Mercurial > repos > tduigou > cloning_simulation
view output.json @ 3:044d36066cb3 draft
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
| author | tduigou |
|---|---|
| date | Fri, 16 May 2025 12:40:59 +0000 |
| parents | dc450979fcd4 |
| children | 254d284a5be9 |
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{ "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": "c02153e44a10e06a", "src": "hda" }, "assembly_plan_name": "Type2sRestrictionAssembly", "genbank_files": { "id": "a7025157dd5d3039", "src": "hdca" }, "topology": "circular" }, "job": { "command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmph0r87skq/files/e/b/4/dataset_eb40ee5e-5155-4303-9230-94926c63daaf.dat,/tmp/tmph0r87skq/files/4/a/9/dataset_4a9a1335-c528-438d-b80a-62b9608dbade.dat,/tmp/tmph0r87skq/files/7/c/a/dataset_7caa4f6a-a734-461f-ac38-c95442632c5a.dat,/tmp/tmph0r87skq/files/9/3/1/dataset_93127db8-2409-4544-93e5-6243a6d253ef.dat,/tmp/tmph0r87skq/files/e/2/9/dataset_e292919e-0a9a-403a-aa6b-30aa552881bd.dat,/tmp/tmph0r87skq/files/4/a/7/dataset_4a7c1e6b-f470-414e-b533-7390f74a64fc.dat,/tmp/tmph0r87skq/files/7/f/3/dataset_7f3df904-0bc5-456a-8679-cc58d06e214e.dat,/tmp/tmph0r87skq/files/a/6/0/dataset_a605738c-9b6d-44c6-891e-01cb729ea4dc.dat,/tmp/tmph0r87skq/files/1/0/c/dataset_10c35405-af25-41d3-9dbd-a411b4b65b98.dat,/tmp/tmph0r87skq/files/1/8/4/dataset_184d9904-3705-424e-b3f7-e5b7b773880f.dat,/tmp/tmph0r87skq/files/4/a/1/dataset_4a10d392-6ebc-413c-bd71-db425aa1aa0a.dat,/tmp/tmph0r87skq/files/8/3/5/dataset_835878c6-84f1-465c-b34e-d177885e567d.dat' --domesticated_seq '' --assembly_csv '/tmp/tmph0r87skq/files/a/5/2/dataset_a522972a-c994-4ec0-a130-e3e1e101d126.dat' --assembly_plan_name 'Type2sRestrictionAssembly' --file_name_mapping '/tmp/tmph0r87skq/files/e/b/4/dataset_eb40ee5e-5155-4303-9230-94926c63daaf.dat:part_A.gb,/tmp/tmph0r87skq/files/4/a/9/dataset_4a9a1335-c528-438d-b80a-62b9608dbade.dat:part_B.gb,/tmp/tmph0r87skq/files/7/c/a/dataset_7caa4f6a-a734-461f-ac38-c95442632c5a.dat:part_C.gb,/tmp/tmph0r87skq/files/9/3/1/dataset_93127db8-2409-4544-93e5-6243a6d253ef.dat:part_D.gb,/tmp/tmph0r87skq/files/e/2/9/dataset_e292919e-0a9a-403a-aa6b-30aa552881bd.dat:part_E.gb,/tmp/tmph0r87skq/files/4/a/7/dataset_4a7c1e6b-f470-414e-b533-7390f74a64fc.dat:part_F.gb,/tmp/tmph0r87skq/files/7/f/3/dataset_7f3df904-0bc5-456a-8679-cc58d06e214e.dat:part_G.gb,/tmp/tmph0r87skq/files/a/6/0/dataset_a605738c-9b6d-44c6-891e-01cb729ea4dc.dat:part_H.gb,/tmp/tmph0r87skq/files/1/0/c/dataset_10c35405-af25-41d3-9dbd-a411b4b65b98.dat:part_I.gb,/tmp/tmph0r87skq/files/1/8/4/dataset_184d9904-3705-424e-b3f7-e5b7b773880f.dat:part_J.gb,/tmp/tmph0r87skq/files/4/a/1/dataset_4a10d392-6ebc-413c-bd71-db425aa1aa0a.dat:part_K.gb,/tmp/tmph0r87skq/files/8/3/5/dataset_835878c6-84f1-465c-b34e-d177885e567d.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/tmph0r87skq/job_working_directory/000/14/outputs/dataset_109d2ac1-716e-4c47-a2b9-25e9d68cd9b7.dat'", "command_version": "", "copied_from_job_id": null, "create_time": "2025-05-16T12:35:55.635805", "dependencies": [], "exit_code": 0, "external_id": "205109", "galaxy_version": "24.2", "handler": null, "history_id": "a7025157dd5d3039", "id": "d49d8be9932a8ee0", "inputs": { "assembly_csv": { "id": "c02153e44a10e06a", "src": "hda", "uuid": "a522972a-c994-4ec0-a130-e3e1e101d126" }, "genbank_files1": { "id": "a7025157dd5d3039", "src": "hda", "uuid": "eb40ee5e-5155-4303-9230-94926c63daaf" }, "genbank_files10": { "id": "26800a0030991202", "src": "hda", "uuid": "184d9904-3705-424e-b3f7-e5b7b773880f" }, "genbank_files11": { "id": "9e9c740782c078df", "src": "hda", "uuid": "4a10d392-6ebc-413c-bd71-db425aa1aa0a" }, "genbank_files12": { "id": "d70a40a14f24deac", "src": "hda", "uuid": "835878c6-84f1-465c-b34e-d177885e567d" }, "genbank_files2": { "id": "ce87194f2a532da8", "src": "hda", "uuid": "4a9a1335-c528-438d-b80a-62b9608dbade" }, "genbank_files3": { "id": "e52e8d0a017d5bd2", "src": "hda", "uuid": "7caa4f6a-a734-461f-ac38-c95442632c5a" }, "genbank_files4": { "id": "4dd0eedec5562f6e", "src": "hda", "uuid": "93127db8-2409-4544-93e5-6243a6d253ef" }, "genbank_files5": { "id": "d1cbd0905c1fc860", "src": "hda", "uuid": "e292919e-0a9a-403a-aa6b-30aa552881bd" }, "genbank_files6": { "id": "0494b81690cb2f5c", "src": "hda", "uuid": "4a7c1e6b-f470-414e-b533-7390f74a64fc" }, "genbank_files7": { "id": "edce0bc0654ca8cc", "src": "hda", "uuid": "7f3df904-0bc5-456a-8679-cc58d06e214e" }, "genbank_files8": { "id": "052d0d471d180256", "src": "hda", "uuid": "a605738c-9b6d-44c6-891e-01cb729ea4dc" }, "genbank_files9": { "id": "5827a0347340e98b", "src": "hda", "uuid": "10c35405-af25-41d3-9dbd-a411b4b65b98" } }, "job_messages": [], "job_metrics": [], "job_runner_name": null, "job_stderr": "", "job_stdout": "", "model_class": "Job", "output_collections": { "construct_gb": { "id": "ce87194f2a532da8", "src": "hdca" } }, "outputs": { "__new_primary_file_construct_gb|construct_1__": { "id": "68bcb17f47b988de", "src": "hda", "uuid": "2c9a5458-38f0-4591-bb2d-452aac86ce0b" }, "__new_primary_file_construct_gb|construct_2__": { "id": "7cb8b41737d3d7aa", "src": "hda", "uuid": "026f0937-350b-4ae7-96da-1e685237a8c8" }, "__new_primary_file_construct_gb|construct_3__": { "id": "e558db6e0f20f34c", "src": "hda", "uuid": "df750e5d-b2f4-43f1-bf95-aa0d980bb98a" }, "__new_primary_file_construct_gb|construct_4__": { "id": "87544afc708050c8", "src": "hda", "uuid": "0ba9a694-1b4e-4ff4-b6f2-87503d04cd66" }, "output_zip": { "id": "d49d8be9932a8ee0", "src": "hda", "uuid": "109d2ac1-716e-4c47-a2b9-25e9d68cd9b7" } }, "params": { "__input_ext": "\"input\"", "adv": "{\"enzyme\": \"auto\", \"use_file_names_as_ids\": true}", "assembly_plan_name": "\"Type2sRestrictionAssembly\"", "chromInfo": "\"/tmp/tmph0r87skq/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, 2.41it/s, now=None]\rassembly: 75%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u258c | 3/4 [00:01<00:00, 2.25it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 4/4 [00:02<00:00, 1.82it/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, 2.41it/s, now=None]\rassembly: 75%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u258c | 3/4 [00:01<00:00, 2.25it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 4/4 [00:02<00:00, 1.82it/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": "2025-05-16T12:36:09.065234", "user_email": "planemo@galaxyproject.org", "user_id": "a7025157dd5d3039" }, "status": "success", "test_index": 0, "time_seconds": 54.82133865356445, "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": "13b114ac662002c6", "src": "hda" }, "assembly_plan_name": "GibsonAssembly", "genbank_files": { "id": "e52e8d0a017d5bd2", "src": "hdca" }, "topology": "circular" }, "job": { "command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmph0r87skq/files/f/2/e/dataset_f2e8406c-fdb7-4b30-aa74-202b93292a26.dat' --domesticated_seq '' --assembly_csv '/tmp/tmph0r87skq/files/5/7/9/dataset_579b13e6-f14d-401c-88ee-b25ed3bf42dc.dat' --assembly_plan_name 'GibsonAssembly' --file_name_mapping '/tmp/tmph0r87skq/files/f/2/e/dataset_f2e8406c-fdb7-4b30-aa74-202b93292a26.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/tmph0r87skq/job_working_directory/000/17/outputs/dataset_36e0457f-1da8-456a-86c9-20ea242688bc.dat'", "command_version": "", "copied_from_job_id": null, "create_time": "2025-05-16T12:36:19.661290", "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": "205459", "galaxy_version": "24.2", "handler": null, "history_id": "ce87194f2a532da8", "id": "e558db6e0f20f34c", "inputs": { "assembly_csv": { "id": "13b114ac662002c6", "src": "hda", "uuid": "579b13e6-f14d-401c-88ee-b25ed3bf42dc" }, "genbank_files1": { "id": "16385471cc722641", "src": "hda", "uuid": "f2e8406c-fdb7-4b30-aa74-202b93292a26" } }, "job_messages": [], "job_metrics": [], "job_runner_name": null, "job_stderr": "", "job_stdout": "", "model_class": "Job", "output_collections": { "construct_gb": { "id": "4dd0eedec5562f6e", "src": "hdca" } }, "outputs": { "__new_primary_file_construct_gb|construct_1__": { "id": "eb4747fb10762624", "src": "hda", "uuid": "8b9f07c0-2a2f-49db-b0b9-e3b27b5d2102" }, "__new_primary_file_construct_gb|construct_2__": { "id": "fa2c1cd7e40ca607", "src": "hda", "uuid": "694f0f93-1c26-4a8b-91ed-bcb7fe4b3784" }, "__new_primary_file_construct_gb|construct_3__": { "id": "2c9180ba70391455", "src": "hda", "uuid": "e57dc6e8-10e6-4527-a375-9ed583735c59" }, "output_zip": { "id": "cf8958f7b0d14fa5", "src": "hda", "uuid": "36e0457f-1da8-456a-86c9-20ea242688bc" } }, "params": { "__input_ext": "\"input\"", "adv": "{\"enzyme\": \"auto\", \"use_file_names_as_ids\": true}", "assembly_plan_name": "\"GibsonAssembly\"", "chromInfo": "\"/tmp/tmph0r87skq/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, 4.71it/s, now=None]\rassembly: 60%|\u2588\u2588\u2588\u2588\u2588\u2588 | 3/5 [00:00<00:00, 4.79it/s, now=None]\rassembly: 80%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588 | 4/5 [00:00<00:00, 4.60it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 5/5 [00:01<00:00, 3.70it/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, 4.71it/s, now=None]\rassembly: 60%|\u2588\u2588\u2588\u2588\u2588\u2588 | 3/5 [00:00<00:00, 4.79it/s, now=None]\rassembly: 80%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588 | 4/5 [00:00<00:00, 4.60it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 5/5 [00:01<00:00, 3.70it/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": "2025-05-16T12:36:31.612352", "user_email": "planemo@galaxyproject.org", "user_id": "a7025157dd5d3039" }, "status": "success", "test_index": 1, "time_seconds": 22.601666688919067, "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": "84906eb14284db27", "src": "hda" }, "assembly_plan_name": "LigaseCyclingReactionAssembly", "genbank_files": { "id": "d1cbd0905c1fc860", "src": "hdca" }, "topology": "circular" }, "job": { "command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmph0r87skq/files/1/5/7/dataset_15741680-9963-4b3d-979e-792be37256f2.dat,/tmp/tmph0r87skq/files/d/3/d/dataset_d3de76b3-3793-46fa-990e-970e1bcb2a72.dat' --domesticated_seq '' --assembly_csv '/tmp/tmph0r87skq/files/2/0/e/dataset_20eb88b1-0fc5-476b-a409-da7f598780b6.dat' --assembly_plan_name 'LigaseCyclingReactionAssembly' --file_name_mapping '/tmp/tmph0r87skq/files/1/5/7/dataset_15741680-9963-4b3d-979e-792be37256f2.dat:RFP_GFP_plasmid_BOs.fa,/tmp/tmph0r87skq/files/d/3/d/dataset_d3de76b3-3793-46fa-990e-970e1bcb2a72.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/tmph0r87skq/job_working_directory/000/21/outputs/dataset_0ffdda24-b80f-4db5-8c10-1467d34eb3a8.dat'", "command_version": "", "copied_from_job_id": null, "create_time": "2025-05-16T12:36:42.888728", "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": "205894", "galaxy_version": "24.2", "handler": null, "history_id": "e52e8d0a017d5bd2", "id": "cf8958f7b0d14fa5", "inputs": { "assembly_csv": { "id": "84906eb14284db27", "src": "hda", "uuid": "20eb88b1-0fc5-476b-a409-da7f598780b6" }, "genbank_files1": { "id": "1fdafe0e70c0e721", "src": "hda", "uuid": "15741680-9963-4b3d-979e-792be37256f2" }, "genbank_files2": { "id": "044728be18fd1186", "src": "hda", "uuid": "d3de76b3-3793-46fa-990e-970e1bcb2a72" } }, "job_messages": [], "job_metrics": [], "job_runner_name": null, "job_stderr": "", "job_stdout": "", "model_class": "Job", "output_collections": { "construct_gb": { "id": "0494b81690cb2f5c", "src": "hdca" } }, "outputs": { "output_zip": { "id": "920c0db56b0a806b", "src": "hda", "uuid": "0ffdda24-b80f-4db5-8c10-1467d34eb3a8" } }, "params": { "__input_ext": "\"input\"", "adv": "{\"enzyme\": \"auto\", \"use_file_names_as_ids\": true}", "assembly_plan_name": "\"LigaseCyclingReactionAssembly\"", "chromInfo": "\"/tmp/tmph0r87skq/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, 2.42it/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, 2.42it/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": "2025-05-16T12:36:54.097489", "user_email": "planemo@galaxyproject.org", "user_id": "a7025157dd5d3039" }, "status": "success", "test_index": 2, "time_seconds": 22.133039951324463, "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": "df13d5ca39cba7c4", "src": "hda" }, "assembly_plan_name": "BASICAssembly", "genbank_files": { "id": "edce0bc0654ca8cc", "src": "hdca" }, "topology": "circular" }, "job": { "command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmph0r87skq/files/4/f/0/dataset_4f0d4258-2f50-4a4e-9271-58e8c272856e.dat,/tmp/tmph0r87skq/files/2/7/f/dataset_27f67c7a-5e38-4103-a00b-a9d8234b6686.dat,/tmp/tmph0r87skq/files/4/e/8/dataset_4e880afa-3f37-43a4-982e-36d750aab3d3.dat,/tmp/tmph0r87skq/files/3/7/4/dataset_3746bcc6-ee0c-4936-832f-ce29f808430d.dat,/tmp/tmph0r87skq/files/7/8/8/dataset_788ebd7b-6247-4f96-a3d3-3c3306c210a0.dat' --domesticated_seq '' --assembly_csv '/tmp/tmph0r87skq/files/e/9/7/dataset_e971a6cf-b13e-4a65-a78d-aa22a0ea1fff.dat' --assembly_plan_name 'BASICAssembly' --file_name_mapping '/tmp/tmph0r87skq/files/4/f/0/dataset_4f0d4258-2f50-4a4e-9271-58e8c272856e.dat:GFP.gb,/tmp/tmph0r87skq/files/2/7/f/dataset_27f67c7a-5e38-4103-a00b-a9d8234b6686.dat:p15A_kan.gb,/tmp/tmph0r87skq/files/4/e/8/dataset_4e880afa-3f37-43a4-982e-36d750aab3d3.dat:promoter.gb,/tmp/tmph0r87skq/files/3/7/4/dataset_3746bcc6-ee0c-4936-832f-ce29f808430d.dat:RFP.gb,/tmp/tmph0r87skq/files/7/8/8/dataset_788ebd7b-6247-4f96-a3d3-3c3306c210a0.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/tmph0r87skq/job_working_directory/000/28/outputs/dataset_5e0faa51-141c-49d1-ba84-ca8aba27508c.dat'", "command_version": "", "copied_from_job_id": null, "create_time": "2025-05-16T12:37:15.245845", "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": "206517", "galaxy_version": "24.2", "handler": null, "history_id": "4dd0eedec5562f6e", "id": "920c0db56b0a806b", "inputs": { "assembly_csv": { "id": "df13d5ca39cba7c4", "src": "hda", "uuid": "e971a6cf-b13e-4a65-a78d-aa22a0ea1fff" }, "genbank_files1": { "id": "caecbbc14917ac69", "src": "hda", "uuid": "4f0d4258-2f50-4a4e-9271-58e8c272856e" }, "genbank_files2": { "id": "10cd084c8017547c", "src": "hda", "uuid": "27f67c7a-5e38-4103-a00b-a9d8234b6686" }, "genbank_files3": { "id": "aa3451be0c94f76e", "src": "hda", "uuid": "4e880afa-3f37-43a4-982e-36d750aab3d3" }, "genbank_files4": { "id": "a5f159065ae97d01", "src": "hda", "uuid": "3746bcc6-ee0c-4936-832f-ce29f808430d" }, "genbank_files5": { "id": "a001a939426dadd1", "src": "hda", "uuid": "788ebd7b-6247-4f96-a3d3-3c3306c210a0" } }, "job_messages": [], "job_metrics": [], "job_runner_name": null, "job_stderr": "", "job_stdout": "", "model_class": "Job", "output_collections": { "construct_gb": { "id": "052d0d471d180256", "src": "hdca" } }, "outputs": { "output_zip": { "id": "081ab14c99ce168b", "src": "hda", "uuid": "5e0faa51-141c-49d1-ba84-ca8aba27508c" } }, "params": { "__input_ext": "\"input\"", "adv": "{\"enzyme\": \"auto\", \"use_file_names_as_ids\": true}", "assembly_plan_name": "\"BASICAssembly\"", "chromInfo": "\"/tmp/tmph0r87skq/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, 49.70it/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, 49.70it/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": "2025-05-16T12:37:25.925491", "user_email": "planemo@galaxyproject.org", "user_id": "a7025157dd5d3039" }, "status": "success", "test_index": 3, "time_seconds": 31.832648515701294, "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": "6af8c0d3c72d39ba", "src": "hda" }, "assembly_plan_name": "BioBrickStandardAssembly", "genbank_files": { "id": "5827a0347340e98b", "src": "hdca" }, "topology": "circular" }, "job": { "command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmph0r87skq/files/7/7/3/dataset_773be428-2d30-4b95-9894-d3758634a3d0.dat,/tmp/tmph0r87skq/files/b/a/c/dataset_bac673f5-074c-4810-9949-59d3b228d83c.dat,/tmp/tmph0r87skq/files/e/5/b/dataset_e5b8dfd0-6e81-47e4-b899-08976d0a1724.dat,/tmp/tmph0r87skq/files/1/5/8/dataset_158cbebb-69fc-4333-b783-e9171b5324d6.dat,/tmp/tmph0r87skq/files/a/5/b/dataset_a5b6ae8b-1068-416f-b0ac-1c44e299cb87.dat' --domesticated_seq '' --assembly_csv '/tmp/tmph0r87skq/files/4/e/d/dataset_4ed60503-3b9f-4204-a8e9-0b96f76b1e49.dat' --assembly_plan_name 'BioBrickStandardAssembly' --file_name_mapping '/tmp/tmph0r87skq/files/7/7/3/dataset_773be428-2d30-4b95-9894-d3758634a3d0.dat:BBa_E0040_GFP.gb,/tmp/tmph0r87skq/files/b/a/c/dataset_bac673f5-074c-4810-9949-59d3b228d83c.dat:BBa_J23119_prom.gb,/tmp/tmph0r87skq/files/e/5/b/dataset_e5b8dfd0-6e81-47e4-b899-08976d0a1724.dat:BBa_J23119_prom_flawed.gb,/tmp/tmph0r87skq/files/1/5/8/dataset_158cbebb-69fc-4333-b783-e9171b5324d6.dat:BBa_J61048_term.gb,/tmp/tmph0r87skq/files/a/5/b/dataset_a5b6ae8b-1068-416f-b0ac-1c44e299cb87.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/tmph0r87skq/job_working_directory/000/35/outputs/dataset_5776ccd7-5dca-4f21-b288-9c15a0b9cdca.dat'", "command_version": "", "copied_from_job_id": null, "create_time": "2025-05-16T12:37:47.708969", "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": "207114", "galaxy_version": "24.2", "handler": null, "history_id": "d1cbd0905c1fc860", "id": "081ab14c99ce168b", "inputs": { "assembly_csv": { "id": "6af8c0d3c72d39ba", "src": "hda", "uuid": "4ed60503-3b9f-4204-a8e9-0b96f76b1e49" }, "genbank_files1": { "id": "06bb6ed11a5684d2", "src": "hda", "uuid": "773be428-2d30-4b95-9894-d3758634a3d0" }, "genbank_files2": { "id": "f34ce69b933b349e", "src": "hda", "uuid": "bac673f5-074c-4810-9949-59d3b228d83c" }, "genbank_files3": { "id": "c295924a5ace6ae8", "src": "hda", "uuid": "e5b8dfd0-6e81-47e4-b899-08976d0a1724" }, "genbank_files4": { "id": "f3a950b5ccc2e145", "src": "hda", "uuid": "158cbebb-69fc-4333-b783-e9171b5324d6" }, "genbank_files5": { "id": "486d488c3f12b41a", "src": "hda", "uuid": "a5b6ae8b-1068-416f-b0ac-1c44e299cb87" } }, "job_messages": [], "job_metrics": [], "job_runner_name": null, "job_stderr": "", "job_stdout": "", "model_class": "Job", "output_collections": { "construct_gb": { "id": "26800a0030991202", "src": "hdca" } }, "outputs": { "__new_primary_file_construct_gb|C1_prom_barcode__": { "id": "62952fe061c1d5d6", "src": "hda", "uuid": "fb185bc3-4c8e-4095-864e-edc42d8c87ab" }, "__new_primary_file_construct_gb|C2_gfp_term__": { "id": "14c055702e438446", "src": "hda", "uuid": "cb6310a2-1237-4f80-9efa-f149cb896f4d" }, "__new_primary_file_construct_gb|C3_final__": { "id": "e9ef3e2f0e439cf2", "src": "hda", "uuid": "13db93e9-4505-4542-845c-57029b5e9a89" }, "output_zip": { "id": "7f1cb49d27c5ee0d", "src": "hda", "uuid": "5776ccd7-5dca-4f21-b288-9c15a0b9cdca" } }, "params": { "__input_ext": "\"input\"", "adv": "{\"enzyme\": \"auto\", \"use_file_names_as_ids\": true}", "assembly_plan_name": "\"BioBrickStandardAssembly\"", "chromInfo": "\"/tmp/tmph0r87skq/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, 1.94it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 3/3 [00:01<00:00, 1.58it/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, 1.94it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 3/3 [00:01<00:00, 1.58it/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": "2025-05-16T12:38:00.688550", "user_email": "planemo@galaxyproject.org", "user_id": "a7025157dd5d3039" }, "status": "success", "test_index": 4, "time_seconds": 34.85270929336548, "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": "4e0765e9771b7fbe", "src": "hda" }, "assembly_plan_name": "Type2sRestrictionAssembly", "domesticated_input": { "id": "9e9c740782c078df", "src": "hdca" }, "genbank_files": { "id": "d70a40a14f24deac", "src": "hdca" }, "topology": "circular" }, "job": { "command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmph0r87skq/files/b/c/d/dataset_bcd311aa-69db-4f2a-9d04-90f34cd78a6f.dat,/tmp/tmph0r87skq/files/0/4/9/dataset_049931ba-600a-46d6-a73e-af6bd3f545e3.dat,/tmp/tmph0r87skq/files/8/6/0/dataset_860e934f-31f6-4ac6-9eac-fd3abf031b08.dat,/tmp/tmph0r87skq/files/a/a/6/dataset_aa6ecd8a-10b8-416a-95ec-bfbe1fa81d21.dat,/tmp/tmph0r87skq/files/3/d/9/dataset_3d97e337-7388-4fab-a6c3-7cb99f371f84.dat,/tmp/tmph0r87skq/files/b/4/5/dataset_b45031f8-71da-4365-9560-b827aa1d6794.dat,/tmp/tmph0r87skq/files/9/e/2/dataset_9e21455c-b124-4c01-8524-949ff16b570e.dat' --domesticated_seq '/tmp/tmph0r87skq/files/a/f/e/dataset_afe4126c-9cc0-45ec-a7d4-37816cb2132d.dat,/tmp/tmph0r87skq/files/f/a/8/dataset_fa8a7e9a-fa40-4e9f-a508-261fd8441292.dat,/tmp/tmph0r87skq/files/7/d/d/dataset_7ddb44a7-da6d-4215-8d11-1ba01c4f6516.dat,/tmp/tmph0r87skq/files/b/f/f/dataset_bff58a1b-e69e-4cb4-b344-79ba8800ac03.dat,/tmp/tmph0r87skq/files/a/f/8/dataset_af806691-7022-4bf2-a42b-7437042cee37.dat' --assembly_csv '/tmp/tmph0r87skq/files/c/6/5/dataset_c652bef1-f073-431c-9e5b-956a58e85d22.dat' --assembly_plan_name 'Type2sRestrictionAssembly' --file_name_mapping '/tmp/tmph0r87skq/files/b/c/d/dataset_bcd311aa-69db-4f2a-9d04-90f34cd78a6f.dat:part_A.gb,/tmp/tmph0r87skq/files/0/4/9/dataset_049931ba-600a-46d6-a73e-af6bd3f545e3.dat:part_B.gb,/tmp/tmph0r87skq/files/8/6/0/dataset_860e934f-31f6-4ac6-9eac-fd3abf031b08.dat:part_C.gb,/tmp/tmph0r87skq/files/a/a/6/dataset_aa6ecd8a-10b8-416a-95ec-bfbe1fa81d21.dat:part_D.gb,/tmp/tmph0r87skq/files/3/d/9/dataset_3d97e337-7388-4fab-a6c3-7cb99f371f84.dat:part_E.gb,/tmp/tmph0r87skq/files/b/4/5/dataset_b45031f8-71da-4365-9560-b827aa1d6794.dat:part_F.gb,/tmp/tmph0r87skq/files/9/e/2/dataset_9e21455c-b124-4c01-8524-949ff16b570e.dat:part_G.gb' --file_name_mapping_dom '/tmp/tmph0r87skq/files/a/f/e/dataset_afe4126c-9cc0-45ec-a7d4-37816cb2132d.dat:part_H.gb,/tmp/tmph0r87skq/files/f/a/8/dataset_fa8a7e9a-fa40-4e9f-a508-261fd8441292.dat:part_I.gb,/tmp/tmph0r87skq/files/7/d/d/dataset_7ddb44a7-da6d-4215-8d11-1ba01c4f6516.dat:part_J.gb,/tmp/tmph0r87skq/files/b/f/f/dataset_bff58a1b-e69e-4cb4-b344-79ba8800ac03.dat:part_K.gb,/tmp/tmph0r87skq/files/a/f/8/dataset_af806691-7022-4bf2-a42b-7437042cee37.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/tmph0r87skq/job_working_directory/000/49/outputs/dataset_a88370aa-4d36-4867-b0d6-613cc59ed01a.dat'", "command_version": "", "copied_from_job_id": null, "create_time": "2025-05-16T12:38:41.107674", "dependencies": [ { "cacheable": false, "dependency_resolver": { "auto_init": true, "auto_install": true, "can_uninstall_dependencies": true, "ensure_channels": 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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, 2.25it/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...\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, 2.46it/s, now=None]\rassembly: 75%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u258c | 3/4 [00:01<00:00, 2.25it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 4/4 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