Mercurial > repos > tduigou > cloning_simulation
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planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit db4ac861e1d03fcdfe94321d858839124e493930-dirty
| author | tduigou |
|---|---|
| date | Wed, 23 Jul 2025 09:46:59 +0000 |
| parents | |
| children |
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{ "summary": { "num_errors": 0, "num_failures": 0, "num_skips": 0, "num_tests": 7 }, "tests": [ { "data": { "inputs": { "adv|use_file_names_as_ids": true, "assembly_csv": { "id": "5251f3a41a1cbe5c", "src": "hda" }, "assembly_plan_name": "Type2sRestrictionAssembly", "genbank_files": { "id": "b685bcc6830b171b", "src": "hdca" }, "topology": "circular" }, "job": { "command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && cp '/tmp/tmp2jitj5ti/files/c/2/9/dataset_c29f7add-5948-4171-8ac2-f87d5bf0f6f6.dat' 'assembly_csv.csv' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmp2jitj5ti/files/e/6/3/dataset_e63928a2-379c-45c8-8839-98a0df69a5cb.dat,/tmp/tmp2jitj5ti/files/4/4/7/dataset_44790451-2c88-485c-b4d5-d0f4bf78a093.dat,/tmp/tmp2jitj5ti/files/7/3/5/dataset_7354b218-2236-4b40-bdcb-3a46917a6e0f.dat,/tmp/tmp2jitj5ti/files/a/8/e/dataset_a8e12f0e-8a7c-48dd-a8ef-6988c90a7e58.dat,/tmp/tmp2jitj5ti/files/a/2/9/dataset_a298e5dd-536e-4652-8690-5132027c738c.dat,/tmp/tmp2jitj5ti/files/d/c/d/dataset_dcd006e1-e03f-42ed-b029-00134dd29dd1.dat,/tmp/tmp2jitj5ti/files/2/a/f/dataset_2aff75ea-f829-4836-a3dc-7cb018e02383.dat,/tmp/tmp2jitj5ti/files/a/1/8/dataset_a180d7ab-0c41-48d4-8941-3d8d251808a6.dat,/tmp/tmp2jitj5ti/files/6/9/2/dataset_692e75b8-b311-48e4-9b81-92c7addf1f79.dat,/tmp/tmp2jitj5ti/files/9/b/3/dataset_9b37829a-f97b-4f67-8243-bf2bd14ae4b6.dat,/tmp/tmp2jitj5ti/files/c/1/2/dataset_c12c0090-a770-4e92-9398-1a66760dc274.dat,/tmp/tmp2jitj5ti/files/5/2/1/dataset_521c5340-7b41-4b46-aa04-9be9ab5e99fd.dat' --domesticated_seq '' --assembly_csv 'assembly_csv.csv' --assembly_plan_name 'Type2sRestrictionAssembly' --file_name_mapping '/tmp/tmp2jitj5ti/files/e/6/3/dataset_e63928a2-379c-45c8-8839-98a0df69a5cb.dat:part_A.gb,/tmp/tmp2jitj5ti/files/4/4/7/dataset_44790451-2c88-485c-b4d5-d0f4bf78a093.dat:part_B.gb,/tmp/tmp2jitj5ti/files/7/3/5/dataset_7354b218-2236-4b40-bdcb-3a46917a6e0f.dat:part_C.gb,/tmp/tmp2jitj5ti/files/a/8/e/dataset_a8e12f0e-8a7c-48dd-a8ef-6988c90a7e58.dat:part_D.gb,/tmp/tmp2jitj5ti/files/a/2/9/dataset_a298e5dd-536e-4652-8690-5132027c738c.dat:part_E.gb,/tmp/tmp2jitj5ti/files/d/c/d/dataset_dcd006e1-e03f-42ed-b029-00134dd29dd1.dat:part_F.gb,/tmp/tmp2jitj5ti/files/2/a/f/dataset_2aff75ea-f829-4836-a3dc-7cb018e02383.dat:part_G.gb,/tmp/tmp2jitj5ti/files/a/1/8/dataset_a180d7ab-0c41-48d4-8941-3d8d251808a6.dat:part_H.gb,/tmp/tmp2jitj5ti/files/6/9/2/dataset_692e75b8-b311-48e4-9b81-92c7addf1f79.dat:part_I.gb,/tmp/tmp2jitj5ti/files/9/b/3/dataset_9b37829a-f97b-4f67-8243-bf2bd14ae4b6.dat:part_J.gb,/tmp/tmp2jitj5ti/files/c/1/2/dataset_c12c0090-a770-4e92-9398-1a66760dc274.dat:part_K.gb,/tmp/tmp2jitj5ti/files/5/2/1/dataset_521c5340-7b41-4b46-aa04-9be9ab5e99fd.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/tmp2jitj5ti/job_working_directory/000/14/outputs/dataset_d929e00d-64fe-466c-820f-898fef1ddd39.dat'", "command_version": "", "copied_from_job_id": null, "create_time": "2025-06-06T10:05:03.918951", "dependencies": [], "exit_code": 0, "external_id": "384868", "galaxy_version": "24.2", "handler": null, "history_id": "b685bcc6830b171b", "id": "382e0b9a3dd586fb", "inputs": { "assembly_csv": { "id": "5251f3a41a1cbe5c", "src": "hda", "uuid": "c29f7add-5948-4171-8ac2-f87d5bf0f6f6" }, "genbank_files1": { "id": "b685bcc6830b171b", "src": "hda", "uuid": "e63928a2-379c-45c8-8839-98a0df69a5cb" }, "genbank_files10": { "id": "07723b52981231a1", "src": "hda", "uuid": "9b37829a-f97b-4f67-8243-bf2bd14ae4b6" }, "genbank_files11": { "id": "830f955cbdf9a561", "src": "hda", "uuid": "c12c0090-a770-4e92-9398-1a66760dc274" }, "genbank_files12": { "id": "71dab170b139725e", "src": "hda", "uuid": "521c5340-7b41-4b46-aa04-9be9ab5e99fd" }, "genbank_files2": { "id": "48e269c64ce4fce2", "src": "hda", "uuid": "44790451-2c88-485c-b4d5-d0f4bf78a093" }, "genbank_files3": { "id": "abbe1d9cd04428c7", "src": "hda", "uuid": "7354b218-2236-4b40-bdcb-3a46917a6e0f" }, "genbank_files4": { "id": "b93fb7c1f8bf7b46", "src": "hda", "uuid": "a8e12f0e-8a7c-48dd-a8ef-6988c90a7e58" }, "genbank_files5": { "id": "45bf0c3ad4473005", "src": "hda", "uuid": "a298e5dd-536e-4652-8690-5132027c738c" }, "genbank_files6": { "id": "4efa4181abcbfe3f", "src": "hda", "uuid": "dcd006e1-e03f-42ed-b029-00134dd29dd1" }, "genbank_files7": { "id": "beb5db8871971f36", "src": "hda", "uuid": "2aff75ea-f829-4836-a3dc-7cb018e02383" }, "genbank_files8": { "id": "bc095eef87c18a70", "src": "hda", "uuid": "a180d7ab-0c41-48d4-8941-3d8d251808a6" }, "genbank_files9": { "id": "9f6ba43f26fd6d3f", "src": "hda", "uuid": "692e75b8-b311-48e4-9b81-92c7addf1f79" } }, "job_messages": [], "job_metrics": [], "job_runner_name": null, "job_stderr": "", "job_stdout": "", "model_class": "Job", "output_collections": { "construct_gb": { "id": "48e269c64ce4fce2", "src": "hdca" } }, "outputs": { "__new_primary_file_construct_gb|construct_1__": { "id": "56254918ce4e0956", "src": "hda", "uuid": "41a51dd8-721c-4361-8c96-d4e737f41eec" }, "__new_primary_file_construct_gb|construct_2__": { "id": "aad815be3bbd2bd5", "src": "hda", "uuid": "956b70c1-92eb-422d-ab4f-808a8b962d1f" }, "__new_primary_file_construct_gb|construct_3__": { "id": "720f24a804e8d612", "src": "hda", "uuid": "998417d6-f292-4477-a81c-962b56e7a0e0" }, "__new_primary_file_construct_gb|construct_4__": { "id": "d6de5bc932d51475", "src": "hda", "uuid": "e7c25803-f52c-4a42-8dc6-c9191701d749" }, "output_zip": { "id": "382e0b9a3dd586fb", "src": "hda", "uuid": "d929e00d-64fe-466c-820f-898fef1ddd39" } }, "params": { "__input_ext": "\"input\"", "adv": "{\"enzyme\": \"auto\", \"use_file_names_as_ids\": true}", "assembly_plan_name": "\"Type2sRestrictionAssembly\"", "chromInfo": "\"/tmp/tmp2jitj5ti/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, 2.12it/s, now=None]\rassembly: 75%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u258c | 3/4 [00:01<00:00, 2.02it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 4/4 [00:02<00:00, 1.70it/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, 2.12it/s, now=None]\rassembly: 75%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u258c | 3/4 [00:01<00:00, 2.02it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 4/4 [00:02<00:00, 1.70it/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": "2025-06-06T10:05:17.649698", "user_email": "planemo@galaxyproject.org", "user_id": "b685bcc6830b171b" }, "status": "success", "test_index": 0, "time_seconds": 56.74104905128479, "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": "d765718fb46383bd", "src": "hda" }, "assembly_plan_name": "GibsonAssembly", "genbank_files": { "id": "abbe1d9cd04428c7", "src": "hdca" }, "topology": "circular" }, "job": { "command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && cp '/tmp/tmp2jitj5ti/files/2/1/9/dataset_219d9b1e-e68c-4fb3-bcfe-e77aba638437.dat' 'assembly_csv.csv' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmp2jitj5ti/files/4/f/b/dataset_4fb22863-853c-4591-9c42-2bb9c71cf261.dat' --domesticated_seq '' --assembly_csv 'assembly_csv.csv' --assembly_plan_name 'GibsonAssembly' --file_name_mapping '/tmp/tmp2jitj5ti/files/4/f/b/dataset_4fb22863-853c-4591-9c42-2bb9c71cf261.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/tmp2jitj5ti/job_working_directory/000/17/outputs/dataset_a64ce795-3e43-4f34-aacf-aee1dd0b1f6e.dat'", "command_version": "", "copied_from_job_id": null, "create_time": "2025-06-06T10:05:28.808016", "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": "385227", "galaxy_version": "24.2", "handler": null, "history_id": "48e269c64ce4fce2", "id": "720f24a804e8d612", "inputs": { "assembly_csv": { "id": "d765718fb46383bd", "src": "hda", "uuid": "219d9b1e-e68c-4fb3-bcfe-e77aba638437" }, "genbank_files1": { "id": "131ab6d9a01aeed2", "src": "hda", "uuid": "4fb22863-853c-4591-9c42-2bb9c71cf261" } }, "job_messages": [], "job_metrics": [], "job_runner_name": null, "job_stderr": "", "job_stdout": "", "model_class": "Job", "output_collections": { "construct_gb": { "id": "b93fb7c1f8bf7b46", "src": "hdca" } }, "outputs": { "__new_primary_file_construct_gb|construct_1__": { "id": "140f14a546d19bc0", "src": "hda", "uuid": "00003b46-ce50-481a-9130-0ec3ae3b7897" }, "__new_primary_file_construct_gb|construct_2__": { "id": "2582d4726cd2a523", "src": "hda", "uuid": "1ac733ac-a271-491e-bd9e-24d18fff78bd" }, "__new_primary_file_construct_gb|construct_3__": { "id": "5e497037d2a37058", "src": "hda", "uuid": "70ddc686-3105-4962-93ca-511e60acfbcd" }, "output_zip": { "id": "26116ea06fd8375c", "src": "hda", "uuid": "a64ce795-3e43-4f34-aacf-aee1dd0b1f6e" } }, "params": { "__input_ext": "\"input\"", "adv": "{\"enzyme\": \"auto\", \"use_file_names_as_ids\": true}", "assembly_plan_name": "\"GibsonAssembly\"", "chromInfo": "\"/tmp/tmp2jitj5ti/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, 4.22it/s, now=None]\rassembly: 60%|\u2588\u2588\u2588\u2588\u2588\u2588 | 3/5 [00:00<00:00, 4.21it/s, now=None]\rassembly: 80%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588 | 4/5 [00:00<00:00, 4.21it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 5/5 [00:01<00:00, 3.48it/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, 4.22it/s, now=None]\rassembly: 60%|\u2588\u2588\u2588\u2588\u2588\u2588 | 3/5 [00:00<00:00, 4.21it/s, now=None]\rassembly: 80%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588 | 4/5 [00:00<00:00, 4.21it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 5/5 [00:01<00:00, 3.48it/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": "2025-06-06T10:05:41.041203", "user_email": "planemo@galaxyproject.org", "user_id": "b685bcc6830b171b" }, "status": "success", "test_index": 1, "time_seconds": 23.27797245979309, "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": "68f713b93b311e6b", "src": "hda" }, "assembly_plan_name": "LigaseCyclingReactionAssembly", "genbank_files": { "id": "45bf0c3ad4473005", "src": "hdca" }, "topology": "circular" }, "job": { "command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && cp '/tmp/tmp2jitj5ti/files/8/0/6/dataset_806117ae-d7a6-43e7-81c7-334a790a0d5e.dat' 'assembly_csv.csv' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmp2jitj5ti/files/c/c/e/dataset_cce9d6d4-372b-484c-9bf5-fe28e7899f4d.dat,/tmp/tmp2jitj5ti/files/c/8/e/dataset_c8e6cbdc-d108-4250-a1c5-1e88ee18d6d1.dat' --domesticated_seq '' --assembly_csv 'assembly_csv.csv' --assembly_plan_name 'LigaseCyclingReactionAssembly' --file_name_mapping '/tmp/tmp2jitj5ti/files/c/c/e/dataset_cce9d6d4-372b-484c-9bf5-fe28e7899f4d.dat:RFP_GFP_plasmid_BOs.fa,/tmp/tmp2jitj5ti/files/c/8/e/dataset_c8e6cbdc-d108-4250-a1c5-1e88ee18d6d1.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/tmp2jitj5ti/job_working_directory/000/21/outputs/dataset_b7f1e2f4-2ca8-443b-8476-c078a5b5f15f.dat'", "command_version": "", "copied_from_job_id": null, "create_time": "2025-06-06T10:05:53.421889", "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": "385648", "galaxy_version": "24.2", "handler": null, "history_id": "abbe1d9cd04428c7", "id": "26116ea06fd8375c", "inputs": { "assembly_csv": { "id": "68f713b93b311e6b", "src": "hda", "uuid": "806117ae-d7a6-43e7-81c7-334a790a0d5e" }, "genbank_files1": { "id": "9573dab05c8aede5", "src": "hda", "uuid": "cce9d6d4-372b-484c-9bf5-fe28e7899f4d" }, "genbank_files2": { "id": "9797c20d21b6409b", "src": "hda", "uuid": "c8e6cbdc-d108-4250-a1c5-1e88ee18d6d1" } }, "job_messages": [], "job_metrics": [], "job_runner_name": null, "job_stderr": "", "job_stdout": "", "model_class": "Job", "output_collections": { "construct_gb": { "id": "4efa4181abcbfe3f", "src": "hdca" } }, "outputs": { "output_zip": { "id": "37fc10922a844411", "src": "hda", "uuid": "b7f1e2f4-2ca8-443b-8476-c078a5b5f15f" } }, "params": { "__input_ext": "\"input\"", "adv": "{\"enzyme\": \"auto\", \"use_file_names_as_ids\": true}", "assembly_plan_name": "\"LigaseCyclingReactionAssembly\"", "chromInfo": "\"/tmp/tmp2jitj5ti/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, 2.30it/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, 2.30it/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": "2025-06-06T10:06:05.965130", "user_email": "planemo@galaxyproject.org", "user_id": "b685bcc6830b171b" }, "status": "success", "test_index": 2, "time_seconds": 24.72797989845276, "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": "a8e6431fd79f2b52", "src": "hda" }, "assembly_plan_name": "BASICAssembly", "genbank_files": { "id": "beb5db8871971f36", "src": "hdca" }, "topology": "circular" }, "job": { "command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && cp '/tmp/tmp2jitj5ti/files/a/8/a/dataset_a8ac250f-f914-442e-b1ba-8cad2b7be6c4.dat' 'assembly_csv.csv' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmp2jitj5ti/files/7/9/d/dataset_79d3620b-c739-4658-a206-77de935d7c60.dat,/tmp/tmp2jitj5ti/files/4/0/3/dataset_403e3d7a-5c6a-475b-9a3d-3c4472aa6a64.dat,/tmp/tmp2jitj5ti/files/5/2/c/dataset_52c35275-6fd5-4c5a-bf8a-a934f837b172.dat,/tmp/tmp2jitj5ti/files/0/4/d/dataset_04dbf80b-1125-481f-bf1c-ffec452c3c03.dat,/tmp/tmp2jitj5ti/files/2/2/2/dataset_222d6a4a-1e02-463b-8f83-1acac5decea9.dat' --domesticated_seq '' --assembly_csv 'assembly_csv.csv' --assembly_plan_name 'BASICAssembly' --file_name_mapping '/tmp/tmp2jitj5ti/files/7/9/d/dataset_79d3620b-c739-4658-a206-77de935d7c60.dat:GFP.gb,/tmp/tmp2jitj5ti/files/4/0/3/dataset_403e3d7a-5c6a-475b-9a3d-3c4472aa6a64.dat:p15A_kan.gb,/tmp/tmp2jitj5ti/files/5/2/c/dataset_52c35275-6fd5-4c5a-bf8a-a934f837b172.dat:promoter.gb,/tmp/tmp2jitj5ti/files/0/4/d/dataset_04dbf80b-1125-481f-bf1c-ffec452c3c03.dat:RFP.gb,/tmp/tmp2jitj5ti/files/2/2/2/dataset_222d6a4a-1e02-463b-8f83-1acac5decea9.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/tmp2jitj5ti/job_working_directory/000/28/outputs/dataset_bd5f0d5e-6a92-4182-b21d-0835394ab658.dat'", "command_version": "", "copied_from_job_id": null, "create_time": "2025-06-06T10:06:28.456243", "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": "386275", "galaxy_version": "24.2", "handler": null, "history_id": "b93fb7c1f8bf7b46", "id": "37fc10922a844411", "inputs": { "assembly_csv": { "id": "a8e6431fd79f2b52", "src": "hda", "uuid": "a8ac250f-f914-442e-b1ba-8cad2b7be6c4" }, "genbank_files1": { "id": "a018d9b816e95d65", "src": "hda", "uuid": "79d3620b-c739-4658-a206-77de935d7c60" }, "genbank_files2": { "id": "e681bc44c9405e4c", "src": "hda", "uuid": "403e3d7a-5c6a-475b-9a3d-3c4472aa6a64" }, "genbank_files3": { "id": "b64509f9b279aeab", "src": "hda", "uuid": "52c35275-6fd5-4c5a-bf8a-a934f837b172" }, "genbank_files4": { "id": "0cded9ae6d76e247", "src": "hda", "uuid": "04dbf80b-1125-481f-bf1c-ffec452c3c03" }, "genbank_files5": { "id": "e7ab3f008685294c", "src": "hda", "uuid": "222d6a4a-1e02-463b-8f83-1acac5decea9" } }, "job_messages": [], "job_metrics": [], "job_runner_name": null, "job_stderr": "", "job_stdout": "", "model_class": "Job", "output_collections": { "construct_gb": { "id": "bc095eef87c18a70", "src": "hdca" } }, "outputs": { "output_zip": { "id": "d2ea46ccc79974d1", "src": "hda", "uuid": "bd5f0d5e-6a92-4182-b21d-0835394ab658" } }, "params": { "__input_ext": "\"input\"", "adv": "{\"enzyme\": \"auto\", \"use_file_names_as_ids\": true}", "assembly_plan_name": "\"BASICAssembly\"", "chromInfo": "\"/tmp/tmp2jitj5ti/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, 47.57it/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, 47.57it/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": "2025-06-06T10:06:39.681856", "user_email": "planemo@galaxyproject.org", "user_id": "b685bcc6830b171b" }, "status": "success", "test_index": 3, "time_seconds": 33.660860538482666, "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": "870b7dd1dbdb30fc", "src": "hda" }, "assembly_plan_name": "BioBrickStandardAssembly", "genbank_files": { "id": "9f6ba43f26fd6d3f", "src": "hdca" }, "topology": "circular" }, "job": { "command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && cp '/tmp/tmp2jitj5ti/files/2/d/8/dataset_2d854388-fb71-4200-9b83-2ce86dc98358.dat' 'assembly_csv.csv' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmp2jitj5ti/files/5/7/3/dataset_57391f80-f9db-4df5-b819-da6d762aece4.dat,/tmp/tmp2jitj5ti/files/3/d/f/dataset_3df8cee0-18b2-40ae-9075-7f585f82e90e.dat,/tmp/tmp2jitj5ti/files/4/3/2/dataset_4322df44-7abe-4c76-9d5f-2c19d97a9117.dat,/tmp/tmp2jitj5ti/files/6/7/1/dataset_67150b86-6b40-4e07-9809-31e5e59ab2f5.dat,/tmp/tmp2jitj5ti/files/4/2/1/dataset_421ffb55-adfd-4e9b-a5cc-8144862c99e4.dat' --domesticated_seq '' --assembly_csv 'assembly_csv.csv' --assembly_plan_name 'BioBrickStandardAssembly' --file_name_mapping '/tmp/tmp2jitj5ti/files/5/7/3/dataset_57391f80-f9db-4df5-b819-da6d762aece4.dat:BBa_E0040_GFP.gb,/tmp/tmp2jitj5ti/files/3/d/f/dataset_3df8cee0-18b2-40ae-9075-7f585f82e90e.dat:BBa_J23119_prom.gb,/tmp/tmp2jitj5ti/files/4/3/2/dataset_4322df44-7abe-4c76-9d5f-2c19d97a9117.dat:BBa_J23119_prom_flawed.gb,/tmp/tmp2jitj5ti/files/6/7/1/dataset_67150b86-6b40-4e07-9809-31e5e59ab2f5.dat:BBa_J61048_term.gb,/tmp/tmp2jitj5ti/files/4/2/1/dataset_421ffb55-adfd-4e9b-a5cc-8144862c99e4.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/tmp2jitj5ti/job_working_directory/000/35/outputs/dataset_7b0034ef-60d7-4a10-b78c-75301b71c879.dat'", "command_version": "", "copied_from_job_id": null, "create_time": "2025-06-06T10:07:01.286437", "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": "386883", "galaxy_version": "24.2", "handler": null, "history_id": "45bf0c3ad4473005", "id": "d2ea46ccc79974d1", "inputs": { "assembly_csv": { "id": "870b7dd1dbdb30fc", "src": "hda", "uuid": "2d854388-fb71-4200-9b83-2ce86dc98358" }, "genbank_files1": { "id": "5d242fab331df92f", "src": "hda", "uuid": "57391f80-f9db-4df5-b819-da6d762aece4" }, "genbank_files2": { "id": "bdeadb8314ea6602", "src": "hda", "uuid": "3df8cee0-18b2-40ae-9075-7f585f82e90e" }, "genbank_files3": { "id": "4b1f0f6cb8a7a593", "src": "hda", "uuid": "4322df44-7abe-4c76-9d5f-2c19d97a9117" }, "genbank_files4": { "id": "1cbd0a844497b2d5", "src": "hda", "uuid": "67150b86-6b40-4e07-9809-31e5e59ab2f5" }, "genbank_files5": { "id": "cd6794c2fc579376", "src": "hda", "uuid": "421ffb55-adfd-4e9b-a5cc-8144862c99e4" } }, "job_messages": [], "job_metrics": [], "job_runner_name": null, "job_stderr": "", "job_stdout": "", "model_class": "Job", "output_collections": { "construct_gb": { "id": "07723b52981231a1", "src": "hdca" } }, "outputs": { "__new_primary_file_construct_gb|C1_prom_barcode__": { "id": "a3d311637d661498", "src": "hda", "uuid": "32cddc11-8c27-4a46-86da-29c2a2b43b49" }, "__new_primary_file_construct_gb|C2_gfp_term__": { "id": "c9508541650f65fa", "src": "hda", "uuid": "b8457751-97a9-4b80-8ce4-987e02aadef4" }, "__new_primary_file_construct_gb|C3_final__": { "id": "2dd6c8d9ce5577ac", "src": "hda", "uuid": "467a54f1-7fa8-48d3-b4f9-253d52e75241" }, "output_zip": { "id": "59f530fda97252d9", "src": "hda", "uuid": "7b0034ef-60d7-4a10-b78c-75301b71c879" } }, "params": { "__input_ext": "\"input\"", "adv": "{\"enzyme\": \"auto\", \"use_file_names_as_ids\": true}", "assembly_plan_name": "\"BioBrickStandardAssembly\"", "chromInfo": "\"/tmp/tmp2jitj5ti/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, 1.86it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 3/3 [00:01<00:00, 1.53it/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, 1.86it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 3/3 [00:01<00:00, 1.53it/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": "2025-06-06T10:07:15.132596", "user_email": "planemo@galaxyproject.org", "user_id": "b685bcc6830b171b" }, "status": "success", "test_index": 4, "time_seconds": 35.4639618396759, "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": "b6eaafbbca788aef", "src": "hda" }, "assembly_plan_name": "Type2sRestrictionAssembly", "domesticated_input": { "id": "830f955cbdf9a561", "src": "hdca" }, "genbank_files": { "id": "71dab170b139725e", "src": "hdca" }, "topology": "circular" }, "job": { "command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && cp '/tmp/tmp2jitj5ti/files/9/d/9/dataset_9d9d9de0-0ef0-45b2-a122-cf3a6b4ad650.dat' 'assembly_csv.csv' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmp2jitj5ti/files/8/3/7/dataset_837c1c85-f287-41c8-9851-10dfb88a9fce.dat,/tmp/tmp2jitj5ti/files/0/9/8/dataset_098eeccf-1536-4ae9-b4ab-e0dfb2b8d0ea.dat,/tmp/tmp2jitj5ti/files/9/6/0/dataset_9607dfc5-cbbf-4445-b2f0-ad0e6b29415c.dat,/tmp/tmp2jitj5ti/files/d/3/3/dataset_d337288e-d007-49d9-a3f0-5ddc75b8c1a7.dat,/tmp/tmp2jitj5ti/files/3/f/0/dataset_3f0b935c-0a99-4d65-9f9e-67077025d92d.dat,/tmp/tmp2jitj5ti/files/5/5/e/dataset_55e788cd-b786-481d-81b3-366b2ca66346.dat,/tmp/tmp2jitj5ti/files/b/2/7/dataset_b275d8fc-8961-49f8-9829-8afe0fb272f6.dat' --domesticated_seq '/tmp/tmp2jitj5ti/files/5/3/a/dataset_53aaa086-f9d0-4702-9104-e1129b9478f5.dat,/tmp/tmp2jitj5ti/files/9/8/3/dataset_98347337-70cf-49bc-a520-7ce28dba7552.dat,/tmp/tmp2jitj5ti/files/4/5/f/dataset_45f979d2-11d9-4eed-81cd-775c9592d31a.dat,/tmp/tmp2jitj5ti/files/3/b/0/dataset_3b0d27f7-3a16-4662-b26b-8fbef1641a3b.dat,/tmp/tmp2jitj5ti/files/0/f/3/dataset_0f35d30e-174f-4177-8881-a8d0e2e56e97.dat' --assembly_csv 'assembly_csv.csv' --assembly_plan_name 'Type2sRestrictionAssembly' --file_name_mapping '/tmp/tmp2jitj5ti/files/8/3/7/dataset_837c1c85-f287-41c8-9851-10dfb88a9fce.dat:part_A.gb,/tmp/tmp2jitj5ti/files/0/9/8/dataset_098eeccf-1536-4ae9-b4ab-e0dfb2b8d0ea.dat:part_B.gb,/tmp/tmp2jitj5ti/files/9/6/0/dataset_9607dfc5-cbbf-4445-b2f0-ad0e6b29415c.dat:part_C.gb,/tmp/tmp2jitj5ti/files/d/3/3/dataset_d337288e-d007-49d9-a3f0-5ddc75b8c1a7.dat:part_D.gb,/tmp/tmp2jitj5ti/files/3/f/0/dataset_3f0b935c-0a99-4d65-9f9e-67077025d92d.dat:part_E.gb,/tmp/tmp2jitj5ti/files/5/5/e/dataset_55e788cd-b786-481d-81b3-366b2ca66346.dat:part_F.gb,/tmp/tmp2jitj5ti/files/b/2/7/dataset_b275d8fc-8961-49f8-9829-8afe0fb272f6.dat:part_G.gb' --file_name_mapping_dom '/tmp/tmp2jitj5ti/files/5/3/a/dataset_53aaa086-f9d0-4702-9104-e1129b9478f5.dat:part_H.gb,/tmp/tmp2jitj5ti/files/9/8/3/dataset_98347337-70cf-49bc-a520-7ce28dba7552.dat:part_I.gb,/tmp/tmp2jitj5ti/files/4/5/f/dataset_45f979d2-11d9-4eed-81cd-775c9592d31a.dat:part_J.gb,/tmp/tmp2jitj5ti/files/3/b/0/dataset_3b0d27f7-3a16-4662-b26b-8fbef1641a3b.dat:part_K.gb,/tmp/tmp2jitj5ti/files/0/f/3/dataset_0f35d30e-174f-4177-8881-a8d0e2e56e97.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/tmp2jitj5ti/job_working_directory/000/49/outputs/dataset_d76108d3-5679-4105-8d35-0311a40cc2bb.dat'", "command_version": "", "copied_from_job_id": null, "create_time": "2025-06-06T10:07:58.337850", "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": "388721", "galaxy_version": "24.2", "handler": null, "history_id": "4efa4181abcbfe3f", "id": "247764bf93430d44", "inputs": { "assembly_csv": { "id": "b6eaafbbca788aef", "src": "hda", "uuid": "9d9d9de0-0ef0-45b2-a122-cf3a6b4ad650" }, "domesticated_input1": { "id": "a1189164982cb43d", "src": "hda", "uuid": "53aaa086-f9d0-4702-9104-e1129b9478f5" }, "domesticated_input2": { "id": "44989d335db736e0", "src": "hda", "uuid": "98347337-70cf-49bc-a520-7ce28dba7552" }, "domesticated_input3": { "id": "03cca6cadcbcac8e", "src": "hda", "uuid": "45f979d2-11d9-4eed-81cd-775c9592d31a" }, "domesticated_input4": { "id": "d642fe61dbbb1956", "src": "hda", "uuid": "3b0d27f7-3a16-4662-b26b-8fbef1641a3b" }, "domesticated_input5": { "id": "0db781d633f10d33", "src": "hda", "uuid": "0f35d30e-174f-4177-8881-a8d0e2e56e97" }, "genbank_files1": { "id": "cf3cf117b1fd29b8", "src": "hda", "uuid": "837c1c85-f287-41c8-9851-10dfb88a9fce" }, "genbank_files2": { "id": "d4b38da3c0d76cb5", "src": "hda", "uuid": "098eeccf-1536-4ae9-b4ab-e0dfb2b8d0ea" }, "genbank_files3": { "id": "2ca78c9590a534f7", "src": "hda", "uuid": "9607dfc5-cbbf-4445-b2f0-ad0e6b29415c" }, "genbank_files4": { "id": "247764bf93430d44", "src": "hda", "uuid": "d337288e-d007-49d9-a3f0-5ddc75b8c1a7" }, "genbank_files5": { "id": "463014d955d5fd42", "src": "hda", "uuid": "3f0b935c-0a99-4d65-9f9e-67077025d92d" }, "genbank_files6": { "id": "a4df66e73e6d9e95", "src": "hda", "uuid": "55e788cd-b786-481d-81b3-366b2ca66346" }, "genbank_files7": { "id": "913dff628ac44951", "src": "hda", "uuid": "b275d8fc-8961-49f8-9829-8afe0fb272f6" } }, "job_messages": [], "job_metrics": [], "job_runner_name": null, "job_stderr": "", "job_stdout": "", "model_class": "Job", "output_collections": { "construct_gb": { "id": "5251f3a41a1cbe5c", "src": "hdca" } }, "outputs": { "__new_primary_file_construct_gb|construct_1__": { "id": "a392596aa79c7e90", "src": "hda", "uuid": "5b1744ae-2358-4704-963c-ae095d2865b9" }, "__new_primary_file_construct_gb|construct_2__": { "id": "f3fa25c91edfe6df", "src": "hda", "uuid": "b1f5b359-a374-4545-bb66-c00344cfca68" }, "__new_primary_file_construct_gb|construct_3__": { "id": "706ccd94442462f8", "src": "hda", "uuid": "691b1282-afae-46f8-8741-4314f28c3613" }, "__new_primary_file_construct_gb|construct_4__": { "id": "ebae0af133eaa0bc", "src": "hda", "uuid": "48ad1713-0702-4178-81bd-20cb2d09349e" }, "output_zip": { "id": "d0372853ed459b21", "src": "hda", "uuid": "d76108d3-5679-4105-8d35-0311a40cc2bb" } }, "params": { "__input_ext": "\"input\"", "adv": "{\"enzyme\": \"auto\", \"use_file_names_as_ids\": true}", "assembly_plan_name": "\"Type2sRestrictionAssembly\"", "chromInfo": "\"/tmp/tmp2jitj5ti/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", "dbkey": "\"?\"", "domesticated_input": "{\"values\": [{\"id\": 11, \"src\": \"hdca\"}]}", "genbank_files": "{\"values\": [{\"id\": 12, \"src\": \"hdca\"}]}", "topology": "\"circular\"" }, "state": "ok", "stderr": "\rassembly: 0%| | 0/4 [00:00<?, ?it/s, now=None]\r \r\rassembly: 0%| | 0/4 [00:00<?, ?it/s, now=None]\rassembly: 50%|\u2588\u2588\u2588\u2588\u2588 | 2/4 [00:00<00:00, 2.42it/s, now=None]\rassembly: 75%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u258c | 3/4 [00:01<00:00, 2.15it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 4/4 [00:02<00:00, 1.75it/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, 2.42it/s, now=None]\rassembly: 75%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u258c | 3/4 [00:01<00:00, 2.15it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 4/4 [00:02<00:00, 1.75it/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": "2025-06-06T10:08:11.535478", "user_email": "planemo@galaxyproject.org", "user_id": "b685bcc6830b171b" }, "status": "success", "test_index": 5, "time_seconds": 56.084434032440186, "tool_id": "cloning_simulation", "tool_version": "0.1.0+galaxy0" }, "has_data": true, "id": "cloning_simulation-5" }, { "data": { "inputs": { "adv|use_file_names_as_ids": true, "assembly_csv": { "id": "85e42f4d247fa0dd", "src": "hda" }, "assembly_plan_name": "Type2sRestrictionAssembly", "domesticated_input": { "id": "382e0b9a3dd586fb", "src": "hdca" }, "topology": "circular" }, "job": { "command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && cp '/tmp/tmp2jitj5ti/files/4/f/5/dataset_4f53254a-8cbc-44ed-b07f-51c7b0ba70bf.dat' 'assembly_csv.csv' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmp2jitj5ti/files/0/3/4/dataset_03437b47-00b6-420f-a71d-dc13cfa4420f.dat,/tmp/tmp2jitj5ti/files/7/3/0/dataset_7302922c-3802-4ec1-8fa6-2aeda8c3f773.dat,/tmp/tmp2jitj5ti/files/4/3/f/dataset_43f8a937-90f1-4ca8-9e1e-ffd4d438b8e3.dat,/tmp/tmp2jitj5ti/files/2/d/a/dataset_2da8d496-7007-408f-8f0d-9bb1bfc6cc89.dat,/tmp/tmp2jitj5ti/files/7/7/e/dataset_77e28f02-e173-4f1b-aa95-ab810151814c.dat,/tmp/tmp2jitj5ti/files/1/d/b/dataset_1db54aac-485c-43e5-b88e-78727df8f24d.dat,/tmp/tmp2jitj5ti/files/e/6/c/dataset_e6c10e1b-4881-49ef-b382-70333c02a312.dat,/tmp/tmp2jitj5ti/files/2/a/7/dataset_2a714c72-017a-4719-b5f6-7258096c4db6.dat,/tmp/tmp2jitj5ti/files/f/5/6/dataset_f56927c8-9d8a-44fc-a5b3-7929dfc14349.dat,/tmp/tmp2jitj5ti/files/7/9/0/dataset_7902eea5-11c6-4d21-950e-e4f1217a3efb.dat,/tmp/tmp2jitj5ti/files/4/9/3/dataset_493c970b-5c95-4af6-afb2-091bbfcad2fb.dat,/tmp/tmp2jitj5ti/files/3/2/a/dataset_32ae37e3-7d24-411c-8633-c253860693e3.dat' --domesticated_seq '' --assembly_csv 'assembly_csv.csv' --assembly_plan_name 'Type2sRestrictionAssembly' --file_name_mapping '/tmp/tmp2jitj5ti/files/0/3/4/dataset_03437b47-00b6-420f-a71d-dc13cfa4420f.dat:part_A.gb,/tmp/tmp2jitj5ti/files/7/3/0/dataset_7302922c-3802-4ec1-8fa6-2aeda8c3f773.dat:part_B.gb,/tmp/tmp2jitj5ti/files/4/3/f/dataset_43f8a937-90f1-4ca8-9e1e-ffd4d438b8e3.dat:part_C.gb,/tmp/tmp2jitj5ti/files/2/d/a/dataset_2da8d496-7007-408f-8f0d-9bb1bfc6cc89.dat:part_D.gb,/tmp/tmp2jitj5ti/files/7/7/e/dataset_77e28f02-e173-4f1b-aa95-ab810151814c.dat:part_E.gb,/tmp/tmp2jitj5ti/files/1/d/b/dataset_1db54aac-485c-43e5-b88e-78727df8f24d.dat:part_F.gb,/tmp/tmp2jitj5ti/files/e/6/c/dataset_e6c10e1b-4881-49ef-b382-70333c02a312.dat:part_G.gb,/tmp/tmp2jitj5ti/files/2/a/7/dataset_2a714c72-017a-4719-b5f6-7258096c4db6.dat:part_H.gb,/tmp/tmp2jitj5ti/files/f/5/6/dataset_f56927c8-9d8a-44fc-a5b3-7929dfc14349.dat:part_I.gb,/tmp/tmp2jitj5ti/files/7/9/0/dataset_7902eea5-11c6-4d21-950e-e4f1217a3efb.dat:part_J.gb,/tmp/tmp2jitj5ti/files/4/9/3/dataset_493c970b-5c95-4af6-afb2-091bbfcad2fb.dat:part_K.gb,/tmp/tmp2jitj5ti/files/3/2/a/dataset_32ae37e3-7d24-411c-8633-c253860693e3.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/tmp2jitj5ti/job_working_directory/000/63/outputs/dataset_0d841edc-5cb0-451d-807c-1e38179edf75.dat'", "command_version": "", "copied_from_job_id": null, "create_time": "2025-06-06T10:08:55.121816", "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": "390797", "galaxy_version": "24.2", "handler": null, "history_id": "beb5db8871971f36", "id": "ebae0af133eaa0bc", "inputs": { "assembly_csv": { "id": "85e42f4d247fa0dd", "src": "hda", "uuid": "4f53254a-8cbc-44ed-b07f-51c7b0ba70bf" }, "domesticated_input1": { "id": "432a266b74c649c8", "src": "hda", "uuid": "03437b47-00b6-420f-a71d-dc13cfa4420f" }, "domesticated_input10": { "id": "e3d9dfc153bf32e3", "src": "hda", 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"output_zip": { "id": "46d30791dc86792c", "src": "hda", "uuid": "0d841edc-5cb0-451d-807c-1e38179edf75" } }, "params": { "__input_ext": "\"input\"", "adv": "{\"enzyme\": \"auto\", \"use_file_names_as_ids\": true}", "assembly_plan_name": "\"Type2sRestrictionAssembly\"", "chromInfo": "\"/tmp/tmp2jitj5ti/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", "dbkey": "\"?\"", "domesticated_input": "{\"values\": [{\"id\": 14, \"src\": \"hdca\"}]}", "genbank_files": null, "topology": "\"circular\"" }, "state": "ok", "stderr": "\rassembly: 0%| | 0/4 [00:00<?, ?it/s, now=None]\r \r\rassembly: 0%| | 0/4 [00:00<?, ?it/s, now=None]\rassembly: 50%|\u2588\u2588\u2588\u2588\u2588 | 2/4 [00:00<00:00, 2.35it/s, now=None]\rassembly: 75%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u258c | 3/4 [00:01<00:00, 2.16it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 4/4 [00:02<00:00, 1.76it/s, now=None]\r \r", "stdout": "Simulating assembly plan assambly...\n{'cancelled_assemblies': 0, 'errored_assemblies': 0, 'valid_assemblies': 4}\nGenerating assemblies reports...\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, 2.35it/s, now=None]\rassembly: 75%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u258c | 3/4 [00:01<00:00, 2.16it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 4/4 [00:02<00:00, 1.76it/s, now=None]\r \r", "tool_stdout": "Simulating assembly plan assambly...\n{'cancelled_assemblies': 0, 'errored_assemblies': 0, 'valid_assemblies': 4}\nGenerating assemblies reports...\n", "update_time": "2025-06-06T10:09:07.953690", "user_email": "planemo@galaxyproject.org", "user_id": "b685bcc6830b171b" }, "status": "success", "test_index": 6, "time_seconds": 56.49321532249451, "tool_id": "cloning_simulation", "tool_version": "0.1.0+galaxy0" }, "has_data": true, "id": "cloning_simulation-6" } ], "version": "0.1" }