligos.fa' --file_name_mapping_dom '' --use_file_names_as_id 'true' --outdir_simulation 'outdir_zip' --output_simulation 'output_zip.zip' --enzyme 'auto' --topology 'circular'&& cp 'output_zip.zip' '/tmp/tmps36anksu/job_working_directory/000/28/outputs/dataset_2ce9e85d-d4e7-4104-833f-9fcac95e2c6d.dat'", | |
| 686 "command_version": "", | |
| 687 "copied_from_job_id": null, | |
| 688 "create_time": "2025-05-16T08:56:09.388287", | |
| 689 "dependencies": [], | |
| 690 "exit_code": 0, | |
| 691 "external_id": "70839", | |
| 692 "galaxy_version": "24.2", | |
| 693 "handler": null, | |
| 694 "history_id": "248d7f69d2402068", | |
| 695 "id": "ecaf8d4d1aeb8c86", | |
| 696 "inputs": { | |
| 697 "assembly_csv": { | |
| 698 "id": "c4d206bede85e5c1", | |
| 699 "src": "hda", | |
| 700 "uuid": "ed3f4797-0002-46e3-a245-70ec97e59118" | |
| 701 }, | |
| 702 "genbank_files1": { | |
| 703 "id": "065a19c3622776e9", | |
| 704 "src": "hda", | |
| 705 "uuid": "09dd12f1-a528-4e2a-a1d3-b9b57e7a02a2" | |
| 706 }, | |
| 707 "genbank_files2": { | |
| 708 "id": "ac67f4a6521db48c", | |
| 709 "src": "hda", | |
| 710 "uuid": "be63c5f6-6c15-43c9-a467-0f00c3395bcf" | |
| 711 }, | |
| 712 "genbank_files3": { | |
| 713 "id": "77ed38528f61eafd", | |
| 714 "src": "hda", | |
| 715 "uuid": "2e03930b-3e9f-45be-9750-42560f39cf14" | |
| 716 }, | |
| 717 "genbank_files4": { | |
| 718 "id": "626b9fd2eae5943c", | |
| 719 "src": "hda", | |
| 720 "uuid": "5bdbe27f-640f-4db1-bc7b-fcedf4b2737a" | |
| 721 }, | |
| 722 "genbank_files5": { | |
| 723 "id": "4a4771cb4e71e8ed", | |
| 724 "src": "hda", | |
| 725 "uuid": "cd53d85a-7ced-4da5-bc73-eb4b74a200e3" | |
| 726 } | |
| 727 }, | |
| 728 "job_messages": [], | |
| 729 "job_metrics": [], | |
| 730 "job_runner_name": null, | |
| 731 "job_stderr": "", | |
| 732 "job_stdout": "", | |
| 733 "model_class": "Job", | |
| 734 "output_collections": {}, | |
| 735 "outputs": { | |
| 736 "output_zip": { | |
| 737 "id": "ecaf8d4d1aeb8c86", | |
| 738 "src": "hda", | |
| 739 "uuid": "2ce9e85d-d4e7-4104-833f-9fcac95e2c6d" | |
| 740 } | |
| 741 }, | |
| 742 "params": { | |
| 743 "__input_ext": "\"input\"", | |
| 744 "adv": "{\"enzyme\": \"auto\", \"use_file_names_as_ids\": true}", | |
| 745 "assembly_plan_name": "\"BASICAssembly\"", | |
| 746 "chromInfo": "\"/tmp/tmps36anksu/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", | |
| 747 "dbkey": "\"?\"", | |
| 748 "domesticated_input": null, | |
| 749 "genbank_files": "{\"values\": [{\"id\": 4, \"src\": \"hdca\"}]}", | |
| 750 "topology": "\"circular\"" | |
| 751 }, | |
| 752 "state": "ok", | |
| 753 "stderr": "\rassembly: 0%| | 0/10 [00:00<?, ?it/s, now=None]\r \r\rassembly: 0%| | 0/8 [00:00<?, ?it/s, now=None]\rassembly: 62%|\u2588\u2588\u2588\u2588\u2588\u2588\u258e | 5/8 [00:00<00:00, 49.95it/s, now=None]\r \r", | |
| 754 "stdout": "Simulating assembly plan assambly...\n{'cancelled_assemblies': 2, 'errored_assemblies': 8, 'valid_assemblies': 0}\nGenerating assemblies reports...\nFiles in the zip archive:\nassambly_simulation/assambly_all_required_parts.txt\nassambly_simulation/assambly_simulation_stats.csv\nassambly_simulation/Report.pdf\nassambly_simulation/assambly_cancelled_assemblies.csv\nassambly_simulation/assambly_errors.csv\nassambly_simulation/assembly_plan_graph.pdf\nassambly_simulation/assambly_summary.csv\nassambly_simulation/LMA-S/error.csv\nassambly_simulation/LMA-S/provided_parts_plots/LMA-S_fwd.pdf\nassambly_simulation/LMA-S/provided_parts_plots/LMA-S_adapter.pdf\nassambly_simulation/LMA-S/provided_parts_records/LMA-S_adapter.gb\nassambly_simulation/LMA-S/provided_parts_records/LMA-S_fwd.gb\nassambly_simulation/L2RBS-xS/error.csv\nassambly_simulation/L2RBS-xS/provided_parts_plots/L2RBS-xS_adapter.pdf\nassambly_simulation/L2RBS-xS/provided_parts_plots/L2RBS-xS_fwd.pdf\nassambly_simulation/L2RBS-xS/provided_parts_records/L2RBS-xS_fwd.gb\nassambly_simulation/L2RBS-xS/provided_parts_records/L2RBS-xS_adapter.gb\nassambly_simulation/L1RBS-xS/error.csv\nassambly_simulation/L1RBS-xS/provided_parts_plots/L1RBS-xS_adapter.pdf\nassambly_simulation/L1RBS-xS/provided_parts_plots/L1RBS-xS_fwd.pdf\nassambly_simulation/L1RBS-xS/provided_parts_records/L1RBS-xS_fwd.gb\nassambly_simulation/L1RBS-xS/provided_parts_records/L1RBS-xS_adapter.gb\nassambly_simulation/LMB-P/error.csv\nassambly_simulation/LMB-P/provided_parts_plots/LMB-P_adapter.pdf\nassambly_simulation/LMB-P/provided_parts_plots/LMB-P_fwd.pdf\nassambly_simulation/LMB-P/provided_parts_records/LMB-P_fwd.gb\nassambly_simulation/LMB-P/provided_parts_records/LMB-P_adapter.gb\nassambly_simulation/L1RBS-1P/error.csv\nassambly_simulation/L1RBS-1P/provided_parts_plots/L1RBS-1P_fwd.pdf\nassambly_simulation/L1RBS-1P/provided_parts_plots/L1RBS-1P_adapter.pdf\nassambly_simulation/L1RBS-1P/provided_parts_records/L1RBS-1P_adapter.gb\nassambly_simulation/L1RBS-1P/provided_parts_records/L1RBS-1P_fwd.gb\nassambly_simulation/L2RBS-1P/error.csv\nassambly_simulation/L2RBS-1P/provided_parts_plots/L2RBS-1P_fwd.pdf\nassambly_simulation/L2RBS-1P/provided_parts_plots/L2RBS-1P_adapter.pdf\nassambly_simulation/L2RBS-1P/provided_parts_records/L2RBS-1P_adapter.gb\nassambly_simulation/L2RBS-1P/provided_parts_records/L2RBS-1P_fwd.gb\nassambly_simulation/LMA-P/error.csv\nassambly_simulation/LMA-P/provided_parts_plots/LMA-P_fwd.pdf\nassambly_simulation/LMA-P/provided_parts_plots/LMA-P_adapter.pdf\nassambly_simulation/LMA-P/provided_parts_records/LMA-P_fwd.gb\nassambly_simulation/LMA-P/provided_parts_records/LMA-P_adapter.gb\nassambly_simulation/LMB-S/error.csv\nassambly_simulation/LMB-S/provided_parts_plots/LMB-S_fwd.pdf\nassambly_simulation/LMB-S/provided_parts_plots/LMB-S_adapter.pdf\nassambly_simulation/LMB-S/provided_parts_records/LMB-S_fwd.gb\nassambly_simulation/LMB-S/provided_parts_records/LMB-S_adapter.gb\n", | |
| 755 "tool_id": "cloning_simulation", | |
| 756 "tool_stderr": "\rassembly: 0%| | 0/10 [00:00<?, ?it/s, now=None]\r \r\rassembly: 0%| | 0/8 [00:00<?, ?it/s, now=None]\rassembly: 62%|\u2588\u2588\u2588\u2588\u2588\u2588\u258e | 5/8 [00:00<00:00, 49.95it/s, now=None]\r \r", | |
| 757 "tool_stdout": "Simulating assembly plan assambly...\n{'cancelled_assemblies': 2, 'errored_assemblies': 8, 'valid_assemblies': 0}\nGenerating assemblies reports...\nFiles in the zip archive:\nassambly_simulation/assambly_all_required_parts.txt\nassambly_simulation/assambly_simulation_stats.csv\nassambly_simulation/Report.pdf\nassambly_simulation/assambly_cancelled_assemblies.csv\nassambly_simulation/assambly_errors.csv\nassambly_simulation/assembly_plan_graph.pdf\nassambly_simulation/assambly_summary.csv\nassambly_simulation/LMA-S/error.csv\nassambly_simulation/LMA-S/provided_parts_plots/LMA-S_fwd.pdf\nassambly_simulation/LMA-S/provided_parts_plots/LMA-S_adapter.pdf\nassambly_simulation/LMA-S/provided_parts_records/LMA-S_adapter.gb\nassambly_simulation/LMA-S/provided_parts_records/LMA-S_fwd.gb\nassambly_simulation/L2RBS-xS/error.csv\nassambly_simulation/L2RBS-xS/provided_parts_plots/L2RBS-xS_adapter.pdf\nassambly_simulation/L2RBS-xS/provided_parts_plots/L2RBS-xS_fwd.pdf\nassambly_simulation/L2RBS-xS/provided_parts_records/L2RBS-xS_fwd.gb\nassambly_simulation/L2RBS-xS/provided_parts_records/L2RBS-xS_adapter.gb\nassambly_simulation/L1RBS-xS/error.csv\nassambly_simulation/L1RBS-xS/provided_parts_plots/L1RBS-xS_adapter.pdf\nassambly_simulation/L1RBS-xS/provided_parts_plots/L1RBS-xS_fwd.pdf\nassambly_simulation/L1RBS-xS/provided_parts_records/L1RBS-xS_fwd.gb\nassambly_simulation/L1RBS-xS/provided_parts_records/L1RBS-xS_adapter.gb\nassambly_simulation/LMB-P/error.csv\nassambly_simulation/LMB-P/provided_parts_plots/LMB-P_adapter.pdf\nassambly_simulation/LMB-P/provided_parts_plots/LMB-P_fwd.pdf\nassambly_simulation/LMB-P/provided_parts_records/LMB-P_fwd.gb\nassambly_simulation/LMB-P/provided_parts_records/LMB-P_adapter.gb\nassambly_simulation/L1RBS-1P/error.csv\nassambly_simulation/L1RBS-1P/provided_parts_plots/L1RBS-1P_fwd.pdf\nassambly_simulation/L1RBS-1P/provided_parts_plots/L1RBS-1P_adapter.pdf\nassambly_simulation/L1RBS-1P/provided_parts_records/L1RBS-1P_adapter.gb\nassambly_simulation/L1RBS-1P/provided_parts_records/L1RBS-1P_fwd.gb\nassambly_simulation/L2RBS-1P/error.csv\nassambly_simulation/L2RBS-1P/provided_parts_plots/L2RBS-1P_fwd.pdf\nassambly_simulation/L2RBS-1P/provided_parts_plots/L2RBS-1P_adapter.pdf\nassambly_simulation/L2RBS-1P/provided_parts_records/L2RBS-1P_adapter.gb\nassambly_simulation/L2RBS-1P/provided_parts_records/L2RBS-1P_fwd.gb\nassambly_simulation/LMA-P/error.csv\nassambly_simulation/LMA-P/provided_parts_plots/LMA-P_fwd.pdf\nassambly_simulation/LMA-P/provided_parts_plots/LMA-P_adapter.pdf\nassambly_simulation/LMA-P/provided_parts_records/LMA-P_fwd.gb\nassambly_simulation/LMA-P/provided_parts_records/LMA-P_adapter.gb\nassambly_simulation/LMB-S/error.csv\nassambly_simulation/LMB-S/provided_parts_plots/LMB-S_fwd.pdf\nassambly_simulation/LMB-S/provided_parts_plots/LMB-S_adapter.pdf\nassambly_simulation/LMB-S/provided_parts_records/LMB-S_fwd.gb\nassambly_simulation/LMB-S/provided_parts_records/LMB-S_adapter.gb\n", | |
| 758 "update_time": "2025-05-16T08:56:20.015826", | |
| 759 "user_email": "planemo@galaxyproject.org", | |
| 760 "user_id": "1d1943aa60deb628" | |
| 761 }, | |
| 762 "status": "success", | |
| 763 "test_index": 3, | |
| 764 "time_seconds": 32.09558367729187, | |
| 765 "tool_id": "cloning_simulation", | |
| 766 "tool_version": "0.1.0+galaxy0" | |
| 767 }, | |
| 768 "has_data": true, | |
| 769 "id": "cloning_simulation-3" | |
| 770 }, | |
| 771 { | |
| 772 "data": { | |
| 773 "inputs": { | |
| 774 "adv|use_file_names_as_ids": true, | |
| 775 "assembly_csv": { | |
| 776 "id": "1b325227d95fdc76", | |
| 777 "src": "hda" | |
| 778 }, | |
| 779 "assembly_plan_name": "BioBrickStandardAssembly", | |
| 780 "genbank_files": { | |
| 781 "id": "a363c57bce5ddac4", | |
| 782 "src": "hdca" | |
| 783 }, | |
| 784 "topology": "circular" | |
| 785 }, | |
| 786 "job": { | |
| 787 "command_line": "mkdir 'outdir_zip' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmps36anksu/files/4/8/f/dataset_48f246fb-df3d-4c65-a99e-cc314c9a2d20.dat,/tmp/tmps36anksu/files/5/0/c/dataset_50cb308d-4eb5-4d9d-ae07-011179d84b2e.dat,/tmp/tmps36anksu/files/1/3/b/dataset_13b514d1-710c-46ef-9b83-939acad72375.dat,/tmp/tmps36anksu/files/3/0/b/dataset_30bef7c3-fecb-40f7-b435-daf794d456c1.dat,/tmp/tmps36anksu/files/a/8/7/dataset_a87d7ba7-2092-45e2-9aff-813bb53a02a6.dat' --domesticated_seq '' --assembly_csv '/tmp/tmps36anksu/files/7/e/6/dataset_7e6259bf-8646-4691-b40d-d91bbe52d6c5.dat' --assembly_plan_name 'BioBrickStandardAssembly' --file_name_mapping '/tmp/tmps36anksu/files/4/8/f/dataset_48f246fb-df3d-4c65-a99e-cc314c9a2d20.dat:BBa_E0040_GFP.gb,/tmp/tmps36anksu/files/5/0/c/dataset_50cb308d-4eb5-4d9d-ae07-011179d84b2e.dat:BBa_J23119_prom.gb,/tmp/tmps36anksu/files/1/3/b/dataset_13b514d1-710c-46ef-9b83-939acad72375.dat:BBa_J23119_prom_flawed.gb,/tmp/tmps36anksu/files/3/0/b/dataset_30bef7c3-fecb-40f7-b435-daf794d456c1.dat:BBa_J61048_term.gb,/tmp/tmps36anksu/files/a/8/7/dataset_a87d7ba7-2092-45e2-9aff-813bb53a02a6.dat:BBa_K611094_bar.gb' --file_name_mapping_dom '' --use_file_names_as_id 'true' --outdir_simulation 'outdir_zip' --output_simulation 'output_zip.zip' --enzyme 'auto' --topology 'circular'&& cp 'output_zip.zip' '/tmp/tmps36anksu/job_working_directory/000/35/outputs/dataset_664a6a95-4ce6-4f74-be51-728a9cbd55da.dat'", | |
| 788 "command_version": "", | |
| 789 "copied_from_job_id": null, | |
| 790 "create_time": "2025-05-16T08:56:41.646034", | |
| 791 "dependencies": [ | |
| 792 { | |
| 793 "cacheable": false, | |
| 794 "dependency_resolver": { | |
| 795 "auto_init": true, | |
| 796 "auto_install": true, | |
| 797 "can_uninstall_dependencies": true, | |
| 798 "ensure_channels": "conda-forge,bioconda", | |
| 799 "model_class": "CondaDependencyResolver", | |
| 800 "prefix": "/home/rkhaled/miniconda3", | |
| 801 "read_only": false, | |
| 802 "resolver_type": "conda", | |
| 803 "resolves_simple_dependencies": true, | |
| 804 "use_local": false, | |
| 805 "versionless": false | |
| 806 }, | |
| 807 "dependency_type": "conda", | |
| 808 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-414e7261396ae5d11be85675e1e19db222325018468f2829061591addd560be0", | |
| 809 "exact": true, | |
| 810 "model_class": "MergedCondaDependency", | |
| 811 "name": "flametree", | |
| 812 "version": "0.1.11" | |
| 813 }, | |
| 814 { | |
| 815 "cacheable": false, | |
| 816 "dependency_resolver": { | |
| 817 "auto_init": true, | |
| 818 "auto_install": true, | |
| 819 "can_uninstall_dependencies": true, | |
| 820 "ensure_channels": "conda-forge,bioconda", | |
| 821 "model_class": "CondaDependencyResolver", | |
| 822 "prefix": "/home/rkhaled/miniconda3", | |
| 823 "read_only": false, | |
| 824 "resolver_type": "conda", | |
| 825 "resolves_simple_dependencies": true, | |
| 826 "use_local": false, | |
| 827 "versionless": false | |
| 828 }, | |
| 829 "dependency_type": "conda", | |
| 830 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-414e7261396ae5d11be85675e1e19db222325018468f2829061591addd560be0", | |
| 831 "exact": true, | |
| 832 "model_class": "MergedCondaDependency", | |
| 833 "name": "biopython", | |
| 834 "version": "1.85" | |
| 835 }, | |
| 836 { | |
| 837 "cacheable": false, | |
| 838 "dependency_resolver": { | |
| 839 "auto_init": true, | |
| 840 "auto_install": true, | |
| 841 "can_uninstall_dependencies": true, | |
| 842 "ensure_channels": "conda-forge,bioconda", | |
| 843 "model_class": "CondaDependencyResolver", | |
| 844 "prefix": "/home/rkhaled/miniconda3", | |
| 845 "read_only": false, | |
| 846 "resolver_type": "conda", | |
| 847 "resolves_simple_dependencies": true, | |
| 848 "use_local": false, | |
| 849 "versionless": false | |
| 850 }, | |
| 851 "dependency_type": "conda", | |
| 852 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-414e7261396ae5d11be85675e1e19db222325018468f2829061591addd560be0", | |
| 853 "exact": true, | |
| 854 "model_class": "MergedCondaDependency", | |
| 855 "name": "proglog", | |
| 856 "version": "0.1.10" | |
| 857 }, | |
| 858 { | |
| 859 "cacheable": false, | |
| 860 "dependency_resolver": { | |
| 861 "auto_init": true, | |
| 862 "auto_install": true, | |
| 863 "can_uninstall_dependencies": true, | |
| 864 "ensure_channels": "conda-forge,bioconda", | |
| 865 "model_class": "CondaDependencyResolver", | |
| 866 "prefix": "/home/rkhaled/miniconda3", | |
| 867 "read_only": false, | |
| 868 "resolver_type": "conda", | |
| 869 "resolves_simple_dependencies": true, | |
| 870 "use_local": false, | |
| 871 "versionless": false | |
| 872 }, | |
| 873 "dependency_type": "conda", | |
| 874 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-414e7261396ae5d11be85675e1e19db222325018468f2829061591addd560be0", | |
| 875 "exact": true, | |
| 876 "model_class": "MergedCondaDependency", | |
| 877 "name": "pandas", | |
| 878 "version": "2.2.3" | |
| 879 }, | |
| 880 { | |
| 881 "cacheable": false, | |
| 882 "dependency_resolver": { | |
| 883 "auto_init": true, | |
| 884 "auto_install": true, | |
| 885 "can_uninstall_dependencies": true, | |
| 886 "ensure_channels": "conda-forge,bioconda", | |
| 887 "model_class": "CondaDependencyResolver", | |
| 888 "prefix": "/home/rkhaled/miniconda3", | |
| 889 "read_only": false, | |
| 890 "resolver_type": "conda", | |
| 891 "resolves_simple_dependencies": true, | |
| 892 "use_local": false, | |
| 893 "versionless": false | |
| 894 }, | |
| 895 "dependency_type": "conda", | |
| 896 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-414e7261396ae5d11be85675e1e19db222325018468f2829061591addd560be0", | |
| 897 "exact": true, | |
| 898 "model_class": "MergedCondaDependency", | |
| 899 "name": "dnacauldron", | |
| 900 "version": "2.0.12" | |
| 901 }, | |
| 902 { | |
| 903 "cacheable": false, | |
| 904 "dependency_resolver": { | |
| 905 "auto_init": true, | |
| 906 "auto_install": true, | |
| 907 "can_uninstall_dependencies": true, | |
| 908 "ensure_channels": "conda-forge,bioconda", | |
| 909 "model_class": "CondaDependencyResolver", | |
| 910 "prefix": "/home/rkhaled/miniconda3", | |
| 911 "read_only": false, | |
| 912 "resolver_type": "conda", | |
| 913 "resolves_simple_dependencies": true, | |
| 914 "use_local": false, | |
| 915 "versionless": false | |
| 916 }, | |
| 917 "dependency_type": "conda", | |
| 918 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-414e7261396ae5d11be85675e1e19db222325018468f2829061591addd560be0", | |
| 919 "exact": true, | |
| 920 "model_class": "MergedCondaDependency", | |
| 921 "name": "pdf-reports", | |
| 922 "version": "0.3.9" | |
| 923 }, | |
| 924 { | |
| 925 "cacheable": false, | |
| 926 "dependency_resolver": { | |
| 927 "auto_init": true, | |
| 928 "auto_install": true, | |
| 929 "can_uninstall_dependencies": true, | |
| 930 "ensure_channels": "conda-forge,bioconda", | |
| 931 "model_class": "CondaDependencyResolver", | |
| 932 "prefix": "/home/rkhaled/miniconda3", | |
| 933 "read_only": false, | |
| 934 "resolver_type": "conda", | |
| 935 "resolves_simple_dependencies": true, | |
| 936 "use_local": false, | |
| 937 "versionless": false | |
| 938 }, | |
| 939 "dependency_type": "conda", | |
| 940 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-414e7261396ae5d11be85675e1e19db222325018468f2829061591addd560be0", | |
| 941 "exact": true, | |
| 942 "model_class": "MergedCondaDependency", | |
| 943 "name": "sequenticon", | |
| 944 "version": "0.1.8" | |
| 945 }, | |
| 946 { | |
| 947 "cacheable": false, | |
| 948 "dependency_resolver": { | |
| 949 "auto_init": true, | |
| 950 "auto_install": true, | |
| 951 "can_uninstall_dependencies": true, | |
| 952 "ensure_channels": "conda-forge,bioconda", | |
| 953 "model_class": "CondaDependencyResolver", | |
| 954 "prefix": "/home/rkhaled/miniconda3", | |
| 955 "read_only": false, | |
| 956 "resolver_type": "conda", | |
| 957 "resolves_simple_dependencies": true, | |
| 958 "use_local": false, | |
| 959 "versionless": false | |
| 960 }, | |
| 961 "dependency_type": "conda", | |
| 962 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-414e7261396ae5d11be85675e1e19db222325018468f2829061591addd560be0", | |
| 963 "exact": true, | |
| 964 "model_class": "MergedCondaDependency", | |
| 965 "name": "dna_features_viewer", | |
| 966 "version": "3.1.4" | |
| 967 } | |
| 968 ], | |
| 969 "exit_code": 0, | |
| 970 "external_id": "71459", | |
| 971 "galaxy_version": "24.2", | |
| 972 "handler": null, | |
| 973 "history_id": "a363c57bce5ddac4", | |
| 974 "id": "4d500d87322140a3", | |
| 975 "inputs": { | |
| 976 "assembly_csv": { | |
| 977 "id": "1b325227d95fdc76", | |
| 978 "src": "hda", | |
| 979 "uuid": "7e6259bf-8646-4691-b40d-d91bbe52d6c5" | |
| 980 }, | |
| 981 "genbank_files1": { | |
| 982 "id": "2d4530cd892a2a69", | |
| 983 "src": "hda", | |
| 984 "uuid": "48f246fb-df3d-4c65-a99e-cc314c9a2d20" | |
| 985 }, | |
| 986 "genbank_files2": { | |
| 987 "id": "afd885e9dc2aeeee", | |
| 988 "src": "hda", | |
| 989 "uuid": "50cb308d-4eb5-4d9d-ae07-011179d84b2e" | |
| 990 }, | |
| 991 "genbank_files3": { | |
| 992 "id": "ae8033db013a49b9", | |
| 993 "src": "hda", | |
| 994 "uuid": "13b514d1-710c-46ef-9b83-939acad72375" | |
| 995 }, | |
| 996 "genbank_files4": { | |
| 997 "id": "0661f11e9507b8a6", | |
| 998 "src": "hda", | |
| 999 "uuid": "30bef7c3-fecb-40f7-b435-daf794d456c1" | |
| 1000 }, | |
| 1001 "genbank_files5": { | |
| 1002 "id": "fcc678ee7e8e9f81", | |
| 1003 "src": "hda", | |
| 1004 "uuid": "a87d7ba7-2092-45e2-9aff-813bb53a02a6" | |
| 1005 } | |
| 1006 }, | |
| 1007 "job_messages": [], | |
| 1008 "job_metrics": [], | |
| 1009 "job_runner_name": null, | |
| 1010 "job_stderr": "", | |
| 1011 "job_stdout": "", | |
| 1012 "model_class": "Job", | |
| 1013 "output_collections": {}, | |
| 1014 "outputs": { | |
| 1015 "output_zip": { | |
| 1016 "id": "4d500d87322140a3", | |
| 1017 "src": "hda", | |
| 1018 "uuid": "664a6a95-4ce6-4f74-be51-728a9cbd55da" | |
| 1019 } | |
| 1020 }, | |
| 1021 "params": { | |
| 1022 "__input_ext": "\"input\"", | |
| 1023 "adv": "{\"enzyme\": \"auto\", \"use_file_names_as_ids\": true}", | |
| 1024 "assembly_plan_name": "\"BioBrickStandardAssembly\"", | |
| 1025 "chromInfo": "\"/tmp/tmps36anksu/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", | |
| 1026 "dbkey": "\"?\"", | |
| 1027 "domesticated_input": null, | |
| 1028 "genbank_files": "{\"values\": [{\"id\": 5, \"src\": \"hdca\"}]}", | |
| 1029 "topology": "\"circular\"" | |
| 1030 }, | |
| 1031 "state": "ok", | |
| 1032 "stderr": "\rassembly: 0%| | 0/3 [00:00<?, ?it/s, now=None]\r \r\rassembly: 0%| | 0/3 [00:00<?, ?it/s, now=None]\rassembly: 67%|\u2588\u2588\u2588\u2588\u2588\u2588\u258b | 2/3 [00:01<00:00, 1.96it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 3/3 [00:01<00:00, 1.59it/s, now=None]\r \r", | |
| 1033 "stdout": "Simulating assembly plan assambly...\n{'cancelled_assemblies': 0, 'errored_assemblies': 0, 'valid_assemblies': 3}\nGenerating assemblies reports...\nFiles in the zip archive:\nassambly_simulation/assambly_all_required_parts.txt\nassambly_simulation/assambly_constructs_level_2.csv\nassambly_simulation/assambly_simulation_stats.csv\nassambly_simulation/assambly_constructs_level_1.csv\nassambly_simulation/Report.pdf\nassambly_simulation/assembly_plan_graph.pdf\nassambly_simulation/assambly_summary.csv\nassambly_simulation/C3_final/C3_final_C1_prom_barcode_E+S_restriction_parts_graph.pdf\nassambly_simulation/C3_final/C3_final_C2_gfp_term_E+X_restriction_connections_graph.pdf\nassambly_simulation/C3_final/C3_final_assembly_mix_connections_graph.pdf\nassambly_simulation/C3_final/C3_final_C1_prom_barcode_E+S_restriction_connections_graph.pdf\nassambly_simulation/C3_final/C3_final_C2_gfp_term_E+X_restriction_parts_graph.pdf\nassambly_simulation/C3_final/C3_final_assembly_mix_parts_graph.pdf\nassambly_simulation/C3_final/C3_final.gb\nassambly_simulation/C3_final/C3_final_summary.csv\nassambly_simulation/C3_final/C3_final.pdf\nassambly_simulation/C3_final/provided_parts_records/C1_prom_barcode.gb\nassambly_simulation/C3_final/provided_parts_records/C2_gfp_term.gb\nassambly_simulation/C2_gfp_term/C2_gfp_term_BBa_E0040_GFP_E+S_restriction_parts_graph.pdf\nassambly_simulation/C2_gfp_term/C2_gfp_term_assembly_mix_parts_graph.pdf\nassambly_simulation/C2_gfp_term/C2_gfp_term_BBa_J61048_term_E+X_restriction_parts_graph.pdf\nassambly_simulation/C2_gfp_term/C2_gfp_term.gb\nassambly_simulation/C2_gfp_term/C2_gfp_term_BBa_J61048_term_E+X_restriction_connections_graph.pdf\nassambly_simulation/C2_gfp_term/C2_gfp_term_assembly_mix_connections_graph.pdf\nassambly_simulation/C2_gfp_term/C2_gfp_term_BBa_E0040_GFP_E+S_restriction_connections_graph.pdf\nassambly_simulation/C2_gfp_term/C2_gfp_term.pdf\nassambly_simulation/C2_gfp_term/C2_gfp_term_summary.csv\nassambly_simulation/C2_gfp_term/provided_parts_records/BBa_J61048_term.gb\nassambly_simulation/C2_gfp_term/provided_parts_records/BBa_E0040_GFP.gb\nassambly_simulation/all_construct_records/C1_prom_barcode.gb\nassambly_simulation/all_construct_records/C2_gfp_term.gb\nassambly_simulation/all_construct_records/C3_final.gb\nassambly_simulation/part_records/BBa_J61048_term.gb\nassambly_simulation/part_records/BBa_K611094_bar.gb\nassambly_simulation/part_records/BBa_E0040_GFP.gb\nassambly_simulation/part_records/BBa_J23119_prom.gb\nassambly_simulation/C1_prom_barcode/C1_prom_barcode_BBa_J23119_prom_E+X_restriction_parts_graph.pdf\nassambly_simulation/C1_prom_barcode/C1_prom_barcode.gb\nassambly_simulation/C1_prom_barcode/C1_prom_barcode_assembly_mix_connections_graph.pdf\nassambly_simulation/C1_prom_barcode/C1_prom_barcode_BBa_K611094_bar_E+S_restriction_parts_graph.pdf\nassambly_simulation/C1_prom_barcode/C1_prom_barcode_BBa_K611094_bar_E+S_restriction_connections_graph.pdf\nassambly_simulation/C1_prom_barcode/C1_prom_barcode.pdf\nassambly_simulation/C1_prom_barcode/C1_prom_barcode_summary.csv\nassambly_simulation/C1_prom_barcode/C1_prom_barcode_assembly_mix_parts_graph.pdf\nassambly_simulation/C1_prom_barcode/C1_prom_barcode_BBa_J23119_prom_E+X_restriction_connections_graph.pdf\nassambly_simulation/C1_prom_barcode/provided_parts_records/BBa_K611094_bar.gb\nassambly_simulation/C1_prom_barcode/provided_parts_records/BBa_J23119_prom.gb\n", | |
| 1034 "tool_id": "cloning_simulation", | |
| 1035 "tool_stderr": "\rassembly: 0%| | 0/3 [00:00<?, ?it/s, now=None]\r \r\rassembly: 0%| | 0/3 [00:00<?, ?it/s, now=None]\rassembly: 67%|\u2588\u2588\u2588\u2588\u2588\u2588\u258b | 2/3 [00:01<00:00, 1.96it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 3/3 [00:01<00:00, 1.59it/s, now=None]\r \r", | |
| 1036 "tool_stdout": "Simulating assembly plan assambly...\n{'cancelled_assemblies': 0, 'errored_assemblies': 0, 'valid_assemblies': 3}\nGenerating assemblies reports...\nFiles in the zip archive:\nassambly_simulation/assambly_all_required_parts.txt\nassambly_simulation/assambly_constructs_level_2.csv\nassambly_simulation/assambly_simulation_stats.csv\nassambly_simulation/assambly_constructs_level_1.csv\nassambly_simulation/Report.pdf\nassambly_simulation/assembly_plan_graph.pdf\nassambly_simulation/assambly_summary.csv\nassambly_simulation/C3_final/C3_final_C1_prom_barcode_E+S_restriction_parts_graph.pdf\nassambly_simulation/C3_final/C3_final_C2_gfp_term_E+X_restriction_connections_graph.pdf\nassambly_simulation/C3_final/C3_final_assembly_mix_connections_graph.pdf\nassambly_simulation/C3_final/C3_final_C1_prom_barcode_E+S_restriction_connections_graph.pdf\nassambly_simulation/C3_final/C3_final_C2_gfp_term_E+X_restriction_parts_graph.pdf\nassambly_simulation/C3_final/C3_final_assembly_mix_parts_graph.pdf\nassambly_simulation/C3_final/C3_final.gb\nassambly_simulation/C3_final/C3_final_summary.csv\nassambly_simulation/C3_final/C3_final.pdf\nassambly_simulation/C3_final/provided_parts_records/C1_prom_barcode.gb\nassambly_simulation/C3_final/provided_parts_records/C2_gfp_term.gb\nassambly_simulation/C2_gfp_term/C2_gfp_term_BBa_E0040_GFP_E+S_restriction_parts_graph.pdf\nassambly_simulation/C2_gfp_term/C2_gfp_term_assembly_mix_parts_graph.pdf\nassambly_simulation/C2_gfp_term/C2_gfp_term_BBa_J61048_term_E+X_restriction_parts_graph.pdf\nassambly_simulation/C2_gfp_term/C2_gfp_term.gb\nassambly_simulation/C2_gfp_term/C2_gfp_term_BBa_J61048_term_E+X_restriction_connections_graph.pdf\nassambly_simulation/C2_gfp_term/C2_gfp_term_assembly_mix_connections_graph.pdf\nassambly_simulation/C2_gfp_term/C2_gfp_term_BBa_E0040_GFP_E+S_restriction_connections_graph.pdf\nassambly_simulation/C2_gfp_term/C2_gfp_term.pdf\nassambly_simulation/C2_gfp_term/C2_gfp_term_summary.csv\nassambly_simulation/C2_gfp_term/provided_parts_records/BBa_J61048_term.gb\nassambly_simulation/C2_gfp_term/provided_parts_records/BBa_E0040_GFP.gb\nassambly_simulation/all_construct_records/C1_prom_barcode.gb\nassambly_simulation/all_construct_records/C2_gfp_term.gb\nassambly_simulation/all_construct_records/C3_final.gb\nassambly_simulation/part_records/BBa_J61048_term.gb\nassambly_simulation/part_records/BBa_K611094_bar.gb\nassambly_simulation/part_records/BBa_E0040_GFP.gb\nassambly_simulation/part_records/BBa_J23119_prom.gb\nassambly_simulation/C1_prom_barcode/C1_prom_barcode_BBa_J23119_prom_E+X_restriction_parts_graph.pdf\nassambly_simulation/C1_prom_barcode/C1_prom_barcode.gb\nassambly_simulation/C1_prom_barcode/C1_prom_barcode_assembly_mix_connections_graph.pdf\nassambly_simulation/C1_prom_barcode/C1_prom_barcode_BBa_K611094_bar_E+S_restriction_parts_graph.pdf\nassambly_simulation/C1_prom_barcode/C1_prom_barcode_BBa_K611094_bar_E+S_restriction_connections_graph.pdf\nassambly_simulation/C1_prom_barcode/C1_prom_barcode.pdf\nassambly_simulation/C1_prom_barcode/C1_prom_barcode_summary.csv\nassambly_simulation/C1_prom_barcode/C1_prom_barcode_assembly_mix_parts_graph.pdf\nassambly_simulation/C1_prom_barcode/C1_prom_barcode_BBa_J23119_prom_E+X_restriction_connections_graph.pdf\nassambly_simulation/C1_prom_barcode/provided_parts_records/BBa_K611094_bar.gb\nassambly_simulation/C1_prom_barcode/provided_parts_records/BBa_J23119_prom.gb\n", | |
| 1037 "update_time": "2025-05-16T08:56:55.140287", | |
| 1038 "user_email": "planemo@galaxyproject.org", | |
| 1039 "user_id": "1d1943aa60deb628" | |
| 1040 }, | |
| 1041 "status": "success", | |
| 1042 "test_index": 4, | |
| 1043 "time_seconds": 34.888214349746704, | |
| 1044 "tool_id": "cloning_simulation", | |
| 1045 "tool_version": "0.1.0+galaxy0" | |
| 1046 }, | |
| 1047 "has_data": true, | |
| 1048 "id": "cloning_simulation-4" | |
| 1049 }, | |
| 1050 { | |
| 1051 "data": { | |
| 1052 "inputs": { | |
| 1053 "adv|use_file_names_as_ids": true, | |
| 1054 "assembly_csv": { | |
| 1055 "id": "a727d841eabfe479", | |
| 1056 "src": "hda" | |
| 1057 }, | |
| 1058 "assembly_plan_name": "Type2sRestrictionAssembly", | |
| 1059 "domesticated_input": { | |
| 1060 "id": "8ab843ac4a5890da", | |
| 1061 "src": "hdca" | |
| 1062 }, | |
| 1063 "genbank_files": { | |
| 1064 "id": "6206f91299006d13", | |
| 1065 "src": "hdca" | |
| 1066 }, | |
| 1067 "topology": "circular" | |
| 1068 }, | |
| 1069 "job": { | |
| 1070 "command_line": "mkdir 'outdir_zip' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmps36anksu/files/2/b/3/dataset_2b34f95b-2776-40a7-ac0a-abdb3d2b151f.dat,/tmp/tmps36anksu/files/8/1/5/dataset_81535329-42d0-4e9d-a713-beb8033e2db9.dat,/tmp/tmps36anksu/files/d/b/b/dataset_dbbc8408-63b6-4265-8878-94942c7b2016.dat,/tmp/tmps36anksu/files/4/1/d/dataset_41d94b9c-f2f0-4253-88bb-896b26fdb7a0.dat,/tmp/tmps36anksu/files/4/8/a/dataset_48a630fc-ea4b-4c19-8b0b-fb78db4bff7d.dat,/tmp/tmps36anksu/files/4/5/9/dataset_459d85d8-4869-4d03-bd2a-d083e4ecf818.dat,/tmp/tmps36anksu/files/1/b/1/dataset_1b189627-18cd-4c7c-8d19-46371420574a.dat' --domesticated_seq '/tmp/tmps36anksu/files/6/a/2/dataset_6a2287bd-1281-4c99-89a6-e4af944c272a.dat,/tmp/tmps36anksu/files/2/c/9/dataset_2c942443-9fa9-48a9-bf35-2f8c2258967b.dat,/tmp/tmps36anksu/files/b/e/c/dataset_becfbff9-15f1-4830-b192-93e7892f371d.dat,/tmp/tmps36anksu/files/8/7/6/dataset_876d6160-fcd5-49e1-ae58-aa8d30c94e09.dat,/tmp/tmps36anksu/files/3/a/8/dataset_3a81169d-4569-4c6d-9417-a3c5924f8649.dat' --assembly_csv '/tmp/tmps36anksu/files/4/a/b/dataset_4abb21a9-cb77-4f0c-9a76-3c01fd662d2a.dat' --assembly_plan_name 'Type2sRestrictionAssembly' --file_name_mapping '/tmp/tmps36anksu/files/2/b/3/dataset_2b34f95b-2776-40a7-ac0a-abdb3d2b151f.dat:part_A.gb,/tmp/tmps36anksu/files/8/1/5/dataset_81535329-42d0-4e9d-a713-beb8033e2db9.dat:part_B.gb,/tmp/tmps36anksu/files/d/b/b/dataset_dbbc8408-63b6-4265-8878-94942c7b2016.dat:part_C.gb,/tmp/tmps36anksu/files/4/1/d/dataset_41d94b9c-f2f0-4253-88bb-896b26fdb7a0.dat:part_D.gb,/tmp/tmps36anksu/files/4/8/a/dataset_48a630fc-ea4b-4c19-8b0b-fb78db4bff7d.dat:part_E.gb,/tmp/tmps36anksu/files/4/5/9/dataset_459d85d8-4869-4d03-bd2a-d083e4ecf818.dat:part_F.gb,/tmp/tmps36anksu/files/1/b/1/dataset_1b189627-18cd-4c7c-8d19-46371420574a.dat:part_G.gb' --file_name_mapping_dom '/tmp/tmps36anksu/files/6/a/2/dataset_6a2287bd-1281-4c99-89a6-e4af944c272a.dat:part_H.gb,/tmp/tmps36anksu/files/2/c/9/dataset_2c942443-9fa9-48a9-bf35-2f8c2258967b.dat:part_I.gb,/tmp/tmps36anksu/files/b/e/c/dataset_becfbff9-15f1-4830-b192-93e7892f371d.dat:part_J.gb,/tmp/tmps36anksu/files/8/7/6/dataset_876d6160-fcd5-49e1-ae58-aa8d30c94e09.dat:part_K.gb,/tmp/tmps36anksu/files/3/a/8/dataset_3a81169d-4569-4c6d-9417-a3c5924f8649.dat:part_L.gb' --use_file_names_as_id 'true' --outdir_simulation 'outdir_zip' --output_simulation 'output_zip.zip' --enzyme 'auto' --topology 'circular'&& cp 'output_zip.zip' '/tmp/tmps36anksu/job_working_directory/000/49/outputs/dataset_891d2044-502b-4e4b-b394-575c9e42a36f.dat'", | |
| 1071 "command_version": "", | |
| 1072 "copied_from_job_id": null, | |
| 1073 "create_time": "2025-05-16T08:57:35.145295", | |
| 1074 "dependencies": [ | |
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| 1080 "can_uninstall_dependencies": true, | |
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| 1082 "model_class": "CondaDependencyResolver", | |
| 1083 "prefix": "/home/rkhaled/miniconda3", | |
| 1084 "read_only": false, | |
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| 1086 "resolves_simple_dependencies": true, | |
| 1087 "use_local": false, | |
| 1088 "versionless": false | |
| 1089 }, | |
| 1090 "dependency_type": "conda", | |
| 1091 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-414e7261396ae5d11be85675e1e19db222325018468f2829061591addd560be0", | |
| 1092 "exact": true, | |
| 1093 "model_class": "MergedCondaDependency", | |
| 1094 "name": "flametree", | |
| 1095 "version": "0.1.11" | |
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| 1105 "prefix": "/home/rkhaled/miniconda3", | |
| 1106 "read_only": false, | |
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| 1108 "resolves_simple_dependencies": true, | |
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| 1110 "versionless": false | |
| 1111 }, | |
| 1112 "dependency_type": "conda", | |
| 1113 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-414e7261396ae5d11be85675e1e19db222325018468f2829061591addd560be0", | |
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| 1125 "ensure_channels": "conda-forge,bioconda", | |
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| 1255 "handler": null, | |
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| 1291 "src": "hda", | |
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| 1322 "uuid": "1b189627-18cd-4c7c-8d19-46371420574a" | |
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| 1328 "job_stderr": "", | |
| 1329 "job_stdout": "", | |
| 1330 "model_class": "Job", | |
| 1331 "output_collections": {}, | |
| 1332 "outputs": { | |
| 1333 "output_zip": { | |
| 1334 "id": "9d82ca4e11899647", | |
| 1335 "src": "hda", | |
| 1336 "uuid": "891d2044-502b-4e4b-b394-575c9e42a36f" | |
| 1337 } | |
| 1338 }, | |
| 1339 "params": { | |
| 1340 "__input_ext": "\"input\"", | |
| 1341 "adv": "{\"enzyme\": \"auto\", \"use_file_names_as_ids\": true}", | |
| 1342 "assembly_plan_name": "\"Type2sRestrictionAssembly\"", | |
| 1343 "chromInfo": "\"/tmp/tmps36anksu/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", | |
| 1344 "dbkey": "\"?\"", | |
| 1345 "domesticated_input": "{\"values\": [{\"id\": 6, \"src\": \"hdca\"}]}", | |
| 1346 "genbank_files": "{\"values\": [{\"id\": 7, \"src\": \"hdca\"}]}", | |
| 1347 "topology": "\"circular\"" | |
| 1348 }, | |
| 1349 "state": "ok", | |
| 1350 "stderr": "\rassembly: 0%| | 0/4 [00:00<?, ?it/s, now=None]\r \r\rassembly: 0%| | 0/4 [00:00<?, ?it/s, now=None]\rassembly: 50%|\u2588\u2588\u2588\u2588\u2588 | 2/4 [00:00<00:00, 2.46it/s, now=None]\rassembly: 75%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u258c | 3/4 [00:01<00:00, 2.24it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 4/4 [00:02<00:00, 1.84it/s, now=None]\r \r", | |
| 1351 "stdout": "Simulating assembly plan assambly...\n{'cancelled_assemblies': 0, 'errored_assemblies': 0, 'valid_assemblies': 4}\nGenerating assemblies reports...\nFiles in the zip archive:\nassambly_simulation/assambly_all_required_parts.txt\nassambly_simulation/assambly_constructs_level_2.csv\nassambly_simulation/assambly_simulation_stats.csv\nassambly_simulation/assambly_constructs_level_1.csv\nassambly_simulation/Report.pdf\nassambly_simulation/assembly_plan_graph.pdf\nassambly_simulation/assambly_summary.csv\nassambly_simulation/construct_3/construct_3_type2s_mix_parts_graph.pdf\nassambly_simulation/construct_3/construct_3_summary.csv\nassambly_simulation/construct_3/construct_3_type2s_mix_connections_graph.pdf\nassambly_simulation/construct_3/construct_3.gb\nassambly_simulation/construct_3/construct_3.pdf\nassambly_simulation/construct_3/provided_parts_records/part_L.gb\nassambly_simulation/construct_3/provided_parts_records/part_K.gb\nassambly_simulation/construct_3/provided_parts_records/part_J.gb\nassambly_simulation/construct_3/provided_parts_records/construct_1.gb\nassambly_simulation/all_construct_records/construct_2.gb\nassambly_simulation/all_construct_records/construct_3.gb\nassambly_simulation/all_construct_records/construct_4.gb\nassambly_simulation/all_construct_records/construct_1.gb\nassambly_simulation/construct_1/construct_1_type2s_mix_connections_graph.pdf\nassambly_simulation/construct_1/construct_1_summary.csv\nassambly_simulation/construct_1/construct_1_type2s_mix_parts_graph.pdf\nassambly_simulation/construct_1/construct_1.pdf\nassambly_simulation/construct_1/construct_1.gb\nassambly_simulation/construct_1/provided_parts_records/part_F.gb\nassambly_simulation/construct_1/provided_parts_records/part_B.gb\nassambly_simulation/construct_1/provided_parts_records/part_D.gb\nassambly_simulation/construct_1/provided_parts_records/part_A.gb\nassambly_simulation/construct_1/provided_parts_records/part_C.gb\nassambly_simulation/construct_1/provided_parts_records/part_E.gb\nassambly_simulation/part_records/part_L.gb\nassambly_simulation/part_records/part_F.gb\nassambly_simulation/part_records/part_B.gb\nassambly_simulation/part_records/part_K.gb\nassambly_simulation/part_records/part_D.gb\nassambly_simulation/part_records/part_A.gb\nassambly_simulation/part_records/part_C.gb\nassambly_simulation/part_records/part_G.gb\nassambly_simulation/part_records/part_I.gb\nassambly_simulation/part_records/part_E.gb\nassambly_simulation/part_records/part_J.gb\nassambly_simulation/part_records/part_H.gb\nassambly_simulation/construct_2/construct_2_type2s_mix_parts_graph.pdf\nassambly_simulation/construct_2/construct_2.pdf\nassambly_simulation/construct_2/construct_2.gb\nassambly_simulation/construct_2/construct_2_summary.csv\nassambly_simulation/construct_2/construct_2_type2s_mix_connections_graph.pdf\nassambly_simulation/construct_2/provided_parts_records/part_F.gb\nassambly_simulation/construct_2/provided_parts_records/part_A.gb\nassambly_simulation/construct_2/provided_parts_records/part_G.gb\nassambly_simulation/construct_2/provided_parts_records/part_I.gb\nassambly_simulation/construct_2/provided_parts_records/part_H.gb\nassambly_simulation/construct_4/construct_4_type2s_mix_parts_graph.pdf\nassambly_simulation/construct_4/construct_4.pdf\nassambly_simulation/construct_4/construct_4.gb\nassambly_simulation/construct_4/construct_4_summary.csv\nassambly_simulation/construct_4/construct_4_type2s_mix_connections_graph.pdf\nassambly_simulation/construct_4/provided_parts_records/part_L.gb\nassambly_simulation/construct_4/provided_parts_records/part_K.gb\nassambly_simulation/construct_4/provided_parts_records/construct_2.gb\nassambly_simulation/construct_4/provided_parts_records/part_J.gb\n", | |
| 1352 "tool_id": "cloning_simulation", | |
| 1353 "tool_stderr": "\rassembly: 0%| | 0/4 [00:00<?, ?it/s, now=None]\r \r\rassembly: 0%| | 0/4 [00:00<?, ?it/s, now=None]\rassembly: 50%|\u2588\u2588\u2588\u2588\u2588 | 2/4 [00:00<00:00, 2.46it/s, now=None]\rassembly: 75%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u258c | 3/4 [00:01<00:00, 2.24it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 4/4 [00:02<00:00, 1.84it/s, now=None]\r \r", | |
| 1354 "tool_stdout": "Simulating assembly plan assambly...\n{'cancelled_assemblies': 0, 'errored_assemblies': 0, 'valid_assemblies': 4}\nGenerating assemblies reports...\nFiles in the zip archive:\nassambly_simulation/assambly_all_required_parts.txt\nassambly_simulation/assambly_constructs_level_2.csv\nassambly_simulation/assambly_simulation_stats.csv\nassambly_simulation/assambly_constructs_level_1.csv\nassambly_simulation/Report.pdf\nassambly_simulation/assembly_plan_graph.pdf\nassambly_simulation/assambly_summary.csv\nassambly_simulation/construct_3/construct_3_type2s_mix_parts_graph.pdf\nassambly_simulation/construct_3/construct_3_summary.csv\nassambly_simulation/construct_3/construct_3_type2s_mix_connections_graph.pdf\nassambly_simulation/construct_3/construct_3.gb\nassambly_simulation/construct_3/construct_3.pdf\nassambly_simulation/construct_3/provided_parts_records/part_L.gb\nassambly_simulation/construct_3/provided_parts_records/part_K.gb\nassambly_simulation/construct_3/provided_parts_records/part_J.gb\nassambly_simulation/construct_3/provided_parts_records/construct_1.gb\nassambly_simulation/all_construct_records/construct_2.gb\nassambly_simulation/all_construct_records/construct_3.gb\nassambly_simulation/all_construct_records/construct_4.gb\nassambly_simulation/all_construct_records/construct_1.gb\nassambly_simulation/construct_1/construct_1_type2s_mix_connections_graph.pdf\nassambly_simulation/construct_1/construct_1_summary.csv\nassambly_simulation/construct_1/construct_1_type2s_mix_parts_graph.pdf\nassambly_simulation/construct_1/construct_1.pdf\nassambly_simulation/construct_1/construct_1.gb\nassambly_simulation/construct_1/provided_parts_records/part_F.gb\nassambly_simulation/construct_1/provided_parts_records/part_B.gb\nassambly_simulation/construct_1/provided_parts_records/part_D.gb\nassambly_simulation/construct_1/provided_parts_records/part_A.gb\nassambly_simulation/construct_1/provided_parts_records/part_C.gb\nassambly_simulation/construct_1/provided_parts_records/part_E.gb\nassambly_simulation/part_records/part_L.gb\nassambly_simulation/part_records/part_F.gb\nassambly_simulation/part_records/part_B.gb\nassambly_simulation/part_records/part_K.gb\nassambly_simulation/part_records/part_D.gb\nassambly_simulation/part_records/part_A.gb\nassambly_simulation/part_records/part_C.gb\nassambly_simulation/part_records/part_G.gb\nassambly_simulation/part_records/part_I.gb\nassambly_simulation/part_records/part_E.gb\nassambly_simulation/part_records/part_J.gb\nassambly_simulation/part_records/part_H.gb\nassambly_simulation/construct_2/construct_2_type2s_mix_parts_graph.pdf\nassambly_simulation/construct_2/construct_2.pdf\nassambly_simulation/construct_2/construct_2.gb\nassambly_simulation/construct_2/construct_2_summary.csv\nassambly_simulation/construct_2/construct_2_type2s_mix_connections_graph.pdf\nassambly_simulation/construct_2/provided_parts_records/part_F.gb\nassambly_simulation/construct_2/provided_parts_records/part_A.gb\nassambly_simulation/construct_2/provided_parts_records/part_G.gb\nassambly_simulation/construct_2/provided_parts_records/part_I.gb\nassambly_simulation/construct_2/provided_parts_records/part_H.gb\nassambly_simulation/construct_4/construct_4_type2s_mix_parts_graph.pdf\nassambly_simulation/construct_4/construct_4.pdf\nassambly_simulation/construct_4/construct_4.gb\nassambly_simulation/construct_4/construct_4_summary.csv\nassambly_simulation/construct_4/construct_4_type2s_mix_connections_graph.pdf\nassambly_simulation/construct_4/provided_parts_records/part_L.gb\nassambly_simulation/construct_4/provided_parts_records/part_K.gb\nassambly_simulation/construct_4/provided_parts_records/construct_2.gb\nassambly_simulation/construct_4/provided_parts_records/part_J.gb\n", | |
| 1355 "update_time": "2025-05-16T08:57:47.925883", | |
| 1356 "user_email": "planemo@galaxyproject.org", | |
| 1357 "user_id": "1d1943aa60deb628" | |
| 1358 }, | |
| 1359 "status": "success", | |
| 1360 "test_index": 5, | |
| 1361 "time_seconds": 52.77062439918518, | |
| 1362 "tool_id": "cloning_simulation", | |
| 1363 "tool_version": "0.1.0+galaxy0" | |
| 1364 }, | |
| 1365 "has_data": true, | |
| 1366 "id": "cloning_simulation-5" | |
| 1367 } | |
| 1368 ], | |
| 1369 "version": "0.1" | |
| 1370 } |