Mercurial > repos > tduigou > cloning_simulation
view output.json @ 7:296e5145a862 draft
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
| author | tduigou |
|---|---|
| date | Fri, 23 May 2025 12:53:50 +0000 |
| parents | e1e985913204 |
| children | 07e902da89ad |
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{ "summary": { "num_errors": 0, "num_failures": 0, "num_skips": 0, "num_tests": 7 }, "tests": [ { "data": { "inputs": { "adv|use_file_names_as_ids": true, "assembly_csv": { "id": "106ff655f8a511fe", "src": "hda" }, "assembly_plan_name": "Type2sRestrictionAssembly", "genbank_files": { "id": "8094a24bdbd328fd", "src": "hdca" }, "topology": "circular" }, "job": { "command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && cp '/tmp/tmpulb7kecp/files/b/1/1/dataset_b114952d-795f-4872-a508-1b68f71f6843.dat' 'assembly_csv.csv' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmpulb7kecp/files/7/7/2/dataset_7728392b-6cec-4864-bb21-79c5330f34db.dat,/tmp/tmpulb7kecp/files/f/9/6/dataset_f96a1c6f-cc5b-4969-947e-d0c5d9bc1861.dat,/tmp/tmpulb7kecp/files/5/d/9/dataset_5d9fa39d-58a0-4385-a52a-cff566ab6569.dat,/tmp/tmpulb7kecp/files/9/2/d/dataset_92d74dbb-3200-4182-b1c1-b916d8b9636a.dat,/tmp/tmpulb7kecp/files/4/e/7/dataset_4e7f3975-e0c4-4043-a1d6-e798d43c88bd.dat,/tmp/tmpulb7kecp/files/9/6/5/dataset_965d5a1c-5b11-44c4-b1bc-392cb2e34bda.dat,/tmp/tmpulb7kecp/files/b/2/9/dataset_b29b6ede-fd7d-4db7-812a-e4719848c9d9.dat,/tmp/tmpulb7kecp/files/d/0/b/dataset_d0b8b55e-d329-4566-b8a2-8708f23d57d2.dat,/tmp/tmpulb7kecp/files/b/c/1/dataset_bc107665-0e38-42fe-8183-edb3b3f22248.dat,/tmp/tmpulb7kecp/files/f/7/e/dataset_f7e084da-7abc-4b0b-a75a-d7be088e30ee.dat,/tmp/tmpulb7kecp/files/6/2/e/dataset_62ece79d-c0cc-454a-bbd8-1c943ff0bcce.dat,/tmp/tmpulb7kecp/files/2/4/7/dataset_2476887f-77e7-4955-8e73-a0b57b50009d.dat' --domesticated_seq '' --assembly_csv 'assembly_csv.csv' --assembly_plan_name 'Type2sRestrictionAssembly' --file_name_mapping '/tmp/tmpulb7kecp/files/7/7/2/dataset_7728392b-6cec-4864-bb21-79c5330f34db.dat:part_A.gb,/tmp/tmpulb7kecp/files/f/9/6/dataset_f96a1c6f-cc5b-4969-947e-d0c5d9bc1861.dat:part_B.gb,/tmp/tmpulb7kecp/files/5/d/9/dataset_5d9fa39d-58a0-4385-a52a-cff566ab6569.dat:part_C.gb,/tmp/tmpulb7kecp/files/9/2/d/dataset_92d74dbb-3200-4182-b1c1-b916d8b9636a.dat:part_D.gb,/tmp/tmpulb7kecp/files/4/e/7/dataset_4e7f3975-e0c4-4043-a1d6-e798d43c88bd.dat:part_E.gb,/tmp/tmpulb7kecp/files/9/6/5/dataset_965d5a1c-5b11-44c4-b1bc-392cb2e34bda.dat:part_F.gb,/tmp/tmpulb7kecp/files/b/2/9/dataset_b29b6ede-fd7d-4db7-812a-e4719848c9d9.dat:part_G.gb,/tmp/tmpulb7kecp/files/d/0/b/dataset_d0b8b55e-d329-4566-b8a2-8708f23d57d2.dat:part_H.gb,/tmp/tmpulb7kecp/files/b/c/1/dataset_bc107665-0e38-42fe-8183-edb3b3f22248.dat:part_I.gb,/tmp/tmpulb7kecp/files/f/7/e/dataset_f7e084da-7abc-4b0b-a75a-d7be088e30ee.dat:part_J.gb,/tmp/tmpulb7kecp/files/6/2/e/dataset_62ece79d-c0cc-454a-bbd8-1c943ff0bcce.dat:part_K.gb,/tmp/tmpulb7kecp/files/2/4/7/dataset_2476887f-77e7-4955-8e73-a0b57b50009d.dat:part_L.gb' --file_name_mapping_dom '' --use_file_names_as_id 'true' --outdir_simulation 'outdir_zip' --outdir_gb 'outdir_gb' --output_simulation 'output_zip.zip' --enzyme 'auto' --topology 'circular' && cp 'output_zip.zip' '/tmp/tmpulb7kecp/job_working_directory/000/14/outputs/dataset_531b5c74-8577-4ba2-86cf-d8f25f16e169.dat'", "command_version": "", "copied_from_job_id": null, "create_time": "2025-05-23T12:13:12.978945", "dependencies": [], "exit_code": 0, "external_id": "178458", "galaxy_version": "24.2", "handler": null, "history_id": "8094a24bdbd328fd", "id": "a843aa6880d39864", "inputs": { "assembly_csv": { "id": "106ff655f8a511fe", "src": "hda", "uuid": "b114952d-795f-4872-a508-1b68f71f6843" }, "genbank_files1": { "id": "8094a24bdbd328fd", "src": "hda", "uuid": "7728392b-6cec-4864-bb21-79c5330f34db" }, "genbank_files10": { "id": "54ed1ed3b165c7b4", "src": "hda", "uuid": "f7e084da-7abc-4b0b-a75a-d7be088e30ee" }, "genbank_files11": { "id": "aa441ebc75addcb0", "src": "hda", "uuid": "62ece79d-c0cc-454a-bbd8-1c943ff0bcce" }, "genbank_files12": { "id": "41108ccf3c813abd", "src": "hda", "uuid": "2476887f-77e7-4955-8e73-a0b57b50009d" }, "genbank_files2": { "id": "6c2020bf7be1ec65", "src": "hda", "uuid": "f96a1c6f-cc5b-4969-947e-d0c5d9bc1861" }, "genbank_files3": { "id": "8a7a2aba20929ed0", "src": "hda", "uuid": "5d9fa39d-58a0-4385-a52a-cff566ab6569" }, "genbank_files4": { "id": "53ad8e2eaf8a05d9", "src": "hda", "uuid": "92d74dbb-3200-4182-b1c1-b916d8b9636a" }, "genbank_files5": { "id": "85b2c5efa0bce20f", "src": "hda", "uuid": "4e7f3975-e0c4-4043-a1d6-e798d43c88bd" }, "genbank_files6": { "id": "3758c7315f184c9a", "src": "hda", "uuid": "965d5a1c-5b11-44c4-b1bc-392cb2e34bda" }, "genbank_files7": { "id": "cc5b73713462c207", "src": "hda", "uuid": "b29b6ede-fd7d-4db7-812a-e4719848c9d9" }, "genbank_files8": { "id": "abedd81ff2360f10", "src": "hda", "uuid": "d0b8b55e-d329-4566-b8a2-8708f23d57d2" }, "genbank_files9": { "id": "83d0643dcafc650b", "src": "hda", "uuid": "bc107665-0e38-42fe-8183-edb3b3f22248" } }, "job_messages": [], "job_metrics": [], "job_runner_name": null, "job_stderr": "", "job_stdout": "", "model_class": "Job", "output_collections": { "construct_gb": { "id": "6c2020bf7be1ec65", "src": "hdca" } }, "outputs": { "__new_primary_file_construct_gb|construct_1__": { "id": "03b30db777cad5e1", "src": "hda", "uuid": "21d43ad8-7969-4897-bade-2bde4913b7c5" }, "__new_primary_file_construct_gb|construct_2__": { "id": "d7483ddd36cf3921", "src": "hda", "uuid": "9420de76-fe00-401e-9cef-039d76b41e8f" }, "__new_primary_file_construct_gb|construct_3__": { "id": "2239b1a77a4b659c", "src": "hda", "uuid": "e360b3e5-97c6-49be-9e0e-4ff44209fb03" }, "__new_primary_file_construct_gb|construct_4__": { "id": "b9f6f443461a8e55", "src": "hda", "uuid": "580f1a4e-e43c-4396-9ae5-d441a0f64d1a" }, "output_zip": { "id": "a843aa6880d39864", "src": "hda", "uuid": "531b5c74-8577-4ba2-86cf-d8f25f16e169" } }, "params": { "__input_ext": "\"input\"", "adv": "{\"enzyme\": \"auto\", \"use_file_names_as_ids\": true}", "assembly_plan_name": "\"Type2sRestrictionAssembly\"", "chromInfo": "\"/tmp/tmpulb7kecp/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, 2.43it/s, now=None]\rassembly: 75%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u258c | 3/4 [00:01<00:00, 2.20it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 4/4 [00:02<00:00, 1.78it/s, now=None]\r \r", "stdout": "Simulating assembly plan assambly...\n{'cancelled_assemblies': 0, 'errored_assemblies': 0, 'valid_assemblies': 4}\nGenerating assemblies reports...\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, 2.43it/s, now=None]\rassembly: 75%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u258c | 3/4 [00:01<00:00, 2.20it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 4/4 [00:02<00:00, 1.78it/s, now=None]\r \r", "tool_stdout": "Simulating assembly plan assambly...\n{'cancelled_assemblies': 0, 'errored_assemblies': 0, 'valid_assemblies': 4}\nGenerating assemblies reports...\n", "update_time": "2025-05-23T12:13:26.150051", "user_email": "planemo@galaxyproject.org", "user_id": "8094a24bdbd328fd" }, "status": "success", "test_index": 0, "time_seconds": 53.7402708530426, "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": "9ebeb50920a3365f", "src": "hda" }, "assembly_plan_name": "GibsonAssembly", "genbank_files": { "id": "8a7a2aba20929ed0", "src": "hdca" }, "topology": "circular" }, "job": { "command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && cp '/tmp/tmpulb7kecp/files/c/b/4/dataset_cb485986-3b87-4675-b3c5-cdb2d0287c2a.dat' 'assembly_csv.csv' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmpulb7kecp/files/a/6/0/dataset_a609f7c2-042e-4412-98a8-2056fe698533.dat' --domesticated_seq '' --assembly_csv 'assembly_csv.csv' --assembly_plan_name 'GibsonAssembly' --file_name_mapping '/tmp/tmpulb7kecp/files/a/6/0/dataset_a609f7c2-042e-4412-98a8-2056fe698533.dat:gibson_sequences.fa' --file_name_mapping_dom '' --use_file_names_as_id 'true' --outdir_simulation 'outdir_zip' --outdir_gb 'outdir_gb' --output_simulation 'output_zip.zip' --enzyme 'auto' --topology 'circular' && cp 'output_zip.zip' '/tmp/tmpulb7kecp/job_working_directory/000/17/outputs/dataset_ff63bc11-8e44-4753-a248-329fb44ee3b1.dat'", "command_version": "", "copied_from_job_id": null, "create_time": "2025-05-23T12:13:37.414073", "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-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf", "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-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf", "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-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf", "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-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf", "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-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf", "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-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf", "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-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf", "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-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf", "exact": true, "model_class": "MergedCondaDependency", "name": "dna_features_viewer", "version": "3.1.5" } ], "exit_code": 0, "external_id": "178806", "galaxy_version": "24.2", "handler": null, "history_id": "6c2020bf7be1ec65", "id": "2239b1a77a4b659c", "inputs": { "assembly_csv": { "id": "9ebeb50920a3365f", "src": "hda", "uuid": "cb485986-3b87-4675-b3c5-cdb2d0287c2a" }, "genbank_files1": { "id": "293d5da1ac833ef3", "src": "hda", "uuid": "a609f7c2-042e-4412-98a8-2056fe698533" } }, "job_messages": [], "job_metrics": [], "job_runner_name": null, "job_stderr": "", "job_stdout": "", "model_class": "Job", "output_collections": { "construct_gb": { "id": "53ad8e2eaf8a05d9", "src": "hdca" } }, "outputs": { "__new_primary_file_construct_gb|construct_1__": { "id": "a21f4c8cc3b535db", "src": "hda", "uuid": "0463b48d-c2d8-42a4-8b6a-ecb4dfc701c4" }, "__new_primary_file_construct_gb|construct_2__": { "id": "c9bb032e1a0e8897", "src": "hda", "uuid": "89f175c4-8e96-49e3-8c45-514b2193b29a" }, "__new_primary_file_construct_gb|construct_3__": { "id": "68281df0cf338722", "src": "hda", "uuid": "2a43a8fd-7b64-4f92-a483-6c716ec2f681" }, "output_zip": { "id": "713969bb307bfc17", "src": "hda", "uuid": "ff63bc11-8e44-4753-a248-329fb44ee3b1" } }, "params": { "__input_ext": "\"input\"", "adv": "{\"enzyme\": \"auto\", \"use_file_names_as_ids\": true}", "assembly_plan_name": "\"GibsonAssembly\"", "chromInfo": "\"/tmp/tmpulb7kecp/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%| | 0/5 [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, 4.37it/s, now=None]\rassembly: 60%|\u2588\u2588\u2588\u2588\u2588\u2588 | 3/5 [00:00<00:00, 4.36it/s, now=None]\rassembly: 80%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588 | 4/5 [00:00<00:00, 4.35it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 5/5 [00:01<00:00, 3.54it/s, now=None]\r \r", "stdout": "Simulating assembly plan assambly...\n{'cancelled_assemblies': 0, 'errored_assemblies': 2, 'valid_assemblies': 3}\nGenerating assemblies reports...\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, 4.37it/s, now=None]\rassembly: 60%|\u2588\u2588\u2588\u2588\u2588\u2588 | 3/5 [00:00<00:00, 4.36it/s, now=None]\rassembly: 80%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588 | 4/5 [00:00<00:00, 4.35it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 5/5 [00:01<00:00, 3.54it/s, now=None]\r \r", "tool_stdout": "Simulating assembly plan assambly...\n{'cancelled_assemblies': 0, 'errored_assemblies': 2, 'valid_assemblies': 3}\nGenerating assemblies reports...\n", "update_time": "2025-05-23T12:13:49.541469", "user_email": "planemo@galaxyproject.org", "user_id": "8094a24bdbd328fd" }, "status": "success", "test_index": 1, "time_seconds": 23.19603419303894, "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": "6ba0e4a0e82495c8", "src": "hda" }, "assembly_plan_name": "LigaseCyclingReactionAssembly", "genbank_files": { "id": "85b2c5efa0bce20f", "src": "hdca" }, "topology": "circular" }, "job": { "command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && cp '/tmp/tmpulb7kecp/files/b/7/7/dataset_b7713227-6c97-4684-ac9a-76650631a0a9.dat' 'assembly_csv.csv' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmpulb7kecp/files/f/e/9/dataset_fe9a8ec6-5d0f-4f89-934f-a46bb9ff8db7.dat,/tmp/tmpulb7kecp/files/4/5/7/dataset_45763854-327e-472f-9cb3-a3cc72b8f76b.dat' --domesticated_seq '' --assembly_csv 'assembly_csv.csv' --assembly_plan_name 'LigaseCyclingReactionAssembly' --file_name_mapping '/tmp/tmpulb7kecp/files/f/e/9/dataset_fe9a8ec6-5d0f-4f89-934f-a46bb9ff8db7.dat:RFP_GFP_plasmid_BOs.fa,/tmp/tmpulb7kecp/files/4/5/7/dataset_45763854-327e-472f-9cb3-a3cc72b8f76b.dat:RFP_GFP_plasmid_parts.fa' --file_name_mapping_dom '' --use_file_names_as_id 'true' --outdir_simulation 'outdir_zip' --outdir_gb 'outdir_gb' --output_simulation 'output_zip.zip' --enzyme 'auto' --topology 'circular' && cp 'output_zip.zip' '/tmp/tmpulb7kecp/job_working_directory/000/21/outputs/dataset_1d53129b-a396-429b-9971-2d00b993e48a.dat'", "command_version": "", "copied_from_job_id": null, "create_time": "2025-05-23T12:14:01.238952", "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-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf", "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-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf", "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-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf", "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-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf", "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-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf", "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-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf", "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-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf", "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-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf", "exact": true, "model_class": "MergedCondaDependency", "name": "dna_features_viewer", "version": "3.1.5" } ], "exit_code": 0, "external_id": "179225", "galaxy_version": "24.2", "handler": null, "history_id": "8a7a2aba20929ed0", "id": "713969bb307bfc17", "inputs": { "assembly_csv": { "id": "6ba0e4a0e82495c8", "src": "hda", "uuid": "b7713227-6c97-4684-ac9a-76650631a0a9" }, "genbank_files1": { "id": "f1fafc006c3c5be7", "src": "hda", "uuid": "fe9a8ec6-5d0f-4f89-934f-a46bb9ff8db7" }, "genbank_files2": { "id": "8c1f52fe6e59f5ac", "src": "hda", "uuid": "45763854-327e-472f-9cb3-a3cc72b8f76b" } }, "job_messages": [], "job_metrics": [], "job_runner_name": null, "job_stderr": "", "job_stdout": "", "model_class": "Job", "output_collections": { "construct_gb": { "id": "3758c7315f184c9a", "src": "hdca" } }, "outputs": { "output_zip": { "id": "db12508970e81a14", "src": "hda", "uuid": "1d53129b-a396-429b-9971-2d00b993e48a" } }, "params": { "__input_ext": "\"input\"", "adv": "{\"enzyme\": \"auto\", \"use_file_names_as_ids\": true}", "assembly_plan_name": "\"LigaseCyclingReactionAssembly\"", "chromInfo": "\"/tmp/tmpulb7kecp/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%| | 0/2 [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, 2.37it/s, now=None]\r \r", "stdout": "Simulating assembly plan assambly...\n{'cancelled_assemblies': 0, 'errored_assemblies': 2, 'valid_assemblies': 0}\nGenerating assemblies reports...\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, 2.37it/s, now=None]\r \r", "tool_stdout": "Simulating assembly plan assambly...\n{'cancelled_assemblies': 0, 'errored_assemblies': 2, 'valid_assemblies': 0}\nGenerating assemblies reports...\n", "update_time": "2025-05-23T12:14:13.046545", "user_email": "planemo@galaxyproject.org", "user_id": "8094a24bdbd328fd" }, "status": "success", "test_index": 2, "time_seconds": 23.21994924545288, "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": "a9ed9e5261104c2a", "src": "hda" }, "assembly_plan_name": "BASICAssembly", "genbank_files": { "id": "cc5b73713462c207", "src": "hdca" }, "topology": "circular" }, "job": { "command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && cp '/tmp/tmpulb7kecp/files/5/1/3/dataset_513294c4-b1bf-4a02-a37d-6f4bd74436d9.dat' 'assembly_csv.csv' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmpulb7kecp/files/a/7/9/dataset_a79829ef-6450-404a-8d59-fa42ddb91ca3.dat,/tmp/tmpulb7kecp/files/7/c/7/dataset_7c74d4c3-38b5-40a7-9c71-482502e6e5f8.dat,/tmp/tmpulb7kecp/files/5/1/c/dataset_51c3184d-fd7e-49a8-af51-e29bbf7a8a37.dat,/tmp/tmpulb7kecp/files/2/4/4/dataset_24493579-a703-4b94-ac09-e283f59035b0.dat,/tmp/tmpulb7kecp/files/c/b/4/dataset_cb4bfd16-db5c-47ce-98f5-a5c5065d4dd4.dat' --domesticated_seq '' --assembly_csv 'assembly_csv.csv' --assembly_plan_name 'BASICAssembly' --file_name_mapping '/tmp/tmpulb7kecp/files/a/7/9/dataset_a79829ef-6450-404a-8d59-fa42ddb91ca3.dat:GFP.gb,/tmp/tmpulb7kecp/files/7/c/7/dataset_7c74d4c3-38b5-40a7-9c71-482502e6e5f8.dat:p15A_kan.gb,/tmp/tmpulb7kecp/files/5/1/c/dataset_51c3184d-fd7e-49a8-af51-e29bbf7a8a37.dat:promoter.gb,/tmp/tmpulb7kecp/files/2/4/4/dataset_24493579-a703-4b94-ac09-e283f59035b0.dat:RFP.gb,/tmp/tmpulb7kecp/files/c/b/4/dataset_cb4bfd16-db5c-47ce-98f5-a5c5065d4dd4.dat:oligos.fa' --file_name_mapping_dom '' --use_file_names_as_id 'true' --outdir_simulation 'outdir_zip' --outdir_gb 'outdir_gb' --output_simulation 'output_zip.zip' --enzyme 'auto' --topology 'circular' && cp 'output_zip.zip' '/tmp/tmpulb7kecp/job_working_directory/000/28/outputs/dataset_47491132-901d-4249-9c1e-dfd12feae17e.dat'", "command_version": "", "copied_from_job_id": null, "create_time": "2025-05-23T12:14:34.083682", "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-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf", "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-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf", "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-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf", "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-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf", "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-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf", "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-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf", "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-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf", "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-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf", "exact": true, "model_class": "MergedCondaDependency", "name": "dna_features_viewer", "version": "3.1.5" } ], "exit_code": 0, "external_id": "179816", "galaxy_version": "24.2", "handler": null, "history_id": "53ad8e2eaf8a05d9", "id": "db12508970e81a14", "inputs": { "assembly_csv": { "id": "a9ed9e5261104c2a", "src": "hda", "uuid": "513294c4-b1bf-4a02-a37d-6f4bd74436d9" }, "genbank_files1": { "id": "ce8e89b55ee6d12d", "src": "hda", "uuid": "a79829ef-6450-404a-8d59-fa42ddb91ca3" }, "genbank_files2": { "id": "9c6b8acc292ccf30", "src": "hda", "uuid": "7c74d4c3-38b5-40a7-9c71-482502e6e5f8" }, "genbank_files3": { "id": "0b252ddd8f79f3ec", "src": "hda", "uuid": "51c3184d-fd7e-49a8-af51-e29bbf7a8a37" }, "genbank_files4": { "id": "757270683c70cddd", "src": "hda", "uuid": "24493579-a703-4b94-ac09-e283f59035b0" }, "genbank_files5": { "id": "3932a26d59be2681", "src": "hda", "uuid": "cb4bfd16-db5c-47ce-98f5-a5c5065d4dd4" } }, "job_messages": [], "job_metrics": [], "job_runner_name": null, "job_stderr": "", "job_stdout": "", "model_class": "Job", "output_collections": { "construct_gb": { "id": "abedd81ff2360f10", "src": "hdca" } }, "outputs": { "output_zip": { "id": "8c26318d49002581", "src": "hda", "uuid": "47491132-901d-4249-9c1e-dfd12feae17e" } }, "params": { "__input_ext": "\"input\"", "adv": "{\"enzyme\": \"auto\", \"use_file_names_as_ids\": true}", "assembly_plan_name": "\"BASICAssembly\"", "chromInfo": "\"/tmp/tmpulb7kecp/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", "dbkey": "\"?\"", "domesticated_input": null, "genbank_files": "{\"values\": [{\"id\": 7, \"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, 49.05it/s, now=None]\r \r", "stdout": "Simulating assembly plan assambly...\n{'cancelled_assemblies': 2, 'errored_assemblies': 8, 'valid_assemblies': 0}\nGenerating assemblies reports...\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, 49.05it/s, now=None]\r \r", "tool_stdout": "Simulating assembly plan assambly...\n{'cancelled_assemblies': 2, 'errored_assemblies': 8, 'valid_assemblies': 0}\nGenerating assemblies reports...\n", "update_time": "2025-05-23T12:14:44.485473", "user_email": "planemo@galaxyproject.org", "user_id": "8094a24bdbd328fd" }, "status": "success", "test_index": 3, "time_seconds": 31.373873472213745, "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": "723f42bbf157272d", "src": "hda" }, "assembly_plan_name": "BioBrickStandardAssembly", "genbank_files": { "id": "83d0643dcafc650b", "src": "hdca" }, "topology": "circular" }, "job": { "command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && cp '/tmp/tmpulb7kecp/files/9/4/0/dataset_940a048a-ec9f-4cc9-9990-f0f1bb9c01db.dat' 'assembly_csv.csv' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmpulb7kecp/files/d/5/9/dataset_d591902b-724d-446d-bad5-1ecf539f4193.dat,/tmp/tmpulb7kecp/files/4/5/7/dataset_457d680a-7fd5-42ce-8747-a78267083da9.dat,/tmp/tmpulb7kecp/files/1/a/9/dataset_1a9aa4c8-4387-4b65-a638-1033465060d7.dat,/tmp/tmpulb7kecp/files/3/f/e/dataset_3feea62b-c35b-4f65-937d-3233db6bf0ec.dat,/tmp/tmpulb7kecp/files/f/9/1/dataset_f917f42d-9d14-4b5e-aa4f-b04e06a56357.dat' --domesticated_seq '' --assembly_csv 'assembly_csv.csv' --assembly_plan_name 'BioBrickStandardAssembly' --file_name_mapping '/tmp/tmpulb7kecp/files/d/5/9/dataset_d591902b-724d-446d-bad5-1ecf539f4193.dat:BBa_E0040_GFP.gb,/tmp/tmpulb7kecp/files/4/5/7/dataset_457d680a-7fd5-42ce-8747-a78267083da9.dat:BBa_J23119_prom.gb,/tmp/tmpulb7kecp/files/1/a/9/dataset_1a9aa4c8-4387-4b65-a638-1033465060d7.dat:BBa_J23119_prom_flawed.gb,/tmp/tmpulb7kecp/files/3/f/e/dataset_3feea62b-c35b-4f65-937d-3233db6bf0ec.dat:BBa_J61048_term.gb,/tmp/tmpulb7kecp/files/f/9/1/dataset_f917f42d-9d14-4b5e-aa4f-b04e06a56357.dat:BBa_K611094_bar.gb' --file_name_mapping_dom '' --use_file_names_as_id 'true' --outdir_simulation 'outdir_zip' --outdir_gb 'outdir_gb' --output_simulation 'output_zip.zip' --enzyme 'auto' --topology 'circular' && cp 'output_zip.zip' '/tmp/tmpulb7kecp/job_working_directory/000/35/outputs/dataset_332a60b5-1b7e-40d6-b4d9-a07f05bc9d4b.dat'", "command_version": "", "copied_from_job_id": null, "create_time": "2025-05-23T12:15:06.093194", "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-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf", "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-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf", "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-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf", "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-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf", "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-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf", "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-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf", "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-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf", "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-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf", "exact": true, "model_class": "MergedCondaDependency", "name": "dna_features_viewer", "version": "3.1.5" } ], "exit_code": 0, "external_id": "180435", "galaxy_version": "24.2", "handler": null, "history_id": "85b2c5efa0bce20f", "id": "8c26318d49002581", "inputs": { "assembly_csv": { "id": "723f42bbf157272d", "src": "hda", "uuid": "940a048a-ec9f-4cc9-9990-f0f1bb9c01db" }, "genbank_files1": { "id": "068bcc8e8d7a762b", "src": "hda", "uuid": "d591902b-724d-446d-bad5-1ecf539f4193" }, "genbank_files2": { "id": "9f11456f5a306175", "src": "hda", "uuid": "457d680a-7fd5-42ce-8747-a78267083da9" }, "genbank_files3": { "id": "4d6d92e009725c02", "src": "hda", "uuid": "1a9aa4c8-4387-4b65-a638-1033465060d7" }, "genbank_files4": { "id": "ba31cade4e4f4bd8", "src": "hda", "uuid": "3feea62b-c35b-4f65-937d-3233db6bf0ec" }, "genbank_files5": { "id": "5c13ba18dcd7e71d", "src": "hda", "uuid": "f917f42d-9d14-4b5e-aa4f-b04e06a56357" } }, "job_messages": [], "job_metrics": [], "job_runner_name": null, "job_stderr": "", "job_stdout": "", "model_class": "Job", "output_collections": { "construct_gb": { "id": "54ed1ed3b165c7b4", "src": "hdca" } }, "outputs": { "__new_primary_file_construct_gb|C1_prom_barcode__": { "id": "165ffecff174f921", "src": "hda", "uuid": "dbf78ec4-1125-4869-b2c7-22ea1e088383" }, "__new_primary_file_construct_gb|C2_gfp_term__": { "id": "68b55cb1abb6ffc8", "src": "hda", "uuid": "eefbb36b-1cb4-4159-a989-674ce4a361d9" }, "__new_primary_file_construct_gb|C3_final__": { "id": "be504c8d89de9ae4", "src": "hda", "uuid": "7c89fcf8-b98f-4719-bedc-509f7d2adbb8" }, "output_zip": { "id": "67dd2dff3a365063", "src": "hda", "uuid": "332a60b5-1b7e-40d6-b4d9-a07f05bc9d4b" } }, "params": { "__input_ext": "\"input\"", "adv": "{\"enzyme\": \"auto\", \"use_file_names_as_ids\": true}", "assembly_plan_name": "\"BioBrickStandardAssembly\"", "chromInfo": "\"/tmp/tmpulb7kecp/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", "dbkey": "\"?\"", "domesticated_input": null, "genbank_files": "{\"values\": [{\"id\": 9, \"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, 1.89it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 3/3 [00:01<00:00, 1.55it/s, now=None]\r \r", "stdout": "Simulating assembly plan assambly...\n{'cancelled_assemblies': 0, 'errored_assemblies': 0, 'valid_assemblies': 3}\nGenerating assemblies reports...\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, 1.89it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 3/3 [00:01<00:00, 1.55it/s, now=None]\r \r", "tool_stdout": "Simulating assembly plan assambly...\n{'cancelled_assemblies': 0, 'errored_assemblies': 0, 'valid_assemblies': 3}\nGenerating assemblies reports...\n", "update_time": "2025-05-23T12:15:19.591969", "user_email": "planemo@galaxyproject.org", "user_id": "8094a24bdbd328fd" }, "status": "success", "test_index": 4, "time_seconds": 35.12441039085388, "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": "8f56f36c2b9f0a7c", "src": "hda" }, "assembly_plan_name": "Type2sRestrictionAssembly", "domesticated_input": { "id": "aa441ebc75addcb0", "src": "hdca" }, "genbank_files": { "id": "41108ccf3c813abd", "src": "hdca" }, "topology": "circular" }, "job": { "command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && cp '/tmp/tmpulb7kecp/files/c/f/a/dataset_cfa1c628-1bad-4864-97c9-f5ff8ae3bb94.dat' 'assembly_csv.csv' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmpulb7kecp/files/0/9/2/dataset_092e3d69-34a0-4c02-9593-859fa17016fb.dat,/tmp/tmpulb7kecp/files/e/d/5/dataset_ed59100d-a4e7-4eb8-9965-8817a8e44000.dat,/tmp/tmpulb7kecp/files/0/1/7/dataset_0172bdce-ca49-45d4-af2d-12a5304b55ca.dat,/tmp/tmpulb7kecp/files/d/2/2/dataset_d22475f3-6c2f-4c52-9164-12248ba5d2a8.dat,/tmp/tmpulb7kecp/files/1/d/9/dataset_1d9b3d4c-eed3-444e-87e6-29c04e915c0d.dat,/tmp/tmpulb7kecp/files/2/4/c/dataset_24c555ec-1536-4ef6-a07d-20d744f3b5fc.dat,/tmp/tmpulb7kecp/files/c/2/3/dataset_c23f475b-f826-4333-8641-66e68bfad42a.dat' --domesticated_seq '/tmp/tmpulb7kecp/files/f/f/a/dataset_ffa8dfa6-df34-412b-84ae-325a3e389a88.dat,/tmp/tmpulb7kecp/files/f/3/3/dataset_f33af6b6-cce3-49b2-a17e-9a168ad065f9.dat,/tmp/tmpulb7kecp/files/2/9/7/dataset_297ec6da-4e55-4534-94c7-903e7e107632.dat,/tmp/tmpulb7kecp/files/3/0/7/dataset_30785c7f-0628-4e63-be45-77272fdedb50.dat,/tmp/tmpulb7kecp/files/f/3/2/dataset_f32a9062-9cf7-48d9-9ddb-ef0c02526564.dat' --assembly_csv 'assembly_csv.csv' --assembly_plan_name 'Type2sRestrictionAssembly' --file_name_mapping '/tmp/tmpulb7kecp/files/0/9/2/dataset_092e3d69-34a0-4c02-9593-859fa17016fb.dat:part_A.gb,/tmp/tmpulb7kecp/files/e/d/5/dataset_ed59100d-a4e7-4eb8-9965-8817a8e44000.dat:part_B.gb,/tmp/tmpulb7kecp/files/0/1/7/dataset_0172bdce-ca49-45d4-af2d-12a5304b55ca.dat:part_C.gb,/tmp/tmpulb7kecp/files/d/2/2/dataset_d22475f3-6c2f-4c52-9164-12248ba5d2a8.dat:part_D.gb,/tmp/tmpulb7kecp/files/1/d/9/dataset_1d9b3d4c-eed3-444e-87e6-29c04e915c0d.dat:part_E.gb,/tmp/tmpulb7kecp/files/2/4/c/dataset_24c555ec-1536-4ef6-a07d-20d744f3b5fc.dat:part_F.gb,/tmp/tmpulb7kecp/files/c/2/3/dataset_c23f475b-f826-4333-8641-66e68bfad42a.dat:part_G.gb' --file_name_mapping_dom '/tmp/tmpulb7kecp/files/f/f/a/dataset_ffa8dfa6-df34-412b-84ae-325a3e389a88.dat:part_H.gb,/tmp/tmpulb7kecp/files/f/3/3/dataset_f33af6b6-cce3-49b2-a17e-9a168ad065f9.dat:part_I.gb,/tmp/tmpulb7kecp/files/2/9/7/dataset_297ec6da-4e55-4534-94c7-903e7e107632.dat:part_J.gb,/tmp/tmpulb7kecp/files/3/0/7/dataset_30785c7f-0628-4e63-be45-77272fdedb50.dat:part_K.gb,/tmp/tmpulb7kecp/files/f/3/2/dataset_f32a9062-9cf7-48d9-9ddb-ef0c02526564.dat:part_L.gb' --use_file_names_as_id 'true' --outdir_simulation 'outdir_zip' --outdir_gb 'outdir_gb' --output_simulation 'output_zip.zip' --enzyme 'auto' --topology 'circular' && cp 'output_zip.zip' '/tmp/tmpulb7kecp/job_working_directory/000/49/outputs/dataset_da6f8b92-03ba-4561-81a4-2ac510aff8c6.dat'", "command_version": "", "copied_from_job_id": null, "create_time": "2025-05-23T12:16:00.836611", "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-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf", "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-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf", "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-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf", "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-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf", "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-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf", "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-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf", "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-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf", "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-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf", "exact": true, "model_class": "MergedCondaDependency", "name": "dna_features_viewer", "version": "3.1.5" } ], "exit_code": 0, "external_id": "181545", "galaxy_version": "24.2", "handler": null, "history_id": "3758c7315f184c9a", "id": "db168591f9c4d2a8", "inputs": { "assembly_csv": { "id": "8f56f36c2b9f0a7c", "src": "hda", "uuid": "cfa1c628-1bad-4864-97c9-f5ff8ae3bb94" }, "domesticated_input1": { "id": "762d85be4105a0e7", "src": "hda", "uuid": "ffa8dfa6-df34-412b-84ae-325a3e389a88" }, "domesticated_input2": { "id": "c453f926cdeee4bd", "src": "hda", "uuid": "f33af6b6-cce3-49b2-a17e-9a168ad065f9" }, "domesticated_input3": { "id": "5bba4dfbf52e531c", "src": "hda", "uuid": "297ec6da-4e55-4534-94c7-903e7e107632" }, "domesticated_input4": { "id": "58e4e52cefa9d689", "src": "hda", "uuid": "30785c7f-0628-4e63-be45-77272fdedb50" }, "domesticated_input5": { "id": "492cbe2cf83388c0", "src": "hda", "uuid": "f32a9062-9cf7-48d9-9ddb-ef0c02526564" }, "genbank_files1": { "id": "5b9f36df99fe7ddd", "src": "hda", "uuid": "092e3d69-34a0-4c02-9593-859fa17016fb" }, "genbank_files2": { "id": "83649da70bd4e994", "src": "hda", "uuid": "ed59100d-a4e7-4eb8-9965-8817a8e44000" }, "genbank_files3": { "id": "9e3a7410afb0cd47", "src": "hda", "uuid": "0172bdce-ca49-45d4-af2d-12a5304b55ca" }, "genbank_files4": { "id": "db168591f9c4d2a8", "src": "hda", "uuid": "d22475f3-6c2f-4c52-9164-12248ba5d2a8" }, "genbank_files5": { "id": "fbc673f3c19d4e8f", "src": "hda", "uuid": "1d9b3d4c-eed3-444e-87e6-29c04e915c0d" }, "genbank_files6": { "id": "612b3112dca3b89a", "src": "hda", "uuid": "24c555ec-1536-4ef6-a07d-20d744f3b5fc" }, "genbank_files7": { "id": "1122563bf7246535", "src": "hda", "uuid": "c23f475b-f826-4333-8641-66e68bfad42a" } }, "job_messages": [], "job_metrics": [], "job_runner_name": null, "job_stderr": "", "job_stdout": "", "model_class": "Job", "output_collections": { "construct_gb": { "id": "106ff655f8a511fe", "src": "hdca" } }, "outputs": { "__new_primary_file_construct_gb|construct_1__": { "id": "4ec2fde3b391b5e9", "src": "hda", "uuid": "65c06a03-7919-4203-8aa0-ee2d6c747da3" }, "__new_primary_file_construct_gb|construct_2__": { "id": "db0ab281fdd171f3", "src": "hda", "uuid": "00b0ee36-bed6-481a-8f87-a3ee2eb3c474" }, "__new_primary_file_construct_gb|construct_3__": { "id": "39bf58b498d37eb0", "src": "hda", "uuid": "c6fb815c-ee68-4263-9e77-86d27f1f5fd9" }, "__new_primary_file_construct_gb|construct_4__": { "id": "54d1dbb833355e05", "src": "hda", "uuid": "af82262d-217d-4952-8d8f-b733d902879c" }, "output_zip": { "id": "7830aac4d222c450", "src": "hda", "uuid": "da6f8b92-03ba-4561-81a4-2ac510aff8c6" } }, "params": { "__input_ext": "\"input\"", "adv": "{\"enzyme\": \"auto\", \"use_file_names_as_ids\": true}", "assembly_plan_name": "\"Type2sRestrictionAssembly\"", "chromInfo": "\"/tmp/tmpulb7kecp/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", "dbkey": "\"?\"", "domesticated_input": "{\"values\": [{\"id\": 11, \"src\": \"hdca\"}]}", "genbank_files": "{\"values\": [{\"id\": 12, \"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, 2.43it/s, now=None]\rassembly: 75%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u258c | 3/4 [00:01<00:00, 2.21it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 4/4 [00:02<00:00, 1.81it/s, now=None]\r \r", "stdout": "Simulating assembly plan assambly...\n{'cancelled_assemblies': 0, 'errored_assemblies': 0, 'valid_assemblies': 4}\nGenerating assemblies reports...\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, 2.43it/s, now=None]\rassembly: 75%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u258c | 3/4 [00:01<00:00, 2.21it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 4/4 [00:02<00:00, 1.81it/s, now=None]\r \r", "tool_stdout": "Simulating assembly plan assambly...\n{'cancelled_assemblies': 0, 'errored_assemblies': 0, 'valid_assemblies': 4}\nGenerating assemblies reports...\n", "update_time": "2025-05-23T12:16:13.850563", "user_email": "planemo@galaxyproject.org", "user_id": "8094a24bdbd328fd" }, "status": "success", "test_index": 5, "time_seconds": 54.179964542388916, "tool_id": "cloning_simulation", "tool_version": "0.1.0+galaxy0" }, "has_data": true, "id": "cloning_simulation-5" }, { "data": { "inputs": { "adv|use_file_names_as_ids": true, "assembly_csv": { "id": "a128918b334a087e", "src": "hda" }, "assembly_plan_name": "Type2sRestrictionAssembly", "domesticated_input": { "id": "a843aa6880d39864", "src": "hdca" }, "topology": "circular" }, "job": { "command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && cp '/tmp/tmpulb7kecp/files/4/d/6/dataset_4d664c21-0606-48f2-a403-c970eada5469.dat' 'assembly_csv.csv' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmpulb7kecp/files/b/f/7/dataset_bf78af79-2d13-4fd5-8858-a0fcf0527125.dat,/tmp/tmpulb7kecp/files/6/c/f/dataset_6cf6f59f-3cee-4539-85e2-0b5786b42a8a.dat,/tmp/tmpulb7kecp/files/8/c/1/dataset_8c1a4509-f793-4b1a-9fc2-599b836e6d1e.dat,/tmp/tmpulb7kecp/files/3/8/1/dataset_3818afb4-1184-43b1-aa48-13efabb7ecc8.dat,/tmp/tmpulb7kecp/files/9/0/e/dataset_90e377b6-c53e-4277-8c54-c361769ee52f.dat,/tmp/tmpulb7kecp/files/4/5/9/dataset_4594442a-8d2b-4f97-a280-8deb7915da9c.dat,/tmp/tmpulb7kecp/files/6/e/9/dataset_6e9767bf-085d-48d0-9ad3-596e435224f3.dat,/tmp/tmpulb7kecp/files/1/4/b/dataset_14bd369b-8410-484e-8402-33aac9998b84.dat,/tmp/tmpulb7kecp/files/1/1/8/dataset_1180d189-8f49-4811-8e79-957c7bf319e4.dat,/tmp/tmpulb7kecp/files/4/9/1/dataset_49140292-5bb2-4b2e-bf02-87402741d120.dat,/tmp/tmpulb7kecp/files/b/4/2/dataset_b4278d16-d56d-4cbf-8fc6-100f10a5a142.dat,/tmp/tmpulb7kecp/files/1/8/0/dataset_18021752-a186-4b63-ba68-b56da64c7e9a.dat' --domesticated_seq '' --assembly_csv 'assembly_csv.csv' --assembly_plan_name 'Type2sRestrictionAssembly' --file_name_mapping '/tmp/tmpulb7kecp/files/b/f/7/dataset_bf78af79-2d13-4fd5-8858-a0fcf0527125.dat:part_A.gb,/tmp/tmpulb7kecp/files/6/c/f/dataset_6cf6f59f-3cee-4539-85e2-0b5786b42a8a.dat:part_B.gb,/tmp/tmpulb7kecp/files/8/c/1/dataset_8c1a4509-f793-4b1a-9fc2-599b836e6d1e.dat:part_C.gb,/tmp/tmpulb7kecp/files/3/8/1/dataset_3818afb4-1184-43b1-aa48-13efabb7ecc8.dat:part_D.gb,/tmp/tmpulb7kecp/files/9/0/e/dataset_90e377b6-c53e-4277-8c54-c361769ee52f.dat:part_E.gb,/tmp/tmpulb7kecp/files/4/5/9/dataset_4594442a-8d2b-4f97-a280-8deb7915da9c.dat:part_F.gb,/tmp/tmpulb7kecp/files/6/e/9/dataset_6e9767bf-085d-48d0-9ad3-596e435224f3.dat:part_G.gb,/tmp/tmpulb7kecp/files/1/4/b/dataset_14bd369b-8410-484e-8402-33aac9998b84.dat:part_H.gb,/tmp/tmpulb7kecp/files/1/1/8/dataset_1180d189-8f49-4811-8e79-957c7bf319e4.dat:part_I.gb,/tmp/tmpulb7kecp/files/4/9/1/dataset_49140292-5bb2-4b2e-bf02-87402741d120.dat:part_J.gb,/tmp/tmpulb7kecp/files/b/4/2/dataset_b4278d16-d56d-4cbf-8fc6-100f10a5a142.dat:part_K.gb,/tmp/tmpulb7kecp/files/1/8/0/dataset_18021752-a186-4b63-ba68-b56da64c7e9a.dat:part_L.gb' --file_name_mapping_dom '' --use_file_names_as_id 'true' --outdir_simulation 'outdir_zip' --outdir_gb 'outdir_gb' --output_simulation 'output_zip.zip' --enzyme 'auto' --topology 'circular' && cp 'output_zip.zip' '/tmp/tmpulb7kecp/job_working_directory/000/63/outputs/dataset_5e972ac3-a1c0-48c4-9db8-648343937891.dat'", "command_version": "", "copied_from_job_id": null, "create_time": "2025-05-23T12:16:53.743706", "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-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf", "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-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf", "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-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf", "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-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf", "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-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf", "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-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf", "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-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf", "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-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf", "exact": true, "model_class": "MergedCondaDependency", "name": "dna_features_viewer", "version": "3.1.5" } ], "exit_code": 0, "external_id": "182633", "galaxy_version": "24.2", "handler": null, "history_id": "cc5b73713462c207", "id": "54d1dbb833355e05", "inputs": { "assembly_csv": { "id": "a128918b334a087e", "src": "hda", "uuid": "4d664c21-0606-48f2-a403-c970eada5469" }, "domesticated_input1": { "id": "7b8eadfe954993cc", "src": "hda", "uuid": "bf78af79-2d13-4fd5-8858-a0fcf0527125" }, "domesticated_input10": { "id": "eadce10583f118a6", "src": "hda", 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"output_zip": { "id": "652ce7490abe3672", "src": "hda", "uuid": "5e972ac3-a1c0-48c4-9db8-648343937891" } }, "params": { "__input_ext": "\"input\"", "adv": "{\"enzyme\": \"auto\", \"use_file_names_as_ids\": true}", "assembly_plan_name": "\"Type2sRestrictionAssembly\"", "chromInfo": "\"/tmp/tmpulb7kecp/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", "dbkey": "\"?\"", "domesticated_input": "{\"values\": [{\"id\": 14, \"src\": \"hdca\"}]}", "genbank_files": null, "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, 2.39it/s, now=None]\rassembly: 75%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u258c | 3/4 [00:01<00:00, 2.19it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 4/4 [00:02<00:00, 1.79it/s, now=None]\r \r", "stdout": "Simulating assembly plan assambly...\n{'cancelled_assemblies': 0, 'errored_assemblies': 0, 'valid_assemblies': 4}\nGenerating assemblies reports...\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, 2.39it/s, now=None]\rassembly: 75%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u258c | 3/4 [00:01<00:00, 2.19it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 4/4 [00:02<00:00, 1.79it/s, now=None]\r \r", "tool_stdout": "Simulating assembly plan assambly...\n{'cancelled_assemblies': 0, 'errored_assemblies': 0, 'valid_assemblies': 4}\nGenerating assemblies reports...\n", "update_time": "2025-05-23T12:17:07.008117", "user_email": "planemo@galaxyproject.org", "user_id": "8094a24bdbd328fd" }, "status": "success", "test_index": 6, "time_seconds": 53.04504728317261, "tool_id": "cloning_simulation", "tool_version": "0.1.0+galaxy0" }, "has_data": true, "id": "cloning_simulation-6" } ], "version": "0.1" }