Mercurial > repos > tduigou > cloning_simulation
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planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit af45e5e0e81535ab0423b0bcff8b5b220bb9b4d0-dirty
| author | tduigou |
|---|---|
| date | Thu, 17 Jul 2025 10:17:24 +0000 |
| parents | 074a76e84b80 |
| children |
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{ "summary": { "num_errors": 0, "num_failures": 0, "num_skips": 0, "num_tests": 8 }, "tests": [ { "data": { "inputs": { "assembly_csv": { "id": "54d710fc68386373", "src": "hda" }, "genbank_files": { "id": "986c9b47c580ae59", "src": "hdca" }, "json_use|assembly_plan_name": "Type2sRestrictionAssembly", "json_use|topology": "circular", "json_use|use_json_paramers": false, "use_file_names_as_ids": true }, "job": { "command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && cp '/tmp/tmpe6pmg7jw/files/0/b/1/dataset_0b1d9a31-e124-42cf-b995-f7c136900f29.dat' 'assembly_csv.csv' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmpe6pmg7jw/files/7/6/9/dataset_76952c3c-fc12-4748-87cb-b6af38db9d3e.dat,/tmp/tmpe6pmg7jw/files/9/a/6/dataset_9a60f4af-d7d4-4bce-ab79-3718dac468ed.dat,/tmp/tmpe6pmg7jw/files/f/e/c/dataset_fec08236-4b1b-4174-af9c-7c3a84487424.dat,/tmp/tmpe6pmg7jw/files/2/0/6/dataset_206ca419-7921-4fc1-9be0-12c35c84bd65.dat,/tmp/tmpe6pmg7jw/files/3/1/b/dataset_31bb0b24-e75c-493f-a016-3796d54eaa18.dat,/tmp/tmpe6pmg7jw/files/6/f/a/dataset_6fa953c7-a9a7-4ba7-a030-da147eadefdc.dat,/tmp/tmpe6pmg7jw/files/7/e/f/dataset_7ef147cb-f331-435c-9a1e-6f0e52abd102.dat,/tmp/tmpe6pmg7jw/files/9/b/6/dataset_9b611c55-c19e-42ce-b45c-40ac049b94cb.dat,/tmp/tmpe6pmg7jw/files/9/b/d/dataset_9bd8627e-0417-475f-b855-352bcd890630.dat,/tmp/tmpe6pmg7jw/files/1/6/4/dataset_164135c0-7b54-4ea0-86d3-e9e928cbc398.dat,/tmp/tmpe6pmg7jw/files/b/e/9/dataset_be927bb4-1a34-43bb-8680-81589459732b.dat,/tmp/tmpe6pmg7jw/files/8/a/4/dataset_8a4bab33-b3e8-4586-b375-ae904dc06793.dat' --domesticated_seq '' --assembly_csv 'assembly_csv.csv' --file_name_mapping '/tmp/tmpe6pmg7jw/files/7/6/9/dataset_76952c3c-fc12-4748-87cb-b6af38db9d3e.dat:part_A.gb,/tmp/tmpe6pmg7jw/files/9/a/6/dataset_9a60f4af-d7d4-4bce-ab79-3718dac468ed.dat:part_B.gb,/tmp/tmpe6pmg7jw/files/f/e/c/dataset_fec08236-4b1b-4174-af9c-7c3a84487424.dat:part_C.gb,/tmp/tmpe6pmg7jw/files/2/0/6/dataset_206ca419-7921-4fc1-9be0-12c35c84bd65.dat:part_D.gb,/tmp/tmpe6pmg7jw/files/3/1/b/dataset_31bb0b24-e75c-493f-a016-3796d54eaa18.dat:part_E.gb,/tmp/tmpe6pmg7jw/files/6/f/a/dataset_6fa953c7-a9a7-4ba7-a030-da147eadefdc.dat:part_F.gb,/tmp/tmpe6pmg7jw/files/7/e/f/dataset_7ef147cb-f331-435c-9a1e-6f0e52abd102.dat:part_G.gb,/tmp/tmpe6pmg7jw/files/9/b/6/dataset_9b611c55-c19e-42ce-b45c-40ac049b94cb.dat:part_H.gb,/tmp/tmpe6pmg7jw/files/9/b/d/dataset_9bd8627e-0417-475f-b855-352bcd890630.dat:part_I.gb,/tmp/tmpe6pmg7jw/files/1/6/4/dataset_164135c0-7b54-4ea0-86d3-e9e928cbc398.dat:part_J.gb,/tmp/tmpe6pmg7jw/files/b/e/9/dataset_be927bb4-1a34-43bb-8680-81589459732b.dat:part_K.gb,/tmp/tmpe6pmg7jw/files/8/a/4/dataset_8a4bab33-b3e8-4586-b375-ae904dc06793.dat:part_L.gb' --file_name_mapping_dom '' --use_json_paramers 'false' --enzyme 'auto' --topology 'circular' --assembly_plan_name 'Type2sRestrictionAssembly' --use_file_names_as_id 'true' --outdir_simulation 'outdir_zip' --outdir_gb 'outdir_gb' --output_simulation 'output_zip.zip' && cp 'output_zip.zip' '/tmp/tmpe6pmg7jw/job_working_directory/000/14/outputs/dataset_95e21ebc-5bff-4544-a5d4-06db22e91066.dat'", "command_version": "", "copied_from_job_id": null, "create_time": "2025-07-17T10:10:24.406223", "dependencies": [], "exit_code": 0, "external_id": "75641", "galaxy_version": "25.0", "handler": null, "history_id": "986c9b47c580ae59", "id": "98a2432f1cff4f91", "inputs": { "assembly_csv": { "id": "54d710fc68386373", "src": "hda", "uuid": "0b1d9a31-e124-42cf-b995-f7c136900f29" }, "genbank_files1": { "id": "986c9b47c580ae59", "src": "hda", "uuid": "76952c3c-fc12-4748-87cb-b6af38db9d3e" }, "genbank_files10": { "id": "8de66704b7df8b5e", "src": "hda", "uuid": "164135c0-7b54-4ea0-86d3-e9e928cbc398" }, "genbank_files11": { "id": "54c6d71c8dc7cb11", "src": "hda", "uuid": "be927bb4-1a34-43bb-8680-81589459732b" }, "genbank_files12": { "id": "2592d2c705ba0baa", "src": "hda", "uuid": "8a4bab33-b3e8-4586-b375-ae904dc06793" }, "genbank_files2": { "id": "8354ecc64d56337d", "src": "hda", "uuid": "9a60f4af-d7d4-4bce-ab79-3718dac468ed" }, "genbank_files3": { "id": "c06bae188baa9490", "src": "hda", "uuid": "fec08236-4b1b-4174-af9c-7c3a84487424" }, "genbank_files4": { "id": "71d208f6d8b613ba", "src": "hda", "uuid": "206ca419-7921-4fc1-9be0-12c35c84bd65" }, "genbank_files5": { "id": "58ad66a9f93223b8", "src": "hda", "uuid": "31bb0b24-e75c-493f-a016-3796d54eaa18" }, "genbank_files6": { "id": "e9003a596293e37c", "src": "hda", "uuid": "6fa953c7-a9a7-4ba7-a030-da147eadefdc" }, "genbank_files7": { "id": "8c39a9a410cc0a00", "src": "hda", "uuid": "7ef147cb-f331-435c-9a1e-6f0e52abd102" }, "genbank_files8": { "id": "f7b25594aba42961", "src": "hda", "uuid": "9b611c55-c19e-42ce-b45c-40ac049b94cb" }, "genbank_files9": { "id": "5f098a2d242af5ee", "src": "hda", "uuid": "9bd8627e-0417-475f-b855-352bcd890630" } }, "job_messages": [], "job_metrics": [], "job_runner_name": null, "job_stderr": "", "job_stdout": "", "model_class": "Job", "output_collections": { "construct_gb": { "id": "8354ecc64d56337d", "src": "hdca" } }, "outputs": { "__new_primary_file_construct_gb|construct_1__": { "id": "172543d29b19f394", "src": "hda", "uuid": "c12d7e47-49c5-4805-8a24-5d4fb0aa8cfa" }, "__new_primary_file_construct_gb|construct_2__": { "id": "018c827a8e5b161a", "src": "hda", "uuid": "be0c60c4-c33d-4855-95d4-ffdb53751eea" }, "__new_primary_file_construct_gb|construct_3__": { "id": "494079827008dff1", "src": "hda", "uuid": "77ec05f3-e147-4ff3-af59-1d173fbc6d27" }, "__new_primary_file_construct_gb|construct_4__": { "id": "665c2a499b613b70", "src": "hda", "uuid": "fd3ed880-c345-47d7-8a38-1ce5c507b417" }, "output_zip": { "id": "98a2432f1cff4f91", "src": "hda", "uuid": "95e21ebc-5bff-4544-a5d4-06db22e91066" } }, "params": { "__input_ext": "\"input\"", "chromInfo": "\"/tmp/tmpe6pmg7jw/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", "dbkey": "\"?\"", "domesticated_input": null, "genbank_files": "{\"values\": [{\"id\": 1, \"src\": \"hdca\"}]}", "json_use": "{\"__current_case__\": 0, \"assembly_plan_name\": \"Type2sRestrictionAssembly\", \"enzyme\": \"auto\", \"topology\": \"circular\", \"use_json_paramers\": false}", "use_file_names_as_ids": "true" }, "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, 2.45it/s, now=None]\rassembly: 75%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u258c | 3/4 [00:01<00:00, 2.23it/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, 2.45it/s, now=None]\rassembly: 75%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u258c | 3/4 [00:01<00:00, 2.23it/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", "tool_stdout": "Simulating assembly plan assambly...\n{'cancelled_assemblies': 0, 'errored_assemblies': 0, 'valid_assemblies': 4}\nGenerating assemblies reports...\n", "update_time": "2025-07-17T10:10:36.297958", "user_email": "planemo@galaxyproject.org", "user_id": "986c9b47c580ae59" }, "status": "success", "test_index": 0, "time_seconds": 52.21098494529724, "tool_id": "cloning_simulation", "tool_version": "0.1.0+galaxy0" }, "has_data": true, "id": "cloning_simulation-0" }, { "data": { "inputs": { "assembly_csv": { "id": "cf7d3dafd862f640", "src": "hda" }, "genbank_files": { "id": "c06bae188baa9490", "src": "hdca" }, "json_use|assembly_plan_name": "GibsonAssembly", "json_use|topology": "circular", "json_use|use_json_paramers": false, "use_file_names_as_ids": true }, "job": { "command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && cp '/tmp/tmpe6pmg7jw/files/2/a/d/dataset_2ad9afbb-7953-4cd9-bff3-482993791028.dat' 'assembly_csv.csv' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmpe6pmg7jw/files/7/0/8/dataset_708e1901-be64-41f9-b767-b1749a71b785.dat' --domesticated_seq '' --assembly_csv 'assembly_csv.csv' --file_name_mapping '/tmp/tmpe6pmg7jw/files/7/0/8/dataset_708e1901-be64-41f9-b767-b1749a71b785.dat:gibson_sequences.fa' --file_name_mapping_dom '' --use_json_paramers 'false' --enzyme 'auto' --topology 'circular' --assembly_plan_name 'GibsonAssembly' --use_file_names_as_id 'true' --outdir_simulation 'outdir_zip' --outdir_gb 'outdir_gb' --output_simulation 'output_zip.zip' && cp 'output_zip.zip' '/tmp/tmpe6pmg7jw/job_working_directory/000/17/outputs/dataset_9a58e169-47f4-4418-8a3b-0fec86242b5c.dat'", "command_version": "", "copied_from_job_id": null, "create_time": "2025-07-17T10:10:47.298570", "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": "76029", "galaxy_version": "25.0", "handler": null, "history_id": "8354ecc64d56337d", "id": "494079827008dff1", "inputs": { "assembly_csv": { "id": "cf7d3dafd862f640", "src": "hda", "uuid": "2ad9afbb-7953-4cd9-bff3-482993791028" }, "genbank_files1": { "id": "ccc90f05d17193c7", "src": "hda", "uuid": "708e1901-be64-41f9-b767-b1749a71b785" } }, "job_messages": [], "job_metrics": [], "job_runner_name": null, "job_stderr": "", "job_stdout": "", "model_class": "Job", "output_collections": { "construct_gb": { "id": "71d208f6d8b613ba", "src": "hdca" } }, "outputs": { "__new_primary_file_construct_gb|construct_1__": { "id": "5c63ea88ecac53b0", "src": "hda", "uuid": "bdd63ae3-8743-4fb8-b62e-15e2dd1b22fe" }, "__new_primary_file_construct_gb|construct_2__": { "id": "56f89f48d02eaad8", "src": "hda", "uuid": "ae8106cf-202a-4ae6-b3be-0af4a59bf28b" }, "__new_primary_file_construct_gb|construct_3__": { "id": "a5c371b6918b1c88", "src": "hda", "uuid": "7085c961-0057-4a6f-93a5-e28a77e87a65" }, "output_zip": { "id": "f0ec65f930df3348", "src": "hda", "uuid": "9a58e169-47f4-4418-8a3b-0fec86242b5c" } }, "params": { "__input_ext": "\"input\"", "chromInfo": "\"/tmp/tmpe6pmg7jw/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", "dbkey": "\"?\"", "domesticated_input": null, "genbank_files": "{\"values\": [{\"id\": 3, \"src\": \"hdca\"}]}", "json_use": "{\"__current_case__\": 0, \"assembly_plan_name\": \"GibsonAssembly\", \"enzyme\": \"auto\", \"topology\": \"circular\", \"use_json_paramers\": false}", "use_file_names_as_ids": "true" }, "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, 4.38it/s, now=None]\rassembly: 80%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588 | 4/5 [00:00<00:00, 4.38it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 5/5 [00:01<00:00, 3.62it/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, 4.38it/s, now=None]\rassembly: 80%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588 | 4/5 [00:00<00:00, 4.38it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 5/5 [00:01<00:00, 3.62it/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": "2025-07-17T10:10:58.876561", "user_email": "planemo@galaxyproject.org", "user_id": "986c9b47c580ae59" }, "status": "success", "test_index": 1, "time_seconds": 22.198808431625366, "tool_id": "cloning_simulation", "tool_version": "0.1.0+galaxy0" }, "has_data": true, "id": "cloning_simulation-1" }, { "data": { "inputs": { "assembly_csv": { "id": "9f199e72d4c8734c", "src": "hda" }, "genbank_files": { "id": "58ad66a9f93223b8", "src": "hdca" }, "json_use|assembly_plan_name": "LigaseCyclingReactionAssembly", "json_use|topology": "circular", "json_use|use_json_paramers": false, "use_file_names_as_ids": true }, "job": { "command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && cp '/tmp/tmpe6pmg7jw/files/d/4/f/dataset_d4f42cf4-85ed-4eb7-ab79-944239671a0c.dat' 'assembly_csv.csv' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmpe6pmg7jw/files/c/6/6/dataset_c66662f5-5307-40f5-b7d8-1ae34e9bc594.dat,/tmp/tmpe6pmg7jw/files/e/b/b/dataset_ebb77d89-fcaf-4aad-ae07-bd6df1cbc75d.dat' --domesticated_seq '' --assembly_csv 'assembly_csv.csv' --file_name_mapping '/tmp/tmpe6pmg7jw/files/c/6/6/dataset_c66662f5-5307-40f5-b7d8-1ae34e9bc594.dat:RFP_GFP_plasmid_BOs.fa,/tmp/tmpe6pmg7jw/files/e/b/b/dataset_ebb77d89-fcaf-4aad-ae07-bd6df1cbc75d.dat:RFP_GFP_plasmid_parts.fa' --file_name_mapping_dom '' --use_json_paramers 'false' --enzyme 'auto' --topology 'circular' --assembly_plan_name 'LigaseCyclingReactionAssembly' --use_file_names_as_id 'true' --outdir_simulation 'outdir_zip' --outdir_gb 'outdir_gb' --output_simulation 'output_zip.zip' && cp 'output_zip.zip' '/tmp/tmpe6pmg7jw/job_working_directory/000/21/outputs/dataset_e37b2d54-bd4d-445c-9171-dd049f49ed36.dat'", "command_version": "", "copied_from_job_id": null, "create_time": "2025-07-17T10:11:10.098701", "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": "76477", "galaxy_version": "25.0", "handler": null, "history_id": "c06bae188baa9490", "id": "f0ec65f930df3348", "inputs": { "assembly_csv": { "id": "9f199e72d4c8734c", "src": "hda", "uuid": "d4f42cf4-85ed-4eb7-ab79-944239671a0c" }, "genbank_files1": { "id": "4eec6dacaee8b95b", "src": "hda", "uuid": "c66662f5-5307-40f5-b7d8-1ae34e9bc594" }, "genbank_files2": { "id": "214d04ae88ac0b41", "src": "hda", "uuid": "ebb77d89-fcaf-4aad-ae07-bd6df1cbc75d" } }, "job_messages": [], "job_metrics": [], "job_runner_name": null, "job_stderr": "", "job_stdout": "", "model_class": "Job", "output_collections": { "construct_gb": { "id": "e9003a596293e37c", "src": "hdca" } }, "outputs": { "output_zip": { "id": "1893df3b29988972", "src": "hda", "uuid": "e37b2d54-bd4d-445c-9171-dd049f49ed36" } }, "params": { "__input_ext": "\"input\"", "chromInfo": "\"/tmp/tmpe6pmg7jw/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", "dbkey": "\"?\"", "domesticated_input": null, "genbank_files": "{\"values\": [{\"id\": 5, \"src\": \"hdca\"}]}", "json_use": "{\"__current_case__\": 0, \"assembly_plan_name\": \"LigaseCyclingReactionAssembly\", \"enzyme\": \"auto\", \"topology\": \"circular\", \"use_json_paramers\": false}", "use_file_names_as_ids": "true" }, "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, 2.35it/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, 2.35it/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": "2025-07-17T10:11:21.625362", "user_email": "planemo@galaxyproject.org", "user_id": "986c9b47c580ae59" }, "status": "success", "test_index": 2, "time_seconds": 22.644192218780518, "tool_id": "cloning_simulation", "tool_version": "0.1.0+galaxy0" }, "has_data": true, "id": "cloning_simulation-2" }, { "data": { "inputs": { "assembly_csv": { "id": "62b2e7c0b424e83e", "src": "hda" }, "genbank_files": { "id": "8c39a9a410cc0a00", "src": "hdca" }, "json_use|assembly_plan_name": "BASICAssembly", "json_use|topology": "circular", "json_use|use_json_paramers": false, "use_file_names_as_ids": true }, "job": { "command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && cp '/tmp/tmpe6pmg7jw/files/b/f/1/dataset_bf11bd3d-ca0e-4756-8106-142184dc57e7.dat' 'assembly_csv.csv' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmpe6pmg7jw/files/a/f/3/dataset_af32db16-e6dc-493f-b6a7-5a3b6725a736.dat,/tmp/tmpe6pmg7jw/files/a/4/9/dataset_a4936e9b-d8be-4cf9-8d6c-1c625676bc58.dat,/tmp/tmpe6pmg7jw/files/0/3/c/dataset_03cda120-0c4d-4452-afab-925df4a5723a.dat,/tmp/tmpe6pmg7jw/files/3/b/1/dataset_3b164cad-fbab-47a9-8965-c95820826daf.dat,/tmp/tmpe6pmg7jw/files/a/b/3/dataset_ab35511d-2fbf-4014-b079-65b270bd9cc8.dat' --domesticated_seq '' --assembly_csv 'assembly_csv.csv' --file_name_mapping '/tmp/tmpe6pmg7jw/files/a/f/3/dataset_af32db16-e6dc-493f-b6a7-5a3b6725a736.dat:GFP.gb,/tmp/tmpe6pmg7jw/files/a/4/9/dataset_a4936e9b-d8be-4cf9-8d6c-1c625676bc58.dat:p15A_kan.gb,/tmp/tmpe6pmg7jw/files/0/3/c/dataset_03cda120-0c4d-4452-afab-925df4a5723a.dat:promoter.gb,/tmp/tmpe6pmg7jw/files/3/b/1/dataset_3b164cad-fbab-47a9-8965-c95820826daf.dat:RFP.gb,/tmp/tmpe6pmg7jw/files/a/b/3/dataset_ab35511d-2fbf-4014-b079-65b270bd9cc8.dat:oligos.fa' --file_name_mapping_dom '' --use_json_paramers 'false' --enzyme 'auto' --topology 'circular' --assembly_plan_name 'BASICAssembly' --use_file_names_as_id 'true' --outdir_simulation 'outdir_zip' --outdir_gb 'outdir_gb' --output_simulation 'output_zip.zip' && cp 'output_zip.zip' '/tmp/tmpe6pmg7jw/job_working_directory/000/28/outputs/dataset_f130e84e-8140-449b-bb7e-8df370a421d1.dat'", "command_version": "", "copied_from_job_id": null, "create_time": "2025-07-17T10:11:42.348377", "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": "77127", "galaxy_version": "25.0", "handler": null, "history_id": "71d208f6d8b613ba", "id": "1893df3b29988972", "inputs": { "assembly_csv": { "id": "62b2e7c0b424e83e", "src": "hda", "uuid": "bf11bd3d-ca0e-4756-8106-142184dc57e7" }, "genbank_files1": { "id": "b20d34fd097d655b", "src": "hda", "uuid": "af32db16-e6dc-493f-b6a7-5a3b6725a736" }, "genbank_files2": { "id": "38d1a5747f8e5978", "src": "hda", "uuid": "a4936e9b-d8be-4cf9-8d6c-1c625676bc58" }, "genbank_files3": { "id": "aa0c2bc050c99399", "src": "hda", "uuid": "03cda120-0c4d-4452-afab-925df4a5723a" }, "genbank_files4": { "id": "7696fc7f810474ba", "src": "hda", "uuid": "3b164cad-fbab-47a9-8965-c95820826daf" }, "genbank_files5": { "id": "bf4065b67294e257", "src": "hda", "uuid": "ab35511d-2fbf-4014-b079-65b270bd9cc8" } }, "job_messages": [], "job_metrics": [], "job_runner_name": null, "job_stderr": "", "job_stdout": "", "model_class": "Job", "output_collections": { "construct_gb": { "id": "f7b25594aba42961", "src": "hdca" } }, "outputs": { "output_zip": { "id": "1f477a8cb4ab1699", "src": "hda", "uuid": "f130e84e-8140-449b-bb7e-8df370a421d1" } }, "params": { "__input_ext": "\"input\"", "chromInfo": "\"/tmp/tmpe6pmg7jw/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", "dbkey": "\"?\"", "domesticated_input": null, "genbank_files": "{\"values\": [{\"id\": 7, \"src\": \"hdca\"}]}", "json_use": "{\"__current_case__\": 0, \"assembly_plan_name\": \"BASICAssembly\", \"enzyme\": \"auto\", \"topology\": \"circular\", \"use_json_paramers\": false}", "use_file_names_as_ids": "true" }, "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: 75%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u258c | 6/8 [00:00<00:00, 49.66it/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: 75%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u258c | 6/8 [00:00<00:00, 49.66it/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": "2025-07-17T10:11:52.291581", "user_email": "planemo@galaxyproject.org", "user_id": "986c9b47c580ae59" }, "status": "success", "test_index": 3, "time_seconds": 30.479472160339355, "tool_id": "cloning_simulation", "tool_version": "0.1.0+galaxy0" }, "has_data": true, "id": "cloning_simulation-3" }, { "data": { "inputs": { "assembly_csv": { "id": "38b6c0c549bf284f", "src": "hda" }, "genbank_files": { "id": "5f098a2d242af5ee", "src": "hdca" }, "json_use|assembly_plan_name": "BioBrickStandardAssembly", "json_use|topology": "circular", "json_use|use_json_paramers": false, "use_file_names_as_ids": true }, "job": { "command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && cp '/tmp/tmpe6pmg7jw/files/3/0/7/dataset_307ff774-78e5-410b-926b-396bf0346f5f.dat' 'assembly_csv.csv' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmpe6pmg7jw/files/8/7/9/dataset_879f6c49-14f5-4f78-8b32-f06d098a7f4f.dat,/tmp/tmpe6pmg7jw/files/a/3/c/dataset_a3cb8cea-16ad-4a33-8e41-a9b378b2974a.dat,/tmp/tmpe6pmg7jw/files/c/7/b/dataset_c7bca70e-0ae9-4062-b185-1e0e5ed116a6.dat,/tmp/tmpe6pmg7jw/files/b/3/a/dataset_b3a11bc9-4c29-470c-8985-d845c2f9e183.dat,/tmp/tmpe6pmg7jw/files/0/8/1/dataset_08129340-240c-4349-af6c-0379d32cae9c.dat' --domesticated_seq '' --assembly_csv 'assembly_csv.csv' --file_name_mapping '/tmp/tmpe6pmg7jw/files/8/7/9/dataset_879f6c49-14f5-4f78-8b32-f06d098a7f4f.dat:BBa_E0040_GFP.gb,/tmp/tmpe6pmg7jw/files/a/3/c/dataset_a3cb8cea-16ad-4a33-8e41-a9b378b2974a.dat:BBa_J23119_prom.gb,/tmp/tmpe6pmg7jw/files/c/7/b/dataset_c7bca70e-0ae9-4062-b185-1e0e5ed116a6.dat:BBa_J23119_prom_flawed.gb,/tmp/tmpe6pmg7jw/files/b/3/a/dataset_b3a11bc9-4c29-470c-8985-d845c2f9e183.dat:BBa_J61048_term.gb,/tmp/tmpe6pmg7jw/files/0/8/1/dataset_08129340-240c-4349-af6c-0379d32cae9c.dat:BBa_K611094_bar.gb' --file_name_mapping_dom '' --use_json_paramers 'false' --enzyme 'auto' --topology 'circular' --assembly_plan_name 'BioBrickStandardAssembly' --use_file_names_as_id 'true' --outdir_simulation 'outdir_zip' --outdir_gb 'outdir_gb' --output_simulation 'output_zip.zip' && cp 'output_zip.zip' '/tmp/tmpe6pmg7jw/job_working_directory/000/35/outputs/dataset_c2f7d71f-de27-48c6-bc1f-b656bc8d53f1.dat'", "command_version": "", "copied_from_job_id": null, "create_time": "2025-07-17T10:12:13.370696", "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": "77757", "galaxy_version": "25.0", "handler": null, "history_id": "58ad66a9f93223b8", "id": "1f477a8cb4ab1699", "inputs": { "assembly_csv": { "id": "38b6c0c549bf284f", "src": "hda", "uuid": "307ff774-78e5-410b-926b-396bf0346f5f" }, "genbank_files1": { "id": "de5166318ad7499c", "src": "hda", "uuid": "879f6c49-14f5-4f78-8b32-f06d098a7f4f" }, "genbank_files2": { "id": "0a0976316513f675", "src": "hda", "uuid": "a3cb8cea-16ad-4a33-8e41-a9b378b2974a" }, "genbank_files3": { "id": "88f51edac3b2f70e", "src": "hda", "uuid": "c7bca70e-0ae9-4062-b185-1e0e5ed116a6" }, "genbank_files4": { "id": "6974b4f354e9f36a", "src": "hda", "uuid": "b3a11bc9-4c29-470c-8985-d845c2f9e183" }, "genbank_files5": { "id": "5b088a1dc26c39a4", "src": "hda", "uuid": "08129340-240c-4349-af6c-0379d32cae9c" } }, "job_messages": [], "job_metrics": [], "job_runner_name": null, "job_stderr": "", "job_stdout": "", "model_class": "Job", "output_collections": { "construct_gb": { "id": "8de66704b7df8b5e", "src": "hdca" } }, "outputs": { "__new_primary_file_construct_gb|C1_prom_barcode__": { "id": "79e58137b38a96f5", "src": "hda", "uuid": "8b1ffa40-fda8-4629-a843-4a17c7d9e983" }, "__new_primary_file_construct_gb|C2_gfp_term__": { "id": "b5ab7a1e4a941d0d", "src": "hda", "uuid": "ef840f10-be08-4855-858c-ee696e852624" }, "__new_primary_file_construct_gb|C3_final__": { "id": "76e4f31bf12269ab", "src": "hda", "uuid": "0eba0e00-8261-4ff7-a40e-46d7fd0b9f62" }, "output_zip": { "id": "8380aea1f9c6b8c9", "src": "hda", "uuid": "c2f7d71f-de27-48c6-bc1f-b656bc8d53f1" } }, "params": { "__input_ext": "\"input\"", "chromInfo": "\"/tmp/tmpe6pmg7jw/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", "dbkey": "\"?\"", "domesticated_input": null, "genbank_files": "{\"values\": [{\"id\": 9, \"src\": \"hdca\"}]}", "json_use": "{\"__current_case__\": 0, \"assembly_plan_name\": \"BioBrickStandardAssembly\", \"enzyme\": \"auto\", \"topology\": \"circular\", \"use_json_paramers\": false}", "use_file_names_as_ids": "true" }, "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, 1.93it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 3/3 [00:01<00:00, 1.59it/s, now=None]\r \r", "stdout": "Simulating assembly plan assambly...\n{'cancelled_assemblies': 0, 'errored_assemblies': 0, 'valid_assemblies': 3}\nGenerating assemblies reports...\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, 1.93it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 3/3 [00:01<00:00, 1.59it/s, now=None]\r \r", "tool_stdout": "Simulating assembly plan assambly...\n{'cancelled_assemblies': 0, 'errored_assemblies': 0, 'valid_assemblies': 3}\nGenerating assemblies reports...\n", "update_time": "2025-07-17T10:12:26.209759", "user_email": "planemo@galaxyproject.org", "user_id": "986c9b47c580ae59" }, "status": "success", "test_index": 4, "time_seconds": 33.86248016357422, "tool_id": "cloning_simulation", "tool_version": "0.1.0+galaxy0" }, "has_data": true, "id": "cloning_simulation-4" }, { "data": { "inputs": { "assembly_csv": { "id": "7b8a6e6b82f35567", "src": "hda" }, "domesticated_input": { "id": "54c6d71c8dc7cb11", "src": "hdca" }, "genbank_files": { "id": "2592d2c705ba0baa", "src": "hdca" }, "json_use|assembly_plan_name": "Type2sRestrictionAssembly", "json_use|topology": "circular", "json_use|use_json_paramers": false, "use_file_names_as_ids": true }, "job": { "command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && cp '/tmp/tmpe6pmg7jw/files/9/b/5/dataset_9b53e736-9aa4-428b-866b-72d2f525f99e.dat' 'assembly_csv.csv' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmpe6pmg7jw/files/d/1/5/dataset_d15ff026-babf-41d1-b9e0-e701e0a51b6b.dat,/tmp/tmpe6pmg7jw/files/2/9/8/dataset_298d983c-3e5c-4b93-944c-b372d4295740.dat,/tmp/tmpe6pmg7jw/files/4/e/3/dataset_4e3c0103-dbb8-465c-abbf-7f9b66a8263b.dat,/tmp/tmpe6pmg7jw/files/1/5/4/dataset_15452284-bc19-43d6-8367-2753056a96ec.dat,/tmp/tmpe6pmg7jw/files/0/f/3/dataset_0f36b33d-8c1c-472b-abbd-c3f63418174a.dat,/tmp/tmpe6pmg7jw/files/a/d/d/dataset_adde970f-87a8-45b0-9303-acf0d7ed7c2e.dat,/tmp/tmpe6pmg7jw/files/9/6/b/dataset_96bd86f4-cd0a-4a34-a1cf-3044a62f77a2.dat' --domesticated_seq '/tmp/tmpe6pmg7jw/files/5/5/8/dataset_5587676a-8c81-4954-bf33-2c965bf7635d.dat,/tmp/tmpe6pmg7jw/files/b/f/b/dataset_bfb815a2-67c8-4cb5-afb8-ea35cfa372eb.dat,/tmp/tmpe6pmg7jw/files/2/1/6/dataset_216a998c-35de-48c2-a017-c3fed9787319.dat,/tmp/tmpe6pmg7jw/files/8/9/1/dataset_89112e3f-e936-4419-938d-b4b4daa68e40.dat,/tmp/tmpe6pmg7jw/files/5/3/2/dataset_53218d73-0f61-4527-b279-62ced98701d1.dat' --assembly_csv 'assembly_csv.csv' --file_name_mapping '/tmp/tmpe6pmg7jw/files/d/1/5/dataset_d15ff026-babf-41d1-b9e0-e701e0a51b6b.dat:part_A.gb,/tmp/tmpe6pmg7jw/files/2/9/8/dataset_298d983c-3e5c-4b93-944c-b372d4295740.dat:part_B.gb,/tmp/tmpe6pmg7jw/files/4/e/3/dataset_4e3c0103-dbb8-465c-abbf-7f9b66a8263b.dat:part_C.gb,/tmp/tmpe6pmg7jw/files/1/5/4/dataset_15452284-bc19-43d6-8367-2753056a96ec.dat:part_D.gb,/tmp/tmpe6pmg7jw/files/0/f/3/dataset_0f36b33d-8c1c-472b-abbd-c3f63418174a.dat:part_E.gb,/tmp/tmpe6pmg7jw/files/a/d/d/dataset_adde970f-87a8-45b0-9303-acf0d7ed7c2e.dat:part_F.gb,/tmp/tmpe6pmg7jw/files/9/6/b/dataset_96bd86f4-cd0a-4a34-a1cf-3044a62f77a2.dat:part_G.gb' --file_name_mapping_dom '/tmp/tmpe6pmg7jw/files/5/5/8/dataset_5587676a-8c81-4954-bf33-2c965bf7635d.dat:part_H.gb,/tmp/tmpe6pmg7jw/files/b/f/b/dataset_bfb815a2-67c8-4cb5-afb8-ea35cfa372eb.dat:part_I.gb,/tmp/tmpe6pmg7jw/files/2/1/6/dataset_216a998c-35de-48c2-a017-c3fed9787319.dat:part_J.gb,/tmp/tmpe6pmg7jw/files/8/9/1/dataset_89112e3f-e936-4419-938d-b4b4daa68e40.dat:part_K.gb,/tmp/tmpe6pmg7jw/files/5/3/2/dataset_53218d73-0f61-4527-b279-62ced98701d1.dat:part_L.gb' --use_json_paramers 'false' --enzyme 'auto' --topology 'circular' --assembly_plan_name 'Type2sRestrictionAssembly' --use_file_names_as_id 'true' --outdir_simulation 'outdir_zip' --outdir_gb 'outdir_gb' --output_simulation 'output_zip.zip' && cp 'output_zip.zip' '/tmp/tmpe6pmg7jw/job_working_directory/000/49/outputs/dataset_85657c38-c9be-421a-8d2e-3ba54dcd1ee1.dat'", "command_version": "", "copied_from_job_id": null, "create_time": "2025-07-17T10:13:06.053332", "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": "78856", "galaxy_version": "25.0", "handler": null, "history_id": "e9003a596293e37c", "id": "c4dd95e8260a7aca", "inputs": { "assembly_csv": { "id": "7b8a6e6b82f35567", "src": "hda", "uuid": "9b53e736-9aa4-428b-866b-72d2f525f99e" }, "domesticated_input1": { "id": "3cae7d055c6a8b90", "src": "hda", "uuid": "5587676a-8c81-4954-bf33-2c965bf7635d" }, "domesticated_input2": { "id": "eb3eeb1f7f0d700b", "src": "hda", "uuid": "bfb815a2-67c8-4cb5-afb8-ea35cfa372eb" }, "domesticated_input3": { "id": "0a842033366cb6f4", "src": "hda", "uuid": "216a998c-35de-48c2-a017-c3fed9787319" }, "domesticated_input4": { "id": "3b0ecfffcd65a433", "src": "hda", "uuid": "89112e3f-e936-4419-938d-b4b4daa68e40" }, "domesticated_input5": { "id": "7b7bd43bd69db4da", "src": "hda", "uuid": "53218d73-0f61-4527-b279-62ced98701d1" }, "genbank_files1": { "id": "b2f60919761cbe66", "src": "hda", "uuid": "d15ff026-babf-41d1-b9e0-e701e0a51b6b" }, "genbank_files2": { "id": "99a09fce7ce0f899", "src": "hda", "uuid": "298d983c-3e5c-4b93-944c-b372d4295740" }, "genbank_files3": { "id": "f6b26195fd7f7f3e", "src": "hda", "uuid": "4e3c0103-dbb8-465c-abbf-7f9b66a8263b" }, "genbank_files4": { "id": "c4dd95e8260a7aca", "src": "hda", "uuid": "15452284-bc19-43d6-8367-2753056a96ec" }, "genbank_files5": { "id": "03de0919cac4bbd5", "src": "hda", "uuid": "0f36b33d-8c1c-472b-abbd-c3f63418174a" }, "genbank_files6": { "id": "8b133a938a16d94a", "src": "hda", "uuid": "adde970f-87a8-45b0-9303-acf0d7ed7c2e" }, "genbank_files7": { "id": "de8340ef2cf62a09", "src": "hda", "uuid": "96bd86f4-cd0a-4a34-a1cf-3044a62f77a2" } }, "job_messages": [], "job_metrics": [], "job_runner_name": null, "job_stderr": "", "job_stdout": "", "model_class": "Job", "output_collections": { "construct_gb": { "id": "54d710fc68386373", "src": "hdca" } }, "outputs": { "__new_primary_file_construct_gb|construct_1__": { "id": "955be7be95972849", "src": "hda", "uuid": "14602eef-eda6-4c3a-8f13-f1cac1adca78" }, "__new_primary_file_construct_gb|construct_2__": { "id": "535a274eb83bb714", "src": "hda", "uuid": "c94a01f0-fd44-4112-be7e-0cc5c48e541d" }, "__new_primary_file_construct_gb|construct_3__": { "id": "b79f0249bac52469", "src": "hda", "uuid": "a4df015a-0bc4-4cec-b8be-67681da9f1b7" }, "__new_primary_file_construct_gb|construct_4__": { "id": "3cafb1bf19a56844", "src": "hda", "uuid": "d38c7640-aa80-4ddd-b16b-6c71f3aaf195" }, "output_zip": { "id": "0d8c106f64e9b667", "src": "hda", "uuid": "85657c38-c9be-421a-8d2e-3ba54dcd1ee1" } }, "params": { "__input_ext": "\"input\"", "chromInfo": "\"/tmp/tmpe6pmg7jw/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", "dbkey": "\"?\"", "domesticated_input": "{\"values\": [{\"id\": 11, \"src\": \"hdca\"}]}", "genbank_files": "{\"values\": [{\"id\": 12, \"src\": \"hdca\"}]}", "json_use": "{\"__current_case__\": 0, \"assembly_plan_name\": \"Type2sRestrictionAssembly\", \"enzyme\": \"auto\", \"topology\": \"circular\", \"use_json_paramers\": false}", "use_file_names_as_ids": "true" }, "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, 2.22it/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, 2.43it/s, now=None]\rassembly: 75%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u258c | 3/4 [00:01<00:00, 2.22it/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": "2025-07-17T10:13:18.198417", "user_email": "planemo@galaxyproject.org", "user_id": "986c9b47c580ae59" }, "status": "success", "test_index": 5, "time_seconds": 51.96266531944275, "tool_id": "cloning_simulation", "tool_version": "0.1.0+galaxy0" }, "has_data": true, "id": "cloning_simulation-5" }, { "data": { "inputs": { "assembly_csv": { "id": "6cceecf1bcab0d5e", "src": "hda" }, "domesticated_input": { "id": "98a2432f1cff4f91", "src": "hdca" }, "json_use|assembly_plan_name": "Type2sRestrictionAssembly", "json_use|topology": "circular", "json_use|use_json_paramers": false, "use_file_names_as_ids": true }, "job": { "command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && cp '/tmp/tmpe6pmg7jw/files/2/8/4/dataset_2844fc99-3db2-458b-9656-9c18962aed13.dat' 'assembly_csv.csv' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmpe6pmg7jw/files/3/6/7/dataset_367c8adb-623b-4fc2-8710-1402b90dc27a.dat,/tmp/tmpe6pmg7jw/files/b/8/c/dataset_b8c15683-a369-4b52-b94d-52e823e2dbc4.dat,/tmp/tmpe6pmg7jw/files/7/b/7/dataset_7b71197b-9cec-4ebc-a0ab-9a9070856680.dat,/tmp/tmpe6pmg7jw/files/0/8/2/dataset_08203bf4-e285-4e41-845d-c7db10709a14.dat,/tmp/tmpe6pmg7jw/files/b/1/7/dataset_b174f6f8-eb0c-44b9-9d1b-89b7a62bc494.dat,/tmp/tmpe6pmg7jw/files/c/5/9/dataset_c598d3b6-58ab-4695-99a5-5fb6197a4823.dat,/tmp/tmpe6pmg7jw/files/0/9/e/dataset_09eec457-37de-4c2c-8b7e-1be1dfbaffd6.dat,/tmp/tmpe6pmg7jw/files/e/8/4/dataset_e84bc66f-f327-4070-8511-c5734161ea4b.dat,/tmp/tmpe6pmg7jw/files/d/b/0/dataset_db0c0f17-0973-48f2-a70a-2760c7521af3.dat,/tmp/tmpe6pmg7jw/files/a/f/1/dataset_af171625-0bb7-4a5f-a858-f92983e9f54e.dat,/tmp/tmpe6pmg7jw/files/3/5/1/dataset_3515fd31-0758-4e14-a6ac-b01ba9941850.dat,/tmp/tmpe6pmg7jw/files/f/2/1/dataset_f2119eb4-c9ca-461f-8d40-6284effbefa1.dat' --domesticated_seq '' --assembly_csv 'assembly_csv.csv' --file_name_mapping '/tmp/tmpe6pmg7jw/files/3/6/7/dataset_367c8adb-623b-4fc2-8710-1402b90dc27a.dat:part_A.gb,/tmp/tmpe6pmg7jw/files/b/8/c/dataset_b8c15683-a369-4b52-b94d-52e823e2dbc4.dat:part_B.gb,/tmp/tmpe6pmg7jw/files/7/b/7/dataset_7b71197b-9cec-4ebc-a0ab-9a9070856680.dat:part_C.gb,/tmp/tmpe6pmg7jw/files/0/8/2/dataset_08203bf4-e285-4e41-845d-c7db10709a14.dat:part_D.gb,/tmp/tmpe6pmg7jw/files/b/1/7/dataset_b174f6f8-eb0c-44b9-9d1b-89b7a62bc494.dat:part_E.gb,/tmp/tmpe6pmg7jw/files/c/5/9/dataset_c598d3b6-58ab-4695-99a5-5fb6197a4823.dat:part_F.gb,/tmp/tmpe6pmg7jw/files/0/9/e/dataset_09eec457-37de-4c2c-8b7e-1be1dfbaffd6.dat:part_G.gb,/tmp/tmpe6pmg7jw/files/e/8/4/dataset_e84bc66f-f327-4070-8511-c5734161ea4b.dat:part_H.gb,/tmp/tmpe6pmg7jw/files/d/b/0/dataset_db0c0f17-0973-48f2-a70a-2760c7521af3.dat:part_I.gb,/tmp/tmpe6pmg7jw/files/a/f/1/dataset_af171625-0bb7-4a5f-a858-f92983e9f54e.dat:part_J.gb,/tmp/tmpe6pmg7jw/files/3/5/1/dataset_3515fd31-0758-4e14-a6ac-b01ba9941850.dat:part_K.gb,/tmp/tmpe6pmg7jw/files/f/2/1/dataset_f2119eb4-c9ca-461f-8d40-6284effbefa1.dat:part_L.gb' --file_name_mapping_dom '' --use_json_paramers 'false' --enzyme 'auto' --topology 'circular' --assembly_plan_name 'Type2sRestrictionAssembly' --use_file_names_as_id 'true' --outdir_simulation 'outdir_zip' --outdir_gb 'outdir_gb' --output_simulation 'output_zip.zip' && cp 'output_zip.zip' '/tmp/tmpe6pmg7jw/job_working_directory/000/63/outputs/dataset_fc4a95ba-4368-4457-b175-ebf26af659aa.dat'", "command_version": "", "copied_from_job_id": null, "create_time": "2025-07-17T10:13:57.903413", "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": "80009", "galaxy_version": "25.0", "handler": null, "history_id": "8c39a9a410cc0a00", "id": "3cafb1bf19a56844", "inputs": { "assembly_csv": { "id": "6cceecf1bcab0d5e", "src": "hda", "uuid": "2844fc99-3db2-458b-9656-9c18962aed13" }, "domesticated_input1": { "id": "95f8e30291b4c724", "src": "hda", "uuid": "367c8adb-623b-4fc2-8710-1402b90dc27a" }, "domesticated_input10": { "id": "5dc7959fa599d57d", "src": "hda", "uuid": "af171625-0bb7-4a5f-a858-f92983e9f54e" }, "domesticated_input11": { "id": "d309b7113a9d8008", "src": "hda", "uuid": "3515fd31-0758-4e14-a6ac-b01ba9941850" }, "domesticated_input12": { "id": "f558e884d7fd7d56", "src": "hda", "uuid": "f2119eb4-c9ca-461f-8d40-6284effbefa1" }, "domesticated_input2": { "id": "e51e45ceb8fc2cce", "src": "hda", "uuid": "b8c15683-a369-4b52-b94d-52e823e2dbc4" }, "domesticated_input3": { "id": "7a147471a754feaa", "src": "hda", "uuid": "7b71197b-9cec-4ebc-a0ab-9a9070856680" }, "domesticated_input4": { "id": "980ee860844f9585", "src": "hda", "uuid": "08203bf4-e285-4e41-845d-c7db10709a14" }, "domesticated_input5": { "id": "fbc8779ea7cd6ed6", "src": "hda", "uuid": "b174f6f8-eb0c-44b9-9d1b-89b7a62bc494" }, "domesticated_input6": { "id": "185e1f0b9b0a67b3", "src": "hda", "uuid": "c598d3b6-58ab-4695-99a5-5fb6197a4823" }, "domesticated_input7": { "id": "37c673ee68b5c3ed", "src": "hda", "uuid": "09eec457-37de-4c2c-8b7e-1be1dfbaffd6" }, "domesticated_input8": { "id": "8a3a0f65c762008d", "src": "hda", "uuid": "e84bc66f-f327-4070-8511-c5734161ea4b" }, "domesticated_input9": { "id": "5033875e970a3799", "src": "hda", "uuid": "db0c0f17-0973-48f2-a70a-2760c7521af3" } }, "job_messages": [], "job_metrics": [], "job_runner_name": null, "job_stderr": "", "job_stdout": "", "model_class": "Job", "output_collections": { "construct_gb": { "id": "172543d29b19f394", "src": "hdca" } }, "outputs": { "__new_primary_file_construct_gb|construct_1__": { "id": "6665d38e10ff581d", "src": "hda", "uuid": "30a2a28d-9d1b-4332-8d5a-acda885308dd" }, "__new_primary_file_construct_gb|construct_2__": { "id": "0788ac4ba66a0bdd", "src": "hda", "uuid": "49f11bec-1e54-49fe-8c44-7cc25273d54d" }, "__new_primary_file_construct_gb|construct_3__": { "id": "f41d1a7bd862df72", "src": "hda", "uuid": "a01def58-86a8-48c3-aabc-d9d5a9367927" }, "__new_primary_file_construct_gb|construct_4__": { "id": "a371069cf8561e3f", "src": "hda", "uuid": "7fd4fd46-1149-4dbe-aaa4-531dc7db5adb" }, "output_zip": { "id": "9df6b2b003837432", "src": "hda", "uuid": "fc4a95ba-4368-4457-b175-ebf26af659aa" } }, "params": { "__input_ext": "\"input\"", "chromInfo": "\"/tmp/tmpe6pmg7jw/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", "dbkey": "\"?\"", "domesticated_input": "{\"values\": [{\"id\": 14, \"src\": \"hdca\"}]}", "genbank_files": null, "json_use": "{\"__current_case__\": 0, \"assembly_plan_name\": \"Type2sRestrictionAssembly\", \"enzyme\": \"auto\", \"topology\": \"circular\", \"use_json_paramers\": false}", "use_file_names_as_ids": "true" }, "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, 2.40it/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, 1.80it/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, 2.40it/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, 1.80it/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": "2025-07-17T10:14:10.606776", "user_email": "planemo@galaxyproject.org", "user_id": "986c9b47c580ae59" }, "status": "success", "test_index": 6, "time_seconds": 52.30599284172058, "tool_id": "cloning_simulation", "tool_version": "0.1.0+galaxy0" }, "has_data": true, "id": "cloning_simulation-6" }, { "data": { "inputs": { "assembly_csv": { "id": "1a15f75791a9be7d", "src": "hda" }, "genbank_files": { "id": "018c827a8e5b161a", "src": "hdca" }, "json_use|json_conf": { "id": "9736c9b0f355f9e7", "src": "hda" }, "json_use|use_json_paramers": true, "use_file_names_as_ids": true }, "job": { "command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && cp '/tmp/tmpe6pmg7jw/files/1/5/e/dataset_15e76393-8b6d-44a4-ad54-61e9090f2281.dat' 'assembly_csv.csv' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmpe6pmg7jw/files/5/9/5/dataset_5952eac7-72c5-4e87-bac4-94a6eb3d7258.dat,/tmp/tmpe6pmg7jw/files/c/6/c/dataset_c6caf0b6-8d07-4998-8d0d-29b5d76faf46.dat,/tmp/tmpe6pmg7jw/files/c/3/e/dataset_c3e1ef9d-d877-4423-9f6d-0c1d109c0101.dat,/tmp/tmpe6pmg7jw/files/8/6/a/dataset_86a24365-6eed-4415-b56f-d0ff9854f0db.dat,/tmp/tmpe6pmg7jw/files/6/9/6/dataset_69698749-ab10-4865-b19a-ef4c5cb47996.dat,/tmp/tmpe6pmg7jw/files/8/e/d/dataset_8eda50dc-6b4b-4af8-9087-c6473e345a47.dat,/tmp/tmpe6pmg7jw/files/f/9/9/dataset_f99ec108-a3c6-4e80-8eff-68d9b8e9f67c.dat,/tmp/tmpe6pmg7jw/files/1/8/7/dataset_187c2c93-0a63-41ce-bf4f-88b7c770557b.dat,/tmp/tmpe6pmg7jw/files/3/d/7/dataset_3d7f0627-ba1c-4541-95f7-27ed41e601fa.dat,/tmp/tmpe6pmg7jw/files/4/c/1/dataset_4c18d9a5-e37c-428e-a5a3-8f698bbd9b3f.dat,/tmp/tmpe6pmg7jw/files/c/d/2/dataset_cd21525e-d4e4-4e03-a632-5a7152529d82.dat,/tmp/tmpe6pmg7jw/files/c/a/a/dataset_caa4a166-f30b-45f5-b1a9-cdacc6b40073.dat' --domesticated_seq '' --assembly_csv 'assembly_csv.csv' --file_name_mapping '/tmp/tmpe6pmg7jw/files/5/9/5/dataset_5952eac7-72c5-4e87-bac4-94a6eb3d7258.dat:part_A.gb,/tmp/tmpe6pmg7jw/files/c/6/c/dataset_c6caf0b6-8d07-4998-8d0d-29b5d76faf46.dat:part_B.gb,/tmp/tmpe6pmg7jw/files/c/3/e/dataset_c3e1ef9d-d877-4423-9f6d-0c1d109c0101.dat:part_C.gb,/tmp/tmpe6pmg7jw/files/8/6/a/dataset_86a24365-6eed-4415-b56f-d0ff9854f0db.dat:part_D.gb,/tmp/tmpe6pmg7jw/files/6/9/6/dataset_69698749-ab10-4865-b19a-ef4c5cb47996.dat:part_E.gb,/tmp/tmpe6pmg7jw/files/8/e/d/dataset_8eda50dc-6b4b-4af8-9087-c6473e345a47.dat:part_F.gb,/tmp/tmpe6pmg7jw/files/f/9/9/dataset_f99ec108-a3c6-4e80-8eff-68d9b8e9f67c.dat:part_G.gb,/tmp/tmpe6pmg7jw/files/1/8/7/dataset_187c2c93-0a63-41ce-bf4f-88b7c770557b.dat:part_H.gb,/tmp/tmpe6pmg7jw/files/3/d/7/dataset_3d7f0627-ba1c-4541-95f7-27ed41e601fa.dat:part_I.gb,/tmp/tmpe6pmg7jw/files/4/c/1/dataset_4c18d9a5-e37c-428e-a5a3-8f698bbd9b3f.dat:part_J.gb,/tmp/tmpe6pmg7jw/files/c/d/2/dataset_cd21525e-d4e4-4e03-a632-5a7152529d82.dat:part_K.gb,/tmp/tmpe6pmg7jw/files/c/a/a/dataset_caa4a166-f30b-45f5-b1a9-cdacc6b40073.dat:part_L.gb' --file_name_mapping_dom '' --use_json_paramers 'true' --json_conf '/tmp/tmpe6pmg7jw/files/9/b/8/dataset_9b899aff-2835-4f10-84f3-52034c55b5dc.dat' --use_file_names_as_id 'true' --outdir_simulation 'outdir_zip' --outdir_gb 'outdir_gb' --output_simulation 'output_zip.zip' && cp 'output_zip.zip' '/tmp/tmpe6pmg7jw/job_working_directory/000/78/outputs/dataset_6ee2cd5c-d43c-4fc7-9ebc-265f89a87696.dat'", "command_version": "", "copied_from_job_id": null, "create_time": "2025-07-17T10:14:50.961634", "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": "81204", "galaxy_version": "25.0", "handler": null, "history_id": "f7b25594aba42961", "id": "6665d38e10ff581d", "inputs": { "assembly_csv": { "id": "1a15f75791a9be7d", "src": "hda", "uuid": "15e76393-8b6d-44a4-ad54-61e9090f2281" }, "genbank_files1": { "id": "59c39a1f7cd89b1b", "src": "hda", "uuid": "5952eac7-72c5-4e87-bac4-94a6eb3d7258" }, "genbank_files10": { "id": "e01657e1b61da6f3", "src": "hda", "uuid": "4c18d9a5-e37c-428e-a5a3-8f698bbd9b3f" }, "genbank_files11": { "id": "ca4aa85e07d14f5a", "src": "hda", "uuid": "cd21525e-d4e4-4e03-a632-5a7152529d82" }, "genbank_files12": { "id": "c041165b2b3d8e70", "src": "hda", "uuid": "caa4a166-f30b-45f5-b1a9-cdacc6b40073" }, "genbank_files2": { "id": "a6194e007a63df57", "src": "hda", "uuid": "c6caf0b6-8d07-4998-8d0d-29b5d76faf46" }, "genbank_files3": { "id": "fa554b79bf343ee0", "src": "hda", "uuid": "c3e1ef9d-d877-4423-9f6d-0c1d109c0101" }, "genbank_files4": { "id": "5a80b8b59c71bb8c", "src": "hda", "uuid": "86a24365-6eed-4415-b56f-d0ff9854f0db" }, "genbank_files5": { "id": "e0d49f429b51fe72", "src": "hda", "uuid": "69698749-ab10-4865-b19a-ef4c5cb47996" }, "genbank_files6": { "id": "78e04b973431c16b", "src": "hda", "uuid": "8eda50dc-6b4b-4af8-9087-c6473e345a47" }, "genbank_files7": { "id": "0582b59361b7ebfc", "src": "hda", "uuid": "f99ec108-a3c6-4e80-8eff-68d9b8e9f67c" }, "genbank_files8": { "id": "d65ee033f23e8216", "src": "hda", "uuid": "187c2c93-0a63-41ce-bf4f-88b7c770557b" }, "genbank_files9": { "id": "eb35258b10e09e8e", "src": "hda", "uuid": "3d7f0627-ba1c-4541-95f7-27ed41e601fa" }, "json_use|json_conf": { "id": "9736c9b0f355f9e7", "src": "hda", "uuid": "9b899aff-2835-4f10-84f3-52034c55b5dc" } }, "job_messages": [], "job_metrics": [], "job_runner_name": null, "job_stderr": "", "job_stdout": "", "model_class": "Job", "output_collections": { "construct_gb": { "id": "494079827008dff1", "src": "hdca" } }, "outputs": { "__new_primary_file_construct_gb|construct_1__": { "id": "042ef984f231298e", "src": "hda", "uuid": "88d735c2-5600-4ed7-942c-07e0ce3b5b4a" }, "__new_primary_file_construct_gb|construct_2__": { "id": "ec93ee31e9126c50", "src": "hda", "uuid": "7b9fee32-94aa-421d-a905-a8a5863047e3" }, "__new_primary_file_construct_gb|construct_3__": { "id": "5cf69b6cb189d4a3", "src": "hda", "uuid": "001a91be-d900-4196-b6b0-fa5ac8e97946" }, "__new_primary_file_construct_gb|construct_4__": { "id": "84d3b22c61ad807e", "src": "hda", "uuid": "e567ccf6-ed3b-4dcb-85e8-8456952d28cc" }, "output_zip": { "id": "985e51699d0cdeaa", "src": "hda", "uuid": "6ee2cd5c-d43c-4fc7-9ebc-265f89a87696" } }, "params": { "__input_ext": "\"input\"", "chromInfo": "\"/tmp/tmpe6pmg7jw/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", "dbkey": "\"?\"", "domesticated_input": null, "genbank_files": "{\"values\": [{\"id\": 16, \"src\": \"hdca\"}]}", "json_use": "{\"__current_case__\": 1, \"json_conf\": {\"values\": [{\"id\": 95, \"src\": \"hda\"}]}, \"use_json_paramers\": true}", "use_file_names_as_ids": "true" }, "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, 1.81it/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, 2.39it/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, 1.81it/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": "2025-07-17T10:15:03.707417", "user_email": "planemo@galaxyproject.org", "user_id": "986c9b47c580ae59" }, "status": "success", "test_index": 7, "time_seconds": 52.973809242248535, "tool_id": "cloning_simulation", "tool_version": "0.1.0+galaxy0" }, "has_data": true, "id": "cloning_simulation-7" } ], "version": "0.1" }