Mercurial > repos > tduigou > cloning_simulation
diff 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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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/output.json Fri May 16 09:39:03 2025 +0000 @@ -0,0 +1,1370 @@ +{ + "summary": { + "num_errors": 0, + "num_failures": 0, + "num_skips": 0, + "num_tests": 6 + }, + "tests": [ + { + "data": { + "inputs": { + "adv|use_file_names_as_ids": true, + "assembly_csv": { + "id": "a2e8f3fd1611e7f5", + "src": "hda" + }, + "assembly_plan_name": "Type2sRestrictionAssembly", + "genbank_files": { + "id": "1d1943aa60deb628", + "src": "hdca" + }, + "topology": "circular" + }, + "job": { + "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'", + "command_version": "", + "copied_from_job_id": null, + "create_time": "2025-05-16T08:54:45.629427", + "dependencies": [], + "exit_code": 0, + "external_id": "69472", + "galaxy_version": "24.2", + "handler": null, + "history_id": "1d1943aa60deb628", + "id": "306d449b91ecb0a3", + "inputs": { + "assembly_csv": { + "id": "a2e8f3fd1611e7f5", + "src": "hda", + "uuid": "420c4b07-ea17-4e63-9f48-4cc364e28432" + }, + "genbank_files1": { + "id": "1d1943aa60deb628", + "src": "hda", + "uuid": "6a407f29-14a2-4358-8781-97a5a60006bf" + }, + "genbank_files10": { + "id": "b55875807068e59e", + "src": "hda", + "uuid": "23c06fae-96cc-4ff8-9e23-111139ce1a92" + }, + "genbank_files11": { + "id": "4b64a67f616af776", + "src": "hda", + "uuid": "d29c16a7-2470-418e-a8f1-1da7c5372dde" + }, + "genbank_files12": { + "id": "1fda217ac9617c88", + "src": "hda", + "uuid": "290bfdf4-f595-42f1-a2f0-0f9a9d8e71df" + }, + "genbank_files2": { + "id": "13a3899f03fff34a", + "src": "hda", + "uuid": "9c05120b-2a93-4298-a718-2db482dec9e0" + }, + "genbank_files3": { + "id": "6872e1ad22eb2e5d", + "src": "hda", + "uuid": "e9dd6c4a-5d1c-48d6-b072-bb67929590f5" + }, + "genbank_files4": { + "id": "248d7f69d2402068", + "src": "hda", + "uuid": "c2a67b9c-bd0d-483b-b229-1f396bc8c275" + }, + "genbank_files5": { + "id": "a363c57bce5ddac4", + "src": "hda", + "uuid": "53dc6b3e-3d2b-4fb7-b279-8b7204ae8d00" + }, + "genbank_files6": { + "id": "8ab843ac4a5890da", + "src": "hda", + "uuid": "40fa89b4-5e49-467e-aa6a-d4b8c9b8a8b0" + }, + "genbank_files7": { + "id": "6206f91299006d13", + "src": "hda", + "uuid": "14b815cb-038e-4836-bb4e-3f049395271c" + }, + "genbank_files8": { + "id": "278f145ab0478700", + "src": "hda", + "uuid": "32719970-8009-4818-a623-ba980af84d70" + }, + "genbank_files9": { + "id": "84aedadb70ef205b", + "src": "hda", + "uuid": "68e30a2d-a44d-40e6-a619-efa1e8cd6e4b" + } + }, + "job_messages": [], + "job_metrics": [], + "job_runner_name": null, + "job_stderr": "", + "job_stdout": "", + "model_class": "Job", + "output_collections": {}, + "outputs": { + "output_zip": { + "id": "306d449b91ecb0a3", + "src": "hda", + "uuid": "19827d46-96d8-48c8-b434-17f9e4732aec" + } + }, + "params": { + "__input_ext": "\"input\"", + "adv": "{\"enzyme\": \"auto\", \"use_file_names_as_ids\": true}", + "assembly_plan_name": "\"Type2sRestrictionAssembly\"", + "chromInfo": "\"/tmp/tmps36anksu/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", + "dbkey": "\"?\"", + "domesticated_input": null, + "genbank_files": "{\"values\": [{\"id\": 1, \"src\": \"hdca\"}]}", + "topology": "\"circular\"" + }, + "state": "ok", + "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", + "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", + "tool_id": "cloning_simulation", + "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", + "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", + "update_time": "2025-05-16T08:54:59.050276", + "user_email": "planemo@galaxyproject.org", + "user_id": "1d1943aa60deb628" + }, + "status": "success", + "test_index": 0, + "time_seconds": 53.80709099769592, + "tool_id": "cloning_simulation", + "tool_version": "0.1.0+galaxy0" + }, + "has_data": true, + "id": "cloning_simulation-0" + }, + { + "data": { + "inputs": { + "adv|use_file_names_as_ids": true, + "assembly_csv": { + "id": "343611dad2e145e6", + "src": "hda" + }, + "assembly_plan_name": "GibsonAssembly", + "genbank_files": { + "id": "13a3899f03fff34a", + "src": "hdca" + }, + "topology": "circular" + }, + "job": { + "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'", + "command_version": "", + "copied_from_job_id": null, + "create_time": "2025-05-16T08:55:10.522461", + "dependencies": [ + { + "cacheable": false, + "dependency_resolver": { + "auto_init": true, + "auto_install": true, + "can_uninstall_dependencies": true, + "ensure_channels": "conda-forge,bioconda", + "model_class": "CondaDependencyResolver", + "prefix": "/home/rkhaled/miniconda3", + "read_only": false, + "resolver_type": "conda", + "resolves_simple_dependencies": true, + "use_local": false, + "versionless": false + }, + "dependency_type": "conda", + "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-414e7261396ae5d11be85675e1e19db222325018468f2829061591addd560be0", + "exact": true, + "model_class": "MergedCondaDependency", + "name": "flametree", + "version": "0.1.11" + }, + { + "cacheable": false, + "dependency_resolver": { + "auto_init": true, + "auto_install": true, + "can_uninstall_dependencies": true, + "ensure_channels": "conda-forge,bioconda", + "model_class": "CondaDependencyResolver", + "prefix": "/home/rkhaled/miniconda3", + "read_only": false, + "resolver_type": "conda", + "resolves_simple_dependencies": true, + "use_local": false, + "versionless": false + }, + "dependency_type": "conda", + "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-414e7261396ae5d11be85675e1e19db222325018468f2829061591addd560be0", + "exact": true, + "model_class": "MergedCondaDependency", + "name": "biopython", + "version": "1.85" + }, + { + "cacheable": false, + "dependency_resolver": { + "auto_init": true, + "auto_install": true, + "can_uninstall_dependencies": true, + "ensure_channels": "conda-forge,bioconda", + "model_class": "CondaDependencyResolver", + "prefix": "/home/rkhaled/miniconda3", + "read_only": false, + "resolver_type": "conda", + "resolves_simple_dependencies": true, + "use_local": false, + "versionless": false + }, + "dependency_type": "conda", + "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-414e7261396ae5d11be85675e1e19db222325018468f2829061591addd560be0", + "exact": true, + "model_class": "MergedCondaDependency", + "name": "proglog", + "version": "0.1.10" + }, + { + "cacheable": false, + "dependency_resolver": { + "auto_init": true, + "auto_install": true, + "can_uninstall_dependencies": true, + "ensure_channels": "conda-forge,bioconda", + "model_class": "CondaDependencyResolver", + "prefix": "/home/rkhaled/miniconda3", + "read_only": false, + "resolver_type": "conda", + "resolves_simple_dependencies": true, + "use_local": false, + "versionless": false + }, + "dependency_type": 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}, + "dependency_type": "conda", + "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-414e7261396ae5d11be85675e1e19db222325018468f2829061591addd560be0", + "exact": true, + "model_class": "MergedCondaDependency", + "name": "sequenticon", + "version": "0.1.8" + }, + { + "cacheable": false, + "dependency_resolver": { + "auto_init": true, + "auto_install": true, + "can_uninstall_dependencies": true, + "ensure_channels": "conda-forge,bioconda", + "model_class": "CondaDependencyResolver", + "prefix": "/home/rkhaled/miniconda3", + "read_only": false, + "resolver_type": "conda", + "resolves_simple_dependencies": true, + "use_local": false, + "versionless": false + }, + "dependency_type": "conda", + "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-414e7261396ae5d11be85675e1e19db222325018468f2829061591addd560be0", + "exact": true, + "model_class": "MergedCondaDependency", + "name": "dna_features_viewer", + "version": "3.1.4" + } + ], + "exit_code": 0, + "external_id": "69816", + "galaxy_version": "24.2", + "handler": null, + "history_id": "13a3899f03fff34a", + "id": "6fff2cd3fd6e4947", + "inputs": { + "assembly_csv": { + "id": "343611dad2e145e6", + "src": "hda", + "uuid": "7a09a16a-a7f7-44ce-8e1d-5f6baf385c44" + }, + "genbank_files1": { + "id": "03c59a54410e4ccf", + "src": "hda", + "uuid": "5c2150b5-537a-4971-98ef-959bb4141fac" + } + }, + "job_messages": [], + "job_metrics": [], + "job_runner_name": null, + "job_stderr": "", + "job_stdout": "", + "model_class": "Job", + "output_collections": {}, + "outputs": { + "output_zip": { + "id": "6fff2cd3fd6e4947", + "src": "hda", + "uuid": "4c70b3f9-9fb4-4e1c-942c-47fd78a5a348" + } + }, + "params": { + "__input_ext": "\"input\"", + "adv": "{\"enzyme\": \"auto\", \"use_file_names_as_ids\": true}", + "assembly_plan_name": "\"GibsonAssembly\"", + "chromInfo": "\"/tmp/tmps36anksu/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", + "dbkey": "\"?\"", + "domesticated_input": null, + "genbank_files": "{\"values\": [{\"id\": 2, \"src\": \"hdca\"}]}", + "topology": "\"circular\"" + }, + "state": "ok", + "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", + "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", + "tool_id": "cloning_simulation", + "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", + "tool_stdout": "Simulating assembly plan assambly...\n{'cancelled_assemblies': 0, 'errored_assemblies': 2, 'valid_assemblies': 3}\nGenerating assemblies reports...\nFiles in the zip 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+ "update_time": "2025-05-16T08:55:23.301357", + "user_email": "planemo@galaxyproject.org", + "user_id": "1d1943aa60deb628" + }, + "status": "success", + "test_index": 1, + "time_seconds": 24.055506706237793, + "tool_id": "cloning_simulation", + "tool_version": "0.1.0+galaxy0" + }, + "has_data": true, + "id": "cloning_simulation-1" + }, + { + "data": { + "inputs": { + "adv|use_file_names_as_ids": true, + "assembly_csv": { + "id": "eae50b1e0ba0bca8", + "src": "hda" + }, + "assembly_plan_name": "LigaseCyclingReactionAssembly", + "genbank_files": { + "id": "6872e1ad22eb2e5d", + "src": "hdca" + }, + "topology": "circular" + }, + "job": { + "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'", + "command_version": "", + "copied_from_job_id": null, + "create_time": "2025-05-16T08:55:35.420052", + "dependencies": [ + { + "cacheable": false, + "dependency_resolver": { + "auto_init": true, + "auto_install": true, + "can_uninstall_dependencies": true, + "ensure_channels": "conda-forge,bioconda", + "model_class": "CondaDependencyResolver", + "prefix": "/home/rkhaled/miniconda3", + "read_only": false, + "resolver_type": "conda", + "resolves_simple_dependencies": true, + "use_local": false, + "versionless": false + }, + "dependency_type": "conda", + "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-414e7261396ae5d11be85675e1e19db222325018468f2829061591addd560be0", + "exact": true, + "model_class": "MergedCondaDependency", + "name": "flametree", + "version": "0.1.11" + }, + { + "cacheable": false, + "dependency_resolver": { + "auto_init": true, + "auto_install": true, + "can_uninstall_dependencies": true, + "ensure_channels": "conda-forge,bioconda", + "model_class": "CondaDependencyResolver", + "prefix": "/home/rkhaled/miniconda3", + "read_only": false, + "resolver_type": "conda", + "resolves_simple_dependencies": true, + "use_local": false, + "versionless": false + }, + "dependency_type": "conda", + "environment_path": 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"can_uninstall_dependencies": true, + "ensure_channels": "conda-forge,bioconda", + "model_class": "CondaDependencyResolver", + "prefix": "/home/rkhaled/miniconda3", + "read_only": false, + "resolver_type": "conda", + "resolves_simple_dependencies": true, + "use_local": false, + "versionless": false + }, + "dependency_type": "conda", + "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-414e7261396ae5d11be85675e1e19db222325018468f2829061591addd560be0", + "exact": true, + "model_class": "MergedCondaDependency", + "name": "pandas", + "version": "2.2.3" + }, + { + "cacheable": false, + "dependency_resolver": { + "auto_init": true, + "auto_install": true, + "can_uninstall_dependencies": true, + "ensure_channels": "conda-forge,bioconda", + "model_class": "CondaDependencyResolver", + "prefix": "/home/rkhaled/miniconda3", + "read_only": false, + "resolver_type": "conda", + "resolves_simple_dependencies": true, + "use_local": false, + "versionless": false + }, + "dependency_type": "conda", + "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-414e7261396ae5d11be85675e1e19db222325018468f2829061591addd560be0", + "exact": true, + "model_class": "MergedCondaDependency", + "name": "dnacauldron", + "version": "2.0.12" + }, + { + "cacheable": false, + "dependency_resolver": { + "auto_init": true, + "auto_install": true, + "can_uninstall_dependencies": true, + "ensure_channels": "conda-forge,bioconda", + "model_class": "CondaDependencyResolver", + "prefix": "/home/rkhaled/miniconda3", + "read_only": false, + "resolver_type": "conda", + "resolves_simple_dependencies": true, + "use_local": false, + "versionless": false + }, + "dependency_type": "conda", + "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-414e7261396ae5d11be85675e1e19db222325018468f2829061591addd560be0", + "exact": true, + "model_class": "MergedCondaDependency", + "name": "pdf-reports", + "version": "0.3.9" + }, + { + "cacheable": false, + "dependency_resolver": { + "auto_init": true, + "auto_install": true, + "can_uninstall_dependencies": true, + "ensure_channels": "conda-forge,bioconda", + "model_class": "CondaDependencyResolver", + "prefix": "/home/rkhaled/miniconda3", + "read_only": false, + "resolver_type": "conda", + "resolves_simple_dependencies": true, + "use_local": false, + "versionless": false + }, + "dependency_type": "conda", + "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-414e7261396ae5d11be85675e1e19db222325018468f2829061591addd560be0", + "exact": true, + "model_class": "MergedCondaDependency", + "name": "sequenticon", + "version": "0.1.8" + }, + { + "cacheable": false, + "dependency_resolver": { + "auto_init": true, + "auto_install": true, + "can_uninstall_dependencies": true, + "ensure_channels": "conda-forge,bioconda", + "model_class": "CondaDependencyResolver", + "prefix": "/home/rkhaled/miniconda3", + "read_only": false, + "resolver_type": "conda", + "resolves_simple_dependencies": true, + "use_local": false, + "versionless": false + }, + "dependency_type": "conda", + "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-414e7261396ae5d11be85675e1e19db222325018468f2829061591addd560be0", + "exact": true, + "model_class": "MergedCondaDependency", + "name": "dna_features_viewer", + "version": "3.1.4" + } + ], + "exit_code": 0, + "external_id": "70205", + "galaxy_version": "24.2", + "handler": null, + "history_id": "6872e1ad22eb2e5d", + "id": "8205956dbdec438f", + "inputs": { + "assembly_csv": { + "id": "eae50b1e0ba0bca8", + "src": "hda", + "uuid": "5af89b00-757d-4606-b6c8-d00d3f0ca39e" + }, + "genbank_files1": { + "id": "e685210c6961cf21", + "src": "hda", + "uuid": "aa035ce9-b3ee-4c4d-a5c1-e2451c4297c2" + }, + "genbank_files2": { + "id": "fb0119a6d133c713", + "src": "hda", + "uuid": "4bb2bf6a-b351-4a80-ab47-d4d56aefa38c" + } + }, + "job_messages": [], + "job_metrics": [], + "job_runner_name": null, + "job_stderr": "", + "job_stdout": "", + "model_class": "Job", + "output_collections": {}, + "outputs": { + "output_zip": { + "id": "8205956dbdec438f", + "src": "hda", + "uuid": "bd5c88b9-1efd-4507-b875-13dfebff9d6a" + } + }, + "params": { + "__input_ext": "\"input\"", + "adv": "{\"enzyme\": \"auto\", \"use_file_names_as_ids\": true}", + "assembly_plan_name": "\"LigaseCyclingReactionAssembly\"", + "chromInfo": "\"/tmp/tmps36anksu/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", + "dbkey": "\"?\"", + "domesticated_input": null, + "genbank_files": "{\"values\": [{\"id\": 3, \"src\": \"hdca\"}]}", + "topology": "\"circular\"" + }, + "state": "ok", + "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", + "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", + "tool_id": "cloning_simulation", + "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", + "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", + "update_time": "2025-05-16T08:55:47.617074", + "user_email": "planemo@galaxyproject.org", + "user_id": "1d1943aa60deb628" + }, + "status": "success", + "test_index": 2, + "time_seconds": 24.352636098861694, + "tool_id": "cloning_simulation", + "tool_version": "0.1.0+galaxy0" + }, + "has_data": true, + "id": "cloning_simulation-2" + }, + { + "data": { + "inputs": { + "adv|use_file_names_as_ids": true, + "assembly_csv": { + "id": "c4d206bede85e5c1", + "src": "hda" + }, + "assembly_plan_name": "BASICAssembly", + "genbank_files": { + "id": "248d7f69d2402068", + "src": "hdca" + }, + "topology": "circular" + }, + "job": { + "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'", + "command_version": "", + "copied_from_job_id": null, + "create_time": "2025-05-16T08:56:09.388287", + "dependencies": [], + "exit_code": 0, + "external_id": "70839", + "galaxy_version": "24.2", + "handler": null, + "history_id": "248d7f69d2402068", + "id": "ecaf8d4d1aeb8c86", + "inputs": { + "assembly_csv": { + "id": "c4d206bede85e5c1", + "src": "hda", + "uuid": "ed3f4797-0002-46e3-a245-70ec97e59118" + }, + "genbank_files1": { + "id": "065a19c3622776e9", + "src": "hda", + "uuid": "09dd12f1-a528-4e2a-a1d3-b9b57e7a02a2" + }, + "genbank_files2": { + "id": "ac67f4a6521db48c", + "src": "hda", + "uuid": "be63c5f6-6c15-43c9-a467-0f00c3395bcf" + }, + "genbank_files3": { + "id": "77ed38528f61eafd", + "src": "hda", + "uuid": "2e03930b-3e9f-45be-9750-42560f39cf14" + }, + "genbank_files4": { + "id": "626b9fd2eae5943c", + "src": "hda", + "uuid": "5bdbe27f-640f-4db1-bc7b-fcedf4b2737a" + }, + "genbank_files5": { + "id": "4a4771cb4e71e8ed", + "src": "hda", + "uuid": "cd53d85a-7ced-4da5-bc73-eb4b74a200e3" + } + }, + "job_messages": [], + "job_metrics": [], + "job_runner_name": null, + "job_stderr": "", + "job_stdout": "", + "model_class": "Job", + "output_collections": {}, + "outputs": { + "output_zip": { + "id": "ecaf8d4d1aeb8c86", + "src": "hda", + "uuid": "2ce9e85d-d4e7-4104-833f-9fcac95e2c6d" + } + }, + "params": { + "__input_ext": "\"input\"", + "adv": "{\"enzyme\": \"auto\", \"use_file_names_as_ids\": true}", + "assembly_plan_name": "\"BASICAssembly\"", + "chromInfo": "\"/tmp/tmps36anksu/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", + "dbkey": "\"?\"", + "domesticated_input": null, + "genbank_files": "{\"values\": [{\"id\": 4, \"src\": \"hdca\"}]}", + "topology": "\"circular\"" + }, + "state": "ok", + "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", + "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", + "tool_id": "cloning_simulation", + "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", + "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", + "update_time": "2025-05-16T08:56:20.015826", + "user_email": "planemo@galaxyproject.org", + "user_id": "1d1943aa60deb628" + }, + "status": "success", + "test_index": 3, + "time_seconds": 32.09558367729187, + "tool_id": "cloning_simulation", + "tool_version": "0.1.0+galaxy0" + }, + "has_data": true, + "id": "cloning_simulation-3" + }, + { + "data": { + "inputs": { + "adv|use_file_names_as_ids": true, + "assembly_csv": { + "id": "1b325227d95fdc76", + "src": "hda" + }, + "assembly_plan_name": "BioBrickStandardAssembly", + "genbank_files": { + "id": "a363c57bce5ddac4", + "src": "hdca" + }, + "topology": "circular" + }, + "job": { + "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'", + "command_version": "", + "copied_from_job_id": null, + "create_time": "2025-05-16T08:56:41.646034", + "dependencies": [ + { + "cacheable": false, + "dependency_resolver": { + "auto_init": true, + "auto_install": true, + "can_uninstall_dependencies": true, + "ensure_channels": "conda-forge,bioconda", + "model_class": "CondaDependencyResolver", + "prefix": "/home/rkhaled/miniconda3", + "read_only": false, + "resolver_type": "conda", + "resolves_simple_dependencies": true, + "use_local": false, + "versionless": false + }, + "dependency_type": "conda", + "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-414e7261396ae5d11be85675e1e19db222325018468f2829061591addd560be0", + "exact": true, + "model_class": "MergedCondaDependency", + "name": "flametree", + "version": "0.1.11" + }, + { + "cacheable": false, + "dependency_resolver": { + "auto_init": true, + "auto_install": true, + "can_uninstall_dependencies": true, + "ensure_channels": "conda-forge,bioconda", + "model_class": "CondaDependencyResolver", + "prefix": "/home/rkhaled/miniconda3", + "read_only": false, + "resolver_type": "conda", + "resolves_simple_dependencies": true, + "use_local": false, + "versionless": false + }, + "dependency_type": "conda", + "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-414e7261396ae5d11be85675e1e19db222325018468f2829061591addd560be0", + "exact": true, + "model_class": "MergedCondaDependency", + "name": "biopython", + "version": "1.85" + }, + { + "cacheable": false, + "dependency_resolver": { + "auto_init": true, + "auto_install": true, + "can_uninstall_dependencies": true, + "ensure_channels": "conda-forge,bioconda", + "model_class": "CondaDependencyResolver", + "prefix": "/home/rkhaled/miniconda3", + "read_only": false, + "resolver_type": "conda", + "resolves_simple_dependencies": true, + "use_local": false, + "versionless": false + }, + "dependency_type": "conda", + "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-414e7261396ae5d11be85675e1e19db222325018468f2829061591addd560be0", + "exact": true, + "model_class": "MergedCondaDependency", + "name": "proglog", + "version": "0.1.10" + }, + { + "cacheable": false, + "dependency_resolver": { + "auto_init": true, + "auto_install": true, + "can_uninstall_dependencies": true, + "ensure_channels": "conda-forge,bioconda", + "model_class": "CondaDependencyResolver", + "prefix": "/home/rkhaled/miniconda3", + "read_only": false, + "resolver_type": "conda", + "resolves_simple_dependencies": true, + "use_local": false, + "versionless": false + }, + "dependency_type": "conda", + "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-414e7261396ae5d11be85675e1e19db222325018468f2829061591addd560be0", + "exact": true, + "model_class": "MergedCondaDependency", + "name": "pandas", + "version": "2.2.3" + }, + { + "cacheable": false, + "dependency_resolver": { + "auto_init": true, + "auto_install": true, + "can_uninstall_dependencies": true, + "ensure_channels": "conda-forge,bioconda", + "model_class": "CondaDependencyResolver", + "prefix": "/home/rkhaled/miniconda3", + "read_only": false, + "resolver_type": "conda", + "resolves_simple_dependencies": true, + "use_local": false, + "versionless": false + }, + "dependency_type": "conda", + "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-414e7261396ae5d11be85675e1e19db222325018468f2829061591addd560be0", + "exact": true, + "model_class": "MergedCondaDependency", + "name": "dnacauldron", + "version": "2.0.12" + }, + { + "cacheable": false, + "dependency_resolver": { + "auto_init": true, + "auto_install": true, + "can_uninstall_dependencies": true, + "ensure_channels": "conda-forge,bioconda", + "model_class": "CondaDependencyResolver", + "prefix": "/home/rkhaled/miniconda3", + "read_only": false, + "resolver_type": "conda", + "resolves_simple_dependencies": true, + "use_local": false, + "versionless": false + }, + "dependency_type": "conda", + "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-414e7261396ae5d11be85675e1e19db222325018468f2829061591addd560be0", + "exact": true, + "model_class": "MergedCondaDependency", + "name": "pdf-reports", + "version": "0.3.9" + }, + { + "cacheable": false, + "dependency_resolver": { + "auto_init": true, + "auto_install": true, + "can_uninstall_dependencies": true, + "ensure_channels": "conda-forge,bioconda", + "model_class": "CondaDependencyResolver", + "prefix": "/home/rkhaled/miniconda3", + "read_only": false, + "resolver_type": "conda", + "resolves_simple_dependencies": true, + "use_local": false, + "versionless": false + }, + "dependency_type": "conda", + "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-414e7261396ae5d11be85675e1e19db222325018468f2829061591addd560be0", + "exact": true, + "model_class": "MergedCondaDependency", + "name": "sequenticon", + "version": "0.1.8" + }, + { + "cacheable": false, + "dependency_resolver": { + "auto_init": true, + "auto_install": true, + "can_uninstall_dependencies": true, + "ensure_channels": "conda-forge,bioconda", + "model_class": "CondaDependencyResolver", + "prefix": "/home/rkhaled/miniconda3", + "read_only": false, + "resolver_type": "conda", + "resolves_simple_dependencies": true, + "use_local": false, + "versionless": false + }, + "dependency_type": "conda", + "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-414e7261396ae5d11be85675e1e19db222325018468f2829061591addd560be0", + "exact": true, + "model_class": "MergedCondaDependency", + "name": "dna_features_viewer", + "version": "3.1.4" + } + ], + "exit_code": 0, + "external_id": "71459", + "galaxy_version": "24.2", + "handler": null, + "history_id": "a363c57bce5ddac4", + "id": "4d500d87322140a3", + "inputs": { + "assembly_csv": { + "id": "1b325227d95fdc76", + "src": "hda", + "uuid": "7e6259bf-8646-4691-b40d-d91bbe52d6c5" + }, + "genbank_files1": { + "id": "2d4530cd892a2a69", + "src": "hda", + "uuid": "48f246fb-df3d-4c65-a99e-cc314c9a2d20" + }, + "genbank_files2": { + "id": "afd885e9dc2aeeee", + "src": "hda", + "uuid": "50cb308d-4eb5-4d9d-ae07-011179d84b2e" + }, + "genbank_files3": { + "id": "ae8033db013a49b9", + "src": "hda", + "uuid": "13b514d1-710c-46ef-9b83-939acad72375" + }, + "genbank_files4": { + "id": "0661f11e9507b8a6", + "src": "hda", + "uuid": "30bef7c3-fecb-40f7-b435-daf794d456c1" + }, + "genbank_files5": { + "id": "fcc678ee7e8e9f81", + "src": "hda", + "uuid": "a87d7ba7-2092-45e2-9aff-813bb53a02a6" + } + }, + "job_messages": [], + "job_metrics": [], + "job_runner_name": null, + "job_stderr": "", + "job_stdout": "", + "model_class": "Job", + "output_collections": {}, + "outputs": { + "output_zip": { + "id": "4d500d87322140a3", + "src": "hda", + "uuid": "664a6a95-4ce6-4f74-be51-728a9cbd55da" + } + }, + "params": { + "__input_ext": "\"input\"", + "adv": "{\"enzyme\": \"auto\", \"use_file_names_as_ids\": true}", + "assembly_plan_name": "\"BioBrickStandardAssembly\"", + "chromInfo": "\"/tmp/tmps36anksu/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", + "dbkey": "\"?\"", + "domesticated_input": null, + "genbank_files": "{\"values\": [{\"id\": 5, \"src\": \"hdca\"}]}", + "topology": "\"circular\"" + }, + "state": "ok", + "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", + "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", + "tool_id": "cloning_simulation", + "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", + "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", + "update_time": "2025-05-16T08:56:55.140287", + "user_email": "planemo@galaxyproject.org", + "user_id": "1d1943aa60deb628" + }, + "status": "success", + "test_index": 4, + "time_seconds": 34.888214349746704, + "tool_id": "cloning_simulation", + "tool_version": "0.1.0+galaxy0" + }, + "has_data": true, + "id": "cloning_simulation-4" + }, + { + "data": { + "inputs": { + "adv|use_file_names_as_ids": true, + "assembly_csv": { + "id": "a727d841eabfe479", + "src": "hda" + }, + "assembly_plan_name": "Type2sRestrictionAssembly", + "domesticated_input": { + "id": "8ab843ac4a5890da", + "src": "hdca" + }, + "genbank_files": { + "id": "6206f91299006d13", + "src": "hdca" + }, + "topology": "circular" + }, + "job": { + "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'", + "command_version": "", + "copied_from_job_id": null, + "create_time": "2025-05-16T08:57:35.145295", + "dependencies": [ + { + "cacheable": false, + "dependency_resolver": { + "auto_init": true, + "auto_install": true, + "can_uninstall_dependencies": true, + "ensure_channels": "conda-forge,bioconda", + "model_class": "CondaDependencyResolver", + "prefix": "/home/rkhaled/miniconda3", + "read_only": false, + "resolver_type": "conda", + "resolves_simple_dependencies": true, + "use_local": false, + "versionless": false + }, + "dependency_type": "conda", + "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-414e7261396ae5d11be85675e1e19db222325018468f2829061591addd560be0", + "exact": true, + "model_class": "MergedCondaDependency", + "name": "flametree", + "version": "0.1.11" + }, + { + "cacheable": false, + "dependency_resolver": { + "auto_init": true, + "auto_install": true, + "can_uninstall_dependencies": true, + "ensure_channels": "conda-forge,bioconda", + "model_class": "CondaDependencyResolver", + "prefix": "/home/rkhaled/miniconda3", + "read_only": false, + "resolver_type": "conda", + "resolves_simple_dependencies": true, + "use_local": false, + "versionless": false + }, + "dependency_type": "conda", + "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-414e7261396ae5d11be85675e1e19db222325018468f2829061591addd560be0", + "exact": true, + "model_class": "MergedCondaDependency", + "name": "biopython", + "version": "1.85" + }, + { + "cacheable": false, + "dependency_resolver": { + "auto_init": true, + "auto_install": true, + "can_uninstall_dependencies": true, + "ensure_channels": "conda-forge,bioconda", + "model_class": "CondaDependencyResolver", + "prefix": "/home/rkhaled/miniconda3", + "read_only": false, + "resolver_type": "conda", + "resolves_simple_dependencies": true, + "use_local": false, + "versionless": false + }, + "dependency_type": "conda", + "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-414e7261396ae5d11be85675e1e19db222325018468f2829061591addd560be0", + "exact": true, + "model_class": "MergedCondaDependency", + "name": "proglog", + "version": "0.1.10" + }, + { + "cacheable": false, + "dependency_resolver": { + "auto_init": true, + "auto_install": true, + "can_uninstall_dependencies": true, + "ensure_channels": "conda-forge,bioconda", + "model_class": "CondaDependencyResolver", + "prefix": "/home/rkhaled/miniconda3", + "read_only": false, + "resolver_type": "conda", + "resolves_simple_dependencies": true, + "use_local": false, + "versionless": false + }, + "dependency_type": "conda", + "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-414e7261396ae5d11be85675e1e19db222325018468f2829061591addd560be0", + "exact": true, + "model_class": "MergedCondaDependency", + "name": "pandas", + "version": "2.2.3" + }, + { + "cacheable": false, + "dependency_resolver": { + "auto_init": true, + "auto_install": true, + "can_uninstall_dependencies": true, + "ensure_channels": "conda-forge,bioconda", + "model_class": "CondaDependencyResolver", + "prefix": "/home/rkhaled/miniconda3", + "read_only": false, + "resolver_type": "conda", + "resolves_simple_dependencies": true, + "use_local": false, + "versionless": false + }, + "dependency_type": 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"cb7d74ca0f50a91c", + "src": "hda", + "uuid": "876d6160-fcd5-49e1-ae58-aa8d30c94e09" + }, + "domesticated_input5": { + "id": "f0efc768d058218e", + "src": "hda", + "uuid": "3a81169d-4569-4c6d-9417-a3c5924f8649" + }, + "genbank_files1": { + "id": "4e56a0aaa45feaf7", + "src": "hda", + "uuid": "2b34f95b-2776-40a7-ac0a-abdb3d2b151f" + }, + "genbank_files2": { + "id": "cb872b8bb704ec40", + "src": "hda", + "uuid": "81535329-42d0-4e9d-a713-beb8033e2db9" + }, + "genbank_files3": { + "id": "90f63057cb36f606", + "src": "hda", + "uuid": "dbbc8408-63b6-4265-8878-94942c7b2016" + }, + "genbank_files4": { + "id": "efde02d124a713a2", + "src": "hda", + "uuid": "41d94b9c-f2f0-4253-88bb-896b26fdb7a0" + }, + "genbank_files5": { + "id": "81a37b9282573f69", + "src": "hda", + "uuid": "48a630fc-ea4b-4c19-8b0b-fb78db4bff7d" + }, + "genbank_files6": { + "id": "9989729bf7df579e", + "src": "hda", + "uuid": "459d85d8-4869-4d03-bd2a-d083e4ecf818" + }, + "genbank_files7": { + "id": "bc2865f07ef20436", + "src": "hda", + "uuid": "1b189627-18cd-4c7c-8d19-46371420574a" + } + }, + "job_messages": [], + "job_metrics": [], + "job_runner_name": null, + "job_stderr": "", + "job_stdout": "", + "model_class": "Job", + "output_collections": {}, + "outputs": { + "output_zip": { + "id": "9d82ca4e11899647", + "src": "hda", + "uuid": "891d2044-502b-4e4b-b394-575c9e42a36f" + } + }, + "params": { + "__input_ext": "\"input\"", + "adv": "{\"enzyme\": \"auto\", \"use_file_names_as_ids\": true}", + "assembly_plan_name": "\"Type2sRestrictionAssembly\"", + "chromInfo": "\"/tmp/tmps36anksu/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", + "dbkey": "\"?\"", + "domesticated_input": "{\"values\": [{\"id\": 6, \"src\": \"hdca\"}]}", + "genbank_files": "{\"values\": [{\"id\": 7, \"src\": \"hdca\"}]}", + "topology": "\"circular\"" + }, + "state": "ok", + "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", + "stdout": "Simulating assembly plan assambly...\n{'cancelled_assemblies': 0, 'errored_assemblies': 0, 'valid_assemblies': 4}\nGenerating assemblies reports...\nFiles in the zip 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+ "update_time": "2025-05-16T08:57:47.925883", + "user_email": "planemo@galaxyproject.org", + "user_id": "1d1943aa60deb628" + }, + "status": "success", + "test_index": 5, + "time_seconds": 52.77062439918518, + "tool_id": "cloning_simulation", + "tool_version": "0.1.0+galaxy0" + }, + "has_data": true, + "id": "cloning_simulation-5" + } + ], + "version": "0.1" +} \ No newline at end of file