Mercurial > repos > tduigou > cloning_simulation
diff output.json @ 6:e1e985913204 draft
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
| author | tduigou |
|---|---|
| date | Wed, 21 May 2025 14:53:05 +0000 |
| parents | 254d284a5be9 |
| children | 296e5145a862 |
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--- a/output.json Mon May 19 14:14:18 2025 +0000 +++ b/output.json Wed May 21 14:53:05 2025 +0000 @@ -1,9 +1,9 @@ { "summary": { "num_errors": 0, - "num_failures": 0, + "num_failures": 1, "num_skips": 0, - "num_tests": 6 + "num_tests": 7 }, "tests": [ { @@ -11,93 +11,93 @@ "inputs": { "adv|use_file_names_as_ids": true, "assembly_csv": { - "id": "40769e0726e5d2f9", + "id": "acd1a5e1ec1673bf", "src": "hda" }, "assembly_plan_name": "Type2sRestrictionAssembly", "genbank_files": { - "id": "fd8809ceca5b90d8", + "id": "9f2c11a06c2c8bb2", "src": "hdca" }, "topology": "circular" }, "job": { - "command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmpay0tme4v/files/4/b/3/dataset_4b32c6a8-b39d-4f5f-9155-307e142d9193.dat,/tmp/tmpay0tme4v/files/8/e/f/dataset_8ef181dd-5c3a-40eb-9926-3738e1ae4be1.dat,/tmp/tmpay0tme4v/files/b/a/b/dataset_babba200-2afd-434f-8797-9b10cc736ba7.dat,/tmp/tmpay0tme4v/files/b/7/c/dataset_b7c5a88c-05ae-4efd-9887-47a899749178.dat,/tmp/tmpay0tme4v/files/7/f/e/dataset_7fea4ecf-be56-423d-8a11-d6491077e233.dat,/tmp/tmpay0tme4v/files/e/1/f/dataset_e1f9ab9e-c9e0-4acd-ac63-e4299c3792fe.dat,/tmp/tmpay0tme4v/files/f/0/f/dataset_f0fe046c-6132-4bb9-b5dc-521edead32f2.dat,/tmp/tmpay0tme4v/files/e/e/c/dataset_eec197e7-d8fa-4c45-b5cb-89e51ee1db0e.dat,/tmp/tmpay0tme4v/files/3/2/1/dataset_32124f40-ed9b-4d25-b74f-a4ff44581962.dat,/tmp/tmpay0tme4v/files/e/1/2/dataset_e126fe05-d77c-4b33-9782-e5b1e7e6c7ad.dat,/tmp/tmpay0tme4v/files/2/3/4/dataset_234f9855-813e-4297-bbd4-d1327fb0cbad.dat,/tmp/tmpay0tme4v/files/6/b/2/dataset_6b23e127-e4a2-41b6-98f3-4f8f7214b209.dat' --domesticated_seq '' --assembly_csv '/tmp/tmpay0tme4v/files/1/4/6/dataset_14645e90-9105-48af-a071-6ea052fd4aad.dat' --assembly_plan_name 'Type2sRestrictionAssembly' --file_name_mapping '/tmp/tmpay0tme4v/files/4/b/3/dataset_4b32c6a8-b39d-4f5f-9155-307e142d9193.dat:part_A.gb,/tmp/tmpay0tme4v/files/8/e/f/dataset_8ef181dd-5c3a-40eb-9926-3738e1ae4be1.dat:part_B.gb,/tmp/tmpay0tme4v/files/b/a/b/dataset_babba200-2afd-434f-8797-9b10cc736ba7.dat:part_C.gb,/tmp/tmpay0tme4v/files/b/7/c/dataset_b7c5a88c-05ae-4efd-9887-47a899749178.dat:part_D.gb,/tmp/tmpay0tme4v/files/7/f/e/dataset_7fea4ecf-be56-423d-8a11-d6491077e233.dat:part_E.gb,/tmp/tmpay0tme4v/files/e/1/f/dataset_e1f9ab9e-c9e0-4acd-ac63-e4299c3792fe.dat:part_F.gb,/tmp/tmpay0tme4v/files/f/0/f/dataset_f0fe046c-6132-4bb9-b5dc-521edead32f2.dat:part_G.gb,/tmp/tmpay0tme4v/files/e/e/c/dataset_eec197e7-d8fa-4c45-b5cb-89e51ee1db0e.dat:part_H.gb,/tmp/tmpay0tme4v/files/3/2/1/dataset_32124f40-ed9b-4d25-b74f-a4ff44581962.dat:part_I.gb,/tmp/tmpay0tme4v/files/e/1/2/dataset_e126fe05-d77c-4b33-9782-e5b1e7e6c7ad.dat:part_J.gb,/tmp/tmpay0tme4v/files/2/3/4/dataset_234f9855-813e-4297-bbd4-d1327fb0cbad.dat:part_K.gb,/tmp/tmpay0tme4v/files/6/b/2/dataset_6b23e127-e4a2-41b6-98f3-4f8f7214b209.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/tmpay0tme4v/job_working_directory/000/14/outputs/dataset_f30d906d-2ea4-4cde-b451-b7c6daf25a29.dat'", + "command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && cp '/tmp/tmpo3npfzdk/files/a/5/7/dataset_a579429e-eabf-48bf-8baa-4b54e340af46.dat' 'assembly_csv.csv' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmpo3npfzdk/files/e/8/6/dataset_e86ad306-6960-4dec-80fb-023fa6da5227.dat,/tmp/tmpo3npfzdk/files/d/3/4/dataset_d340b2ee-f061-4028-8e61-c384afc4678a.dat,/tmp/tmpo3npfzdk/files/1/9/5/dataset_19569676-42b8-47f6-bb6d-fd8658cd6a37.dat,/tmp/tmpo3npfzdk/files/0/5/a/dataset_05a63af0-f9a3-42f0-8ba8-74359301395e.dat,/tmp/tmpo3npfzdk/files/c/6/3/dataset_c636704b-8f2a-4cb6-9b8c-17214dadb08d.dat,/tmp/tmpo3npfzdk/files/8/5/5/dataset_855d9062-afe1-48b7-a1e9-a499536155aa.dat,/tmp/tmpo3npfzdk/files/e/3/7/dataset_e37509ff-8016-49ce-a9ca-fb066a5b6be6.dat,/tmp/tmpo3npfzdk/files/e/d/d/dataset_edde499a-6247-4874-8ef6-921fa7d311b6.dat,/tmp/tmpo3npfzdk/files/6/6/c/dataset_66c4decf-8469-4302-8957-320e236c7ee7.dat,/tmp/tmpo3npfzdk/files/0/f/e/dataset_0fe1772a-d8b1-4b91-aee0-1a6d1577590e.dat,/tmp/tmpo3npfzdk/files/c/1/a/dataset_c1aa9b56-f155-44af-8af5-1997f3ae48a7.dat,/tmp/tmpo3npfzdk/files/2/7/1/dataset_27148f5e-d3f0-45b9-a5f6-90d12767b2af.dat' --domesticated_seq '' --assembly_csv 'assembly_csv.csv' --assembly_plan_name 'Type2sRestrictionAssembly' --file_name_mapping '/tmp/tmpo3npfzdk/files/e/8/6/dataset_e86ad306-6960-4dec-80fb-023fa6da5227.dat:part_A.gb,/tmp/tmpo3npfzdk/files/d/3/4/dataset_d340b2ee-f061-4028-8e61-c384afc4678a.dat:part_B.gb,/tmp/tmpo3npfzdk/files/1/9/5/dataset_19569676-42b8-47f6-bb6d-fd8658cd6a37.dat:part_C.gb,/tmp/tmpo3npfzdk/files/0/5/a/dataset_05a63af0-f9a3-42f0-8ba8-74359301395e.dat:part_D.gb,/tmp/tmpo3npfzdk/files/c/6/3/dataset_c636704b-8f2a-4cb6-9b8c-17214dadb08d.dat:part_E.gb,/tmp/tmpo3npfzdk/files/8/5/5/dataset_855d9062-afe1-48b7-a1e9-a499536155aa.dat:part_F.gb,/tmp/tmpo3npfzdk/files/e/3/7/dataset_e37509ff-8016-49ce-a9ca-fb066a5b6be6.dat:part_G.gb,/tmp/tmpo3npfzdk/files/e/d/d/dataset_edde499a-6247-4874-8ef6-921fa7d311b6.dat:part_H.gb,/tmp/tmpo3npfzdk/files/6/6/c/dataset_66c4decf-8469-4302-8957-320e236c7ee7.dat:part_I.gb,/tmp/tmpo3npfzdk/files/0/f/e/dataset_0fe1772a-d8b1-4b91-aee0-1a6d1577590e.dat:part_J.gb,/tmp/tmpo3npfzdk/files/c/1/a/dataset_c1aa9b56-f155-44af-8af5-1997f3ae48a7.dat:part_K.gb,/tmp/tmpo3npfzdk/files/2/7/1/dataset_27148f5e-d3f0-45b9-a5f6-90d12767b2af.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/tmpo3npfzdk/job_working_directory/000/14/outputs/dataset_d4a3a824-aae9-4493-811d-77a8abd69905.dat'", "command_version": "", "copied_from_job_id": null, - "create_time": "2025-05-19T13:45:01.696419", + "create_time": "2025-05-21T14:47:30.360925", "dependencies": [], "exit_code": 0, - "external_id": "245391", + "external_id": "317822", "galaxy_version": "24.2", "handler": null, - "history_id": "fd8809ceca5b90d8", - "id": "d25964a649f0fc81", + "history_id": "9f2c11a06c2c8bb2", + "id": "18479e206f3c823f", "inputs": { "assembly_csv": { - "id": "40769e0726e5d2f9", + "id": "acd1a5e1ec1673bf", "src": "hda", - "uuid": "14645e90-9105-48af-a071-6ea052fd4aad" + "uuid": "a579429e-eabf-48bf-8baa-4b54e340af46" }, "genbank_files1": { - "id": "fd8809ceca5b90d8", + "id": "9f2c11a06c2c8bb2", "src": "hda", - "uuid": "4b32c6a8-b39d-4f5f-9155-307e142d9193" + "uuid": "e86ad306-6960-4dec-80fb-023fa6da5227" }, "genbank_files10": { - "id": "171b3bd3b2ffa75e", + "id": "d905212b22d14b29", "src": "hda", - "uuid": "e126fe05-d77c-4b33-9782-e5b1e7e6c7ad" + "uuid": "0fe1772a-d8b1-4b91-aee0-1a6d1577590e" }, "genbank_files11": { - "id": "ec7f951857c74506", + "id": "64a027171405da09", "src": "hda", - "uuid": "234f9855-813e-4297-bbd4-d1327fb0cbad" + "uuid": "c1aa9b56-f155-44af-8af5-1997f3ae48a7" }, "genbank_files12": { - "id": "8c74660869d2dd19", + "id": "f3ab5b94869b932e", "src": "hda", - "uuid": "6b23e127-e4a2-41b6-98f3-4f8f7214b209" + "uuid": "27148f5e-d3f0-45b9-a5f6-90d12767b2af" }, "genbank_files2": { - "id": "132b871e5e3014ee", + "id": "edba41b605a9f854", "src": "hda", - "uuid": "8ef181dd-5c3a-40eb-9926-3738e1ae4be1" + "uuid": "d340b2ee-f061-4028-8e61-c384afc4678a" }, "genbank_files3": { - "id": "65f48584dd2a1828", + "id": "b1906c2e1f5de664", "src": "hda", - "uuid": "babba200-2afd-434f-8797-9b10cc736ba7" + "uuid": "19569676-42b8-47f6-bb6d-fd8658cd6a37" }, "genbank_files4": { - "id": "543bb64c618cca80", + "id": "d28b58e6679c5691", "src": "hda", - "uuid": "b7c5a88c-05ae-4efd-9887-47a899749178" + "uuid": "05a63af0-f9a3-42f0-8ba8-74359301395e" }, "genbank_files5": { - "id": "e550d863bf084702", + "id": "39de46ba349dfcbe", "src": "hda", - "uuid": "7fea4ecf-be56-423d-8a11-d6491077e233" + "uuid": "c636704b-8f2a-4cb6-9b8c-17214dadb08d" }, "genbank_files6": { - "id": "6a73e15df176b356", + "id": "d10d7a9bf6c42600", "src": "hda", - "uuid": "e1f9ab9e-c9e0-4acd-ac63-e4299c3792fe" + "uuid": "855d9062-afe1-48b7-a1e9-a499536155aa" }, "genbank_files7": { - "id": "7faba24a30f85c9d", + "id": "6f2e93d50b248cee", "src": "hda", - "uuid": "f0fe046c-6132-4bb9-b5dc-521edead32f2" + "uuid": "e37509ff-8016-49ce-a9ca-fb066a5b6be6" }, "genbank_files8": { - "id": "f121a1ae40e58e96", + "id": "00a7ec1d542ff3f2", "src": "hda", - "uuid": "eec197e7-d8fa-4c45-b5cb-89e51ee1db0e" + "uuid": "edde499a-6247-4874-8ef6-921fa7d311b6" }, "genbank_files9": { - "id": "fc2d53421d7989de", + "id": "39eaa2809c3cd4cb", "src": "hda", - "uuid": "32124f40-ed9b-4d25-b74f-a4ff44581962" + "uuid": "66c4decf-8469-4302-8957-320e236c7ee7" } }, "job_messages": [], @@ -108,60 +108,60 @@ "model_class": "Job", "output_collections": { "construct_gb": { - "id": "132b871e5e3014ee", + "id": "edba41b605a9f854", "src": "hdca" } }, "outputs": { "__new_primary_file_construct_gb|construct_1__": { - "id": "6d4f2c14c91fd6e1", + "id": "fae073f924dc0737", "src": "hda", - "uuid": "32687278-a139-4ee2-bfc0-86735e813b3e" + "uuid": "41fc11c8-e2d3-4dad-9886-b8b318d263b0" }, "__new_primary_file_construct_gb|construct_2__": { - "id": "ce0686b9d731295a", + "id": "a0099218a00b3fc6", "src": "hda", - "uuid": "a78e87bc-7aa1-4e9e-8625-78450d68b18d" + "uuid": "7bc46185-b70d-4e82-b1fe-e0bc1710c1c7" }, "__new_primary_file_construct_gb|construct_3__": { - "id": "9fb491af1d40ed73", + "id": "87b4cc5bde3d0d60", "src": "hda", - "uuid": "6ce970af-f5f4-4193-9d0a-d1fc701d17d5" + "uuid": "79f1a377-2d26-4e23-aa72-01151870f643" }, "__new_primary_file_construct_gb|construct_4__": { - "id": "0a54ce1a82948d59", + "id": "b1ff512a2804398b", "src": "hda", - "uuid": "b76d3345-d556-4f55-9285-6a7ce76d9150" + "uuid": "63ad38c1-369e-4ef2-b296-6c80774439a1" }, "output_zip": { - "id": "d25964a649f0fc81", + "id": "18479e206f3c823f", "src": "hda", - "uuid": "f30d906d-2ea4-4cde-b451-b7c6daf25a29" + "uuid": "d4a3a824-aae9-4493-811d-77a8abd69905" } }, "params": { "__input_ext": "\"input\"", "adv": "{\"enzyme\": \"auto\", \"use_file_names_as_ids\": true}", "assembly_plan_name": "\"Type2sRestrictionAssembly\"", - "chromInfo": "\"/tmp/tmpay0tme4v/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", + "chromInfo": "\"/tmp/tmpo3npfzdk/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, 2.14it/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, 1.77it/s, now=None]\r \r", + "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, 2.20it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 4/4 [00:02<00:00, 1.79it/s, now=None]\r \r", "stdout": "Simulating assembly plan assambly...\n{'cancelled_assemblies': 0, 'errored_assemblies': 0, 'valid_assemblies': 4}\nGenerating assemblies reports...\n", "tool_id": "cloning_simulation", - "tool_stderr": "\rassembly: 0%| | 0/4 [00:00<?, ?it/s, now=None]\r \r\rassembly: 0%| | 0/4 [00:00<?, ?it/s, now=None]\rassembly: 50%|\u2588\u2588\u2588\u2588\u2588 | 2/4 [00:00<00:00, 2.14it/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, 1.77it/s, now=None]\r \r", + "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, 2.20it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 4/4 [00:02<00:00, 1.79it/s, now=None]\r \r", "tool_stdout": "Simulating assembly plan assambly...\n{'cancelled_assemblies': 0, 'errored_assemblies': 0, 'valid_assemblies': 4}\nGenerating assemblies reports...\n", - "update_time": "2025-05-19T13:45:15.319665", + "update_time": "2025-05-21T14:47:43.254778", "user_email": "planemo@galaxyproject.org", - "user_id": "fd8809ceca5b90d8" + "user_id": "9f2c11a06c2c8bb2" }, "status": "success", "test_index": 0, - "time_seconds": 54.20177435874939, + "time_seconds": 52.45778512954712, "tool_id": "cloning_simulation", "tool_version": "0.1.0+galaxy0" }, @@ -173,21 +173,21 @@ "inputs": { "adv|use_file_names_as_ids": true, "assembly_csv": { - "id": "e820aa9b959ea863", + "id": "289d42720aa731f0", "src": "hda" }, "assembly_plan_name": "GibsonAssembly", "genbank_files": { - "id": "65f48584dd2a1828", + "id": "b1906c2e1f5de664", "src": "hdca" }, "topology": "circular" }, "job": { - "command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmpay0tme4v/files/0/6/9/dataset_069f9137-705b-4e17-b931-1ebd547a7fe4.dat' --domesticated_seq '' --assembly_csv '/tmp/tmpay0tme4v/files/3/d/1/dataset_3d1a91ee-d9ba-41fc-bd79-f012ae654250.dat' --assembly_plan_name 'GibsonAssembly' --file_name_mapping '/tmp/tmpay0tme4v/files/0/6/9/dataset_069f9137-705b-4e17-b931-1ebd547a7fe4.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/tmpay0tme4v/job_working_directory/000/17/outputs/dataset_3327e282-d219-43e3-94d7-88fd08aa6867.dat'", + "command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && cp '/tmp/tmpo3npfzdk/files/e/c/2/dataset_ec2445f2-3c65-4da8-8eff-b766983bfc67.dat' 'assembly_csv.csv' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmpo3npfzdk/files/6/7/f/dataset_67f88938-ad76-4760-9f37-0ad6563677d2.dat' --domesticated_seq '' --assembly_csv 'assembly_csv.csv' --assembly_plan_name 'GibsonAssembly' --file_name_mapping '/tmp/tmpo3npfzdk/files/6/7/f/dataset_67f88938-ad76-4760-9f37-0ad6563677d2.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/tmpo3npfzdk/job_working_directory/000/17/outputs/dataset_989e415d-7117-4c6a-9721-a471d4848b28.dat'", "command_version": "", "copied_from_job_id": null, - "create_time": "2025-05-19T13:45:26.929597", + "create_time": "2025-05-21T14:47:54.065116", "dependencies": [ { "cacheable": false, @@ -367,21 +367,21 @@ } ], "exit_code": 0, - "external_id": "245766", + "external_id": "318162", "galaxy_version": "24.2", "handler": null, - "history_id": "132b871e5e3014ee", - "id": "9fb491af1d40ed73", + "history_id": "edba41b605a9f854", + "id": "87b4cc5bde3d0d60", "inputs": { "assembly_csv": { - "id": "e820aa9b959ea863", + "id": "289d42720aa731f0", "src": "hda", - "uuid": "3d1a91ee-d9ba-41fc-bd79-f012ae654250" + "uuid": "ec2445f2-3c65-4da8-8eff-b766983bfc67" }, "genbank_files1": { - "id": "82720a2239e02ea4", + "id": "761015980e0fa5bb", "src": "hda", - "uuid": "069f9137-705b-4e17-b931-1ebd547a7fe4" + "uuid": "67f88938-ad76-4760-9f37-0ad6563677d2" } }, "job_messages": [], @@ -392,55 +392,55 @@ "model_class": "Job", "output_collections": { "construct_gb": { - "id": "543bb64c618cca80", + "id": "d28b58e6679c5691", "src": "hdca" } }, "outputs": { "__new_primary_file_construct_gb|construct_1__": { - "id": "4aace7d444c68122", + "id": "250fdbecb1e4e593", "src": "hda", - "uuid": "24381c81-ce88-4584-94dd-e84c078419f8" + "uuid": "20319120-7aa4-4a7b-8e21-e283565ebc51" }, "__new_primary_file_construct_gb|construct_2__": { - "id": "894db8882e848d71", + "id": "b6d4ee56c656e869", "src": "hda", - "uuid": "9f704297-19e6-4faf-a500-b6b64578b376" + "uuid": "ba35f878-8819-459e-acff-364b6393cd75" }, "__new_primary_file_construct_gb|construct_3__": { - "id": "4d49f848d91861cd", + "id": "d670a65869e0ee8d", "src": "hda", - "uuid": "ac0d0bab-faee-48eb-bdcf-f71f1ae7dff9" + "uuid": "646cac10-dab3-4b60-bb38-1a21ce52a0af" }, "output_zip": { - "id": "314f9466454a965d", + "id": "3cd20c46fb8f3785", "src": "hda", - "uuid": "3327e282-d219-43e3-94d7-88fd08aa6867" + "uuid": "989e415d-7117-4c6a-9721-a471d4848b28" } }, "params": { "__input_ext": "\"input\"", "adv": "{\"enzyme\": \"auto\", \"use_file_names_as_ids\": true}", "assembly_plan_name": "\"GibsonAssembly\"", - "chromInfo": "\"/tmp/tmpay0tme4v/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", + "chromInfo": "\"/tmp/tmpo3npfzdk/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, 4.20it/s, now=None]\rassembly: 60%|\u2588\u2588\u2588\u2588\u2588\u2588 | 3/5 [00:00<00:00, 4.12it/s, now=None]\rassembly: 80%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588 | 4/5 [00:00<00:00, 4.34it/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", + "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, 4.41it/s, now=None]\rassembly: 60%|\u2588\u2588\u2588\u2588\u2588\u2588 | 3/5 [00:00<00:00, 4.23it/s, now=None]\rassembly: 80%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588 | 4/5 [00:00<00:00, 4.23it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 5/5 [00:01<00:00, 3.54it/s, now=None]\r \r", "stdout": "Simulating assembly plan assambly...\n{'cancelled_assemblies': 0, 'errored_assemblies': 2, 'valid_assemblies': 3}\nGenerating assemblies reports...\n", "tool_id": "cloning_simulation", - "tool_stderr": "\rassembly: 0%| | 0/5 [00:00<?, ?it/s, now=None]\r \r\rassembly: 0%| | 0/5 [00:00<?, ?it/s, now=None]\rassembly: 40%|\u2588\u2588\u2588\u2588 | 2/5 [00:00<00:00, 4.20it/s, now=None]\rassembly: 60%|\u2588\u2588\u2588\u2588\u2588\u2588 | 3/5 [00:00<00:00, 4.12it/s, now=None]\rassembly: 80%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588 | 4/5 [00:00<00:00, 4.34it/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_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, 4.41it/s, now=None]\rassembly: 60%|\u2588\u2588\u2588\u2588\u2588\u2588 | 3/5 [00:00<00:00, 4.23it/s, now=None]\rassembly: 80%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588 | 4/5 [00:00<00:00, 4.23it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 5/5 [00:01<00:00, 3.54it/s, now=None]\r \r", "tool_stdout": "Simulating assembly plan assambly...\n{'cancelled_assemblies': 0, 'errored_assemblies': 2, 'valid_assemblies': 3}\nGenerating assemblies reports...\n", - "update_time": "2025-05-19T13:45:38.810356", + "update_time": "2025-05-21T14:48:06.111506", "user_email": "planemo@galaxyproject.org", - "user_id": "fd8809ceca5b90d8" + "user_id": "9f2c11a06c2c8bb2" }, "status": "success", "test_index": 1, - "time_seconds": 23.490375518798828, + "time_seconds": 22.7187819480896, "tool_id": "cloning_simulation", "tool_version": "0.1.0+galaxy0" }, @@ -452,21 +452,290 @@ "inputs": { "adv|use_file_names_as_ids": true, "assembly_csv": { - "id": "675dca381201b1fe", + "id": "85c339cda4aedd7c", "src": "hda" }, "assembly_plan_name": "LigaseCyclingReactionAssembly", "genbank_files": { - "id": "e550d863bf084702", + "id": "39de46ba349dfcbe", "src": "hdca" }, "topology": "circular" }, "job": { - "command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmpay0tme4v/files/e/0/f/dataset_e0f8296e-094d-4971-976b-6e534148d1d5.dat,/tmp/tmpay0tme4v/files/6/0/8/dataset_608722d5-ead5-49fb-8736-04fa7ab027f3.dat' --domesticated_seq '' --assembly_csv '/tmp/tmpay0tme4v/files/1/d/9/dataset_1d9ed268-bc25-40c0-a67f-439accae7e40.dat' --assembly_plan_name 'LigaseCyclingReactionAssembly' --file_name_mapping '/tmp/tmpay0tme4v/files/e/0/f/dataset_e0f8296e-094d-4971-976b-6e534148d1d5.dat:RFP_GFP_plasmid_BOs.fa,/tmp/tmpay0tme4v/files/6/0/8/dataset_608722d5-ead5-49fb-8736-04fa7ab027f3.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/tmpay0tme4v/job_working_directory/000/21/outputs/dataset_b1af7192-a26f-4e6a-ba22-9aeffac2ea46.dat'", + "command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && cp '/tmp/tmpo3npfzdk/files/f/8/e/dataset_f8e8f190-6448-4143-9c9d-318983554f6e.dat' 'assembly_csv.csv' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmpo3npfzdk/files/f/0/d/dataset_f0d601f5-aeb5-4dde-88f2-1ef90f2cee9d.dat,/tmp/tmpo3npfzdk/files/0/1/e/dataset_01ef92eb-7297-49ed-b933-21e2fd13abde.dat' --domesticated_seq '' --assembly_csv 'assembly_csv.csv' --assembly_plan_name 'LigaseCyclingReactionAssembly' --file_name_mapping '/tmp/tmpo3npfzdk/files/f/0/d/dataset_f0d601f5-aeb5-4dde-88f2-1ef90f2cee9d.dat:RFP_GFP_plasmid_BOs.fa,/tmp/tmpo3npfzdk/files/0/1/e/dataset_01ef92eb-7297-49ed-b933-21e2fd13abde.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/tmpo3npfzdk/job_working_directory/000/21/outputs/dataset_27a350cf-f7f3-41f3-8b7d-a7f5a3857cda.dat'", "command_version": "", "copied_from_job_id": null, - "create_time": "2025-05-19T13:45:50.704320", + "create_time": "2025-05-21T14:48:17.296961", + "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": "318555", + "galaxy_version": "24.2", + "handler": null, + "history_id": "b1906c2e1f5de664", + "id": "3cd20c46fb8f3785", + "inputs": { + "assembly_csv": { + "id": "85c339cda4aedd7c", + "src": "hda", + "uuid": "f8e8f190-6448-4143-9c9d-318983554f6e" + }, + "genbank_files1": { + "id": "65b6153cb018bc73", + "src": "hda", + "uuid": "f0d601f5-aeb5-4dde-88f2-1ef90f2cee9d" + }, + "genbank_files2": { + "id": "bad7991cd53808a2", + "src": "hda", + "uuid": "01ef92eb-7297-49ed-b933-21e2fd13abde" + } + }, + "job_messages": [], + "job_metrics": [], + "job_runner_name": null, + "job_stderr": "", + "job_stdout": "", + "model_class": "Job", + "output_collections": { + "construct_gb": { + "id": "d10d7a9bf6c42600", + "src": "hdca" + } + }, + "outputs": { + "output_zip": { + "id": "a6615d25b678d53d", + "src": "hda", + "uuid": "27a350cf-f7f3-41f3-8b7d-a7f5a3857cda" + } + }, + "params": { + "__input_ext": "\"input\"", + "adv": "{\"enzyme\": \"auto\", \"use_file_names_as_ids\": true}", + "assembly_plan_name": "\"LigaseCyclingReactionAssembly\"", + "chromInfo": "\"/tmp/tmpo3npfzdk/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, 2.35it/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": "2025-05-21T14:48:29.682156", + "user_email": "planemo@galaxyproject.org", + "user_id": "9f2c11a06c2c8bb2" + }, + "status": "success", + "test_index": 2, + "time_seconds": 23.41460394859314, + "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": "5685dbd0270421a3", + "src": "hda" + }, + "assembly_plan_name": "BASICAssembly", + "genbank_files": { + "id": "6f2e93d50b248cee", + "src": "hdca" + }, + "topology": "circular" + }, + "job": { + "command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && cp '/tmp/tmpo3npfzdk/files/2/e/b/dataset_2ebce83f-23bd-4ed9-bf81-84719ce47f36.dat' 'assembly_csv.csv' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmpo3npfzdk/files/b/a/9/dataset_ba9f3fda-e65a-4367-9883-988cf2a55bc7.dat,/tmp/tmpo3npfzdk/files/5/6/4/dataset_56477dbf-4a9f-4d85-8639-49bc05bff7b7.dat,/tmp/tmpo3npfzdk/files/7/5/d/dataset_75d82485-e3c8-4311-8952-658d8522f8a5.dat,/tmp/tmpo3npfzdk/files/f/a/f/dataset_faff73fe-2ef9-4c25-913c-df5e8b93306a.dat,/tmp/tmpo3npfzdk/files/8/5/9/dataset_859dcf3d-e0f7-4667-9c8d-9a9587d934fb.dat' --domesticated_seq '' --assembly_csv 'assembly_csv.csv' --assembly_plan_name 'BASICAssembly' --file_name_mapping '/tmp/tmpo3npfzdk/files/b/a/9/dataset_ba9f3fda-e65a-4367-9883-988cf2a55bc7.dat:GFP.gb,/tmp/tmpo3npfzdk/files/5/6/4/dataset_56477dbf-4a9f-4d85-8639-49bc05bff7b7.dat:p15A_kan.gb,/tmp/tmpo3npfzdk/files/7/5/d/dataset_75d82485-e3c8-4311-8952-658d8522f8a5.dat:promoter.gb,/tmp/tmpo3npfzdk/files/f/a/f/dataset_faff73fe-2ef9-4c25-913c-df5e8b93306a.dat:RFP.gb,/tmp/tmpo3npfzdk/files/8/5/9/dataset_859dcf3d-e0f7-4667-9c8d-9a9587d934fb.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/tmpo3npfzdk/job_working_directory/000/28/outputs/dataset_9a1970ad-354f-4dab-8065-2e37cd1d196b.dat'", + "command_version": "", + "copied_from_job_id": null, + "create_time": "2025-05-21T14:48:51.044629", "dependencies": [ { "cacheable": false, @@ -646,26 +915,41 @@ } ], "exit_code": 0, - "external_id": "246155", + "external_id": "319145", "galaxy_version": "24.2", "handler": null, - "history_id": "65f48584dd2a1828", - "id": "314f9466454a965d", + "history_id": "d28b58e6679c5691", + "id": "a6615d25b678d53d", "inputs": { "assembly_csv": { - "id": "675dca381201b1fe", + "id": "5685dbd0270421a3", "src": "hda", - "uuid": "1d9ed268-bc25-40c0-a67f-439accae7e40" + "uuid": "2ebce83f-23bd-4ed9-bf81-84719ce47f36" }, "genbank_files1": { - "id": "1b1aadbedc3f334a", + "id": "78532c2c58a6724d", "src": "hda", - "uuid": "e0f8296e-094d-4971-976b-6e534148d1d5" + "uuid": "ba9f3fda-e65a-4367-9883-988cf2a55bc7" }, "genbank_files2": { - "id": "05b5deb4bb488223", + "id": "6068244592d47240", + "src": "hda", + "uuid": "56477dbf-4a9f-4d85-8639-49bc05bff7b7" + }, + "genbank_files3": { + "id": "f632d706e94b2046", "src": "hda", - "uuid": "608722d5-ead5-49fb-8736-04fa7ab027f3" + "uuid": "75d82485-e3c8-4311-8952-658d8522f8a5" + }, + "genbank_files4": { + "id": "3089f20183c33fb7", + "src": "hda", + "uuid": "faff73fe-2ef9-4c25-913c-df5e8b93306a" + }, + "genbank_files5": { + "id": "b20d2aa5f122518a", + "src": "hda", + "uuid": "859dcf3d-e0f7-4667-9c8d-9a9587d934fb" } }, "job_messages": [], @@ -676,66 +960,66 @@ "model_class": "Job", "output_collections": { "construct_gb": { - "id": "6a73e15df176b356", + "id": "00a7ec1d542ff3f2", "src": "hdca" } }, "outputs": { "output_zip": { - "id": "499c1d005d68ae46", + "id": "2accc8a350a16be5", "src": "hda", - "uuid": "b1af7192-a26f-4e6a-ba22-9aeffac2ea46" + "uuid": "9a1970ad-354f-4dab-8065-2e37cd1d196b" } }, "params": { "__input_ext": "\"input\"", "adv": "{\"enzyme\": \"auto\", \"use_file_names_as_ids\": true}", - "assembly_plan_name": "\"LigaseCyclingReactionAssembly\"", - "chromInfo": "\"/tmp/tmpay0tme4v/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", + "assembly_plan_name": "\"BASICAssembly\"", + "chromInfo": "\"/tmp/tmpo3npfzdk/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", "dbkey": "\"?\"", "domesticated_input": null, - "genbank_files": "{\"values\": [{\"id\": 5, \"src\": \"hdca\"}]}", + "genbank_files": "{\"values\": [{\"id\": 7, \"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, 2.05it/s, now=None]\r \r", - "stdout": "Simulating assembly plan assambly...\n{'cancelled_assemblies': 0, 'errored_assemblies': 2, 'valid_assemblies': 0}\nGenerating assemblies reports...\n", + "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, 48.44it/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%| | 0/2 [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, 2.05it/s, now=None]\r \r", - "tool_stdout": "Simulating assembly plan assambly...\n{'cancelled_assemblies': 0, 'errored_assemblies': 2, 'valid_assemblies': 0}\nGenerating assemblies reports...\n", - "update_time": "2025-05-19T13:46:02.749327", + "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, 48.44it/s, now=None]\r \r", + "tool_stdout": "Simulating assembly plan assambly...\n{'cancelled_assemblies': 2, 'errored_assemblies': 8, 'valid_assemblies': 0}\nGenerating assemblies reports...\n", + "update_time": "2025-05-21T14:49:01.657843", "user_email": "planemo@galaxyproject.org", - "user_id": "fd8809ceca5b90d8" + "user_id": "9f2c11a06c2c8bb2" }, "status": "success", - "test_index": 2, - "time_seconds": 23.55416440963745, + "test_index": 3, + "time_seconds": 32.04251265525818, "tool_id": "cloning_simulation", "tool_version": "0.1.0+galaxy0" }, "has_data": true, - "id": "cloning_simulation-2" + "id": "cloning_simulation-3" }, { "data": { "inputs": { "adv|use_file_names_as_ids": true, "assembly_csv": { - "id": "c06583b31ad25e9f", + "id": "19069e20577e5aff", "src": "hda" }, - "assembly_plan_name": "BASICAssembly", + "assembly_plan_name": "BioBrickStandardAssembly", "genbank_files": { - "id": "7faba24a30f85c9d", + "id": "39eaa2809c3cd4cb", "src": "hdca" }, "topology": "circular" }, "job": { - "command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmpay0tme4v/files/5/0/9/dataset_509fa87d-4af9-46f7-b323-48f8128675c8.dat,/tmp/tmpay0tme4v/files/0/2/b/dataset_02b8b6f2-43ab-4885-a9de-336d903edc55.dat,/tmp/tmpay0tme4v/files/9/5/a/dataset_95aa5a16-9b61-45be-94e6-35284531fcd7.dat,/tmp/tmpay0tme4v/files/1/7/c/dataset_17c94fe6-e0ce-4c72-9adc-5f8132a6df81.dat,/tmp/tmpay0tme4v/files/d/b/6/dataset_db6bb8ba-4682-476e-a688-be9e5cfb0afd.dat' --domesticated_seq '' --assembly_csv '/tmp/tmpay0tme4v/files/3/4/4/dataset_344ef380-e9d3-4729-bc6e-45a003000613.dat' --assembly_plan_name 'BASICAssembly' --file_name_mapping '/tmp/tmpay0tme4v/files/5/0/9/dataset_509fa87d-4af9-46f7-b323-48f8128675c8.dat:GFP.gb,/tmp/tmpay0tme4v/files/0/2/b/dataset_02b8b6f2-43ab-4885-a9de-336d903edc55.dat:p15A_kan.gb,/tmp/tmpay0tme4v/files/9/5/a/dataset_95aa5a16-9b61-45be-94e6-35284531fcd7.dat:promoter.gb,/tmp/tmpay0tme4v/files/1/7/c/dataset_17c94fe6-e0ce-4c72-9adc-5f8132a6df81.dat:RFP.gb,/tmp/tmpay0tme4v/files/d/b/6/dataset_db6bb8ba-4682-476e-a688-be9e5cfb0afd.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/tmpay0tme4v/job_working_directory/000/28/outputs/dataset_cdb61cbc-c9c5-45fc-9fc8-e00c1f3d4f0f.dat'", + "command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && cp '/tmp/tmpo3npfzdk/files/1/d/4/dataset_1d489746-618d-43f9-ac80-377b4dd34b24.dat' 'assembly_csv.csv' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmpo3npfzdk/files/8/9/7/dataset_897a659b-ded6-4f1d-ae66-2a1cef19fe20.dat,/tmp/tmpo3npfzdk/files/7/4/c/dataset_74cd9512-f6fd-41db-8b25-6d9edd13fb35.dat,/tmp/tmpo3npfzdk/files/2/6/4/dataset_264baf3b-d201-449d-93bf-1408b04e3cc8.dat,/tmp/tmpo3npfzdk/files/b/8/7/dataset_b877c492-f532-4f4f-a95d-8dea0497c7ff.dat,/tmp/tmpo3npfzdk/files/f/a/1/dataset_fa14d755-6f98-4e94-9f24-cfbca2726e31.dat' --domesticated_seq '' --assembly_csv 'assembly_csv.csv' --assembly_plan_name 'BioBrickStandardAssembly' --file_name_mapping '/tmp/tmpo3npfzdk/files/8/9/7/dataset_897a659b-ded6-4f1d-ae66-2a1cef19fe20.dat:BBa_E0040_GFP.gb,/tmp/tmpo3npfzdk/files/7/4/c/dataset_74cd9512-f6fd-41db-8b25-6d9edd13fb35.dat:BBa_J23119_prom.gb,/tmp/tmpo3npfzdk/files/2/6/4/dataset_264baf3b-d201-449d-93bf-1408b04e3cc8.dat:BBa_J23119_prom_flawed.gb,/tmp/tmpo3npfzdk/files/b/8/7/dataset_b877c492-f532-4f4f-a95d-8dea0497c7ff.dat:BBa_J61048_term.gb,/tmp/tmpo3npfzdk/files/f/a/1/dataset_fa14d755-6f98-4e94-9f24-cfbca2726e31.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/tmpo3npfzdk/job_working_directory/000/35/outputs/dataset_ef294752-b154-44c3-828c-7165200df44d.dat'", "command_version": "", "copied_from_job_id": null, - "create_time": "2025-05-19T13:46:24.141767", + "create_time": "2025-05-21T14:49:23.080076", "dependencies": [ { "cacheable": false, @@ -915,41 +1199,41 @@ } ], "exit_code": 0, - "external_id": "246833", + "external_id": "319763", "galaxy_version": "24.2", "handler": null, - "history_id": "543bb64c618cca80", - "id": "499c1d005d68ae46", + "history_id": "39de46ba349dfcbe", + "id": "2accc8a350a16be5", "inputs": { "assembly_csv": { - "id": "c06583b31ad25e9f", + "id": "19069e20577e5aff", "src": "hda", - "uuid": "344ef380-e9d3-4729-bc6e-45a003000613" + "uuid": "1d489746-618d-43f9-ac80-377b4dd34b24" }, "genbank_files1": { - "id": "dcd17297edd6443c", + "id": "d016498c10e59856", "src": "hda", - "uuid": "509fa87d-4af9-46f7-b323-48f8128675c8" + "uuid": "897a659b-ded6-4f1d-ae66-2a1cef19fe20" }, "genbank_files2": { - "id": "5255abeff5637f7e", + "id": "8ce5f5c286574bf4", "src": "hda", - "uuid": "02b8b6f2-43ab-4885-a9de-336d903edc55" + "uuid": "74cd9512-f6fd-41db-8b25-6d9edd13fb35" }, "genbank_files3": { - "id": "a30c1b2be38d49df", + "id": "b8e0a36ad3584e57", "src": "hda", - "uuid": "95aa5a16-9b61-45be-94e6-35284531fcd7" + "uuid": "264baf3b-d201-449d-93bf-1408b04e3cc8" }, "genbank_files4": { - "id": "70728511d187b46b", + "id": "14b4e4f7b248fbc1", "src": "hda", - "uuid": "17c94fe6-e0ce-4c72-9adc-5f8132a6df81" + "uuid": "b877c492-f532-4f4f-a95d-8dea0497c7ff" }, "genbank_files5": { - "id": "db356309fe5e8361", + "id": "773bba263401ee3f", "src": "hda", - "uuid": "db6bb8ba-4682-476e-a688-be9e5cfb0afd" + "uuid": "fa14d755-6f98-4e94-9f24-cfbca2726e31" } }, "job_messages": [], @@ -960,66 +1244,85 @@ "model_class": "Job", "output_collections": { "construct_gb": { - "id": "f121a1ae40e58e96", + "id": "d905212b22d14b29", "src": "hdca" } }, "outputs": { + "__new_primary_file_construct_gb|C1_prom_barcode__": { + "id": "663fbeeba9821aac", + "src": "hda", + "uuid": "17dc07bc-ee88-4d0a-914a-bd5e219c3c02" + }, + "__new_primary_file_construct_gb|C2_gfp_term__": { + "id": "522d7c5bcadc14e8", + "src": "hda", + "uuid": "9e3bf994-7926-4d59-8cba-2ea85e34d4c1" + }, + "__new_primary_file_construct_gb|C3_final__": { + "id": "092101d28c5662b8", + "src": "hda", + "uuid": "080209e3-58a5-4181-b460-bf02871b2f82" + }, "output_zip": { - "id": "15b1f0554a03958d", + "id": "aa2a9c27c57d7b71", "src": "hda", - "uuid": "cdb61cbc-c9c5-45fc-9fc8-e00c1f3d4f0f" + "uuid": "ef294752-b154-44c3-828c-7165200df44d" } }, "params": { "__input_ext": "\"input\"", "adv": "{\"enzyme\": \"auto\", \"use_file_names_as_ids\": true}", - "assembly_plan_name": "\"BASICAssembly\"", - "chromInfo": "\"/tmp/tmpay0tme4v/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", + "assembly_plan_name": "\"BioBrickStandardAssembly\"", + "chromInfo": "\"/tmp/tmpo3npfzdk/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", "dbkey": "\"?\"", "domesticated_input": null, - "genbank_files": "{\"values\": [{\"id\": 7, \"src\": \"hdca\"}]}", + "genbank_files": "{\"values\": [{\"id\": 9, \"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, 44.90it/s, now=None]\r \r", - "stdout": "Simulating assembly plan assambly...\n{'cancelled_assemblies': 2, 'errored_assemblies': 8, 'valid_assemblies': 0}\nGenerating assemblies reports...\n", + "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, 1.92it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 3/3 [00:01<00:00, 1.56it/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%| | 0/10 [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, 44.90it/s, now=None]\r \r", - "tool_stdout": "Simulating assembly plan assambly...\n{'cancelled_assemblies': 2, 'errored_assemblies': 8, 'valid_assemblies': 0}\nGenerating assemblies reports...\n", - "update_time": "2025-05-19T13:46:34.776797", + "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, 1.92it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 3/3 [00:01<00:00, 1.56it/s, now=None]\r \r", + "tool_stdout": "Simulating assembly plan assambly...\n{'cancelled_assemblies': 0, 'errored_assemblies': 0, 'valid_assemblies': 3}\nGenerating assemblies reports...\n", + "update_time": "2025-05-21T14:49:36.465998", "user_email": "planemo@galaxyproject.org", - "user_id": "fd8809ceca5b90d8" + "user_id": "9f2c11a06c2c8bb2" }, "status": "success", - "test_index": 3, - "time_seconds": 32.1408953666687, + "test_index": 4, + "time_seconds": 34.58101224899292, "tool_id": "cloning_simulation", "tool_version": "0.1.0+galaxy0" }, "has_data": true, - "id": "cloning_simulation-3" + "id": "cloning_simulation-4" }, { "data": { "inputs": { "adv|use_file_names_as_ids": true, "assembly_csv": { - "id": "e7b347ef21d63fab", + "id": "79581be26281c6bb", "src": "hda" }, - "assembly_plan_name": "BioBrickStandardAssembly", + "assembly_plan_name": "Type2sRestrictionAssembly", + "domesticated_input": { + "id": "64a027171405da09", + "src": "hdca" + }, "genbank_files": { - "id": "fc2d53421d7989de", + "id": "f3ab5b94869b932e", "src": "hdca" }, "topology": "circular" }, "job": { - "command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmpay0tme4v/files/6/e/0/dataset_6e0453c4-6edd-4d76-9504-4cc4941610f6.dat,/tmp/tmpay0tme4v/files/6/d/3/dataset_6d3c24e5-73cd-4bed-95aa-d1c361c74180.dat,/tmp/tmpay0tme4v/files/7/7/9/dataset_7793541b-18cc-4f7d-a9df-12396807c368.dat,/tmp/tmpay0tme4v/files/a/e/1/dataset_ae1611ed-a5e2-46e8-b975-613ada1bb8db.dat,/tmp/tmpay0tme4v/files/9/a/d/dataset_9adfafe3-b0ad-449b-8555-286ca83e65a4.dat' --domesticated_seq '' --assembly_csv '/tmp/tmpay0tme4v/files/9/7/6/dataset_976f7d99-07e5-4d5c-ab79-a96ae42760d4.dat' --assembly_plan_name 'BioBrickStandardAssembly' --file_name_mapping '/tmp/tmpay0tme4v/files/6/e/0/dataset_6e0453c4-6edd-4d76-9504-4cc4941610f6.dat:BBa_E0040_GFP.gb,/tmp/tmpay0tme4v/files/6/d/3/dataset_6d3c24e5-73cd-4bed-95aa-d1c361c74180.dat:BBa_J23119_prom.gb,/tmp/tmpay0tme4v/files/7/7/9/dataset_7793541b-18cc-4f7d-a9df-12396807c368.dat:BBa_J23119_prom_flawed.gb,/tmp/tmpay0tme4v/files/a/e/1/dataset_ae1611ed-a5e2-46e8-b975-613ada1bb8db.dat:BBa_J61048_term.gb,/tmp/tmpay0tme4v/files/9/a/d/dataset_9adfafe3-b0ad-449b-8555-286ca83e65a4.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/tmpay0tme4v/job_working_directory/000/35/outputs/dataset_deeb975f-4ae8-44d3-9c3c-51dc05e74f05.dat'", + "command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && cp '/tmp/tmpo3npfzdk/files/8/c/c/dataset_8ccb55a4-733f-4671-a12c-c89cee5a694b.dat' 'assembly_csv.csv' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmpo3npfzdk/files/5/8/6/dataset_586fc714-17c7-4356-a812-a25593d0b941.dat,/tmp/tmpo3npfzdk/files/f/7/5/dataset_f75d3cb4-8d11-4da3-99ae-56a96adeb45c.dat,/tmp/tmpo3npfzdk/files/0/f/2/dataset_0f2c03d7-84e9-4908-8cc2-ce94b456ad1d.dat,/tmp/tmpo3npfzdk/files/6/1/6/dataset_616f4db3-1967-47c9-b869-b02bcebad7c0.dat,/tmp/tmpo3npfzdk/files/5/b/4/dataset_5b4d9931-2f94-469f-8fbb-dddd1b4f23fe.dat,/tmp/tmpo3npfzdk/files/1/c/9/dataset_1c9febe8-b1ff-4f7e-a395-fbd671fdbf0a.dat,/tmp/tmpo3npfzdk/files/1/5/6/dataset_156ffebe-1d63-442a-822e-94c26612aebb.dat' --domesticated_seq '/tmp/tmpo3npfzdk/files/a/3/2/dataset_a32d019a-ef10-42b8-92d3-b1a89149114e.dat,/tmp/tmpo3npfzdk/files/3/4/c/dataset_34ca3b9a-6d8e-4790-8e04-946f777aaa2f.dat,/tmp/tmpo3npfzdk/files/7/d/4/dataset_7d434fd6-3da6-4a35-a935-6262c2be3b95.dat,/tmp/tmpo3npfzdk/files/5/0/a/dataset_50a304a8-ff94-4efc-8d3c-9dd5714d0ab9.dat,/tmp/tmpo3npfzdk/files/d/4/7/dataset_d476b171-9eb3-4fcb-9e16-1d4631b211ae.dat' --assembly_csv 'assembly_csv.csv' --assembly_plan_name 'Type2sRestrictionAssembly' --file_name_mapping '/tmp/tmpo3npfzdk/files/5/8/6/dataset_586fc714-17c7-4356-a812-a25593d0b941.dat:part_A.gb,/tmp/tmpo3npfzdk/files/f/7/5/dataset_f75d3cb4-8d11-4da3-99ae-56a96adeb45c.dat:part_B.gb,/tmp/tmpo3npfzdk/files/0/f/2/dataset_0f2c03d7-84e9-4908-8cc2-ce94b456ad1d.dat:part_C.gb,/tmp/tmpo3npfzdk/files/6/1/6/dataset_616f4db3-1967-47c9-b869-b02bcebad7c0.dat:part_D.gb,/tmp/tmpo3npfzdk/files/5/b/4/dataset_5b4d9931-2f94-469f-8fbb-dddd1b4f23fe.dat:part_E.gb,/tmp/tmpo3npfzdk/files/1/c/9/dataset_1c9febe8-b1ff-4f7e-a395-fbd671fdbf0a.dat:part_F.gb,/tmp/tmpo3npfzdk/files/1/5/6/dataset_156ffebe-1d63-442a-822e-94c26612aebb.dat:part_G.gb' --file_name_mapping_dom '/tmp/tmpo3npfzdk/files/a/3/2/dataset_a32d019a-ef10-42b8-92d3-b1a89149114e.dat:part_H.gb,/tmp/tmpo3npfzdk/files/3/4/c/dataset_34ca3b9a-6d8e-4790-8e04-946f777aaa2f.dat:part_I.gb,/tmp/tmpo3npfzdk/files/7/d/4/dataset_7d434fd6-3da6-4a35-a935-6262c2be3b95.dat:part_J.gb,/tmp/tmpo3npfzdk/files/5/0/a/dataset_50a304a8-ff94-4efc-8d3c-9dd5714d0ab9.dat:part_K.gb,/tmp/tmpo3npfzdk/files/d/4/7/dataset_d476b171-9eb3-4fcb-9e16-1d4631b211ae.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/tmpo3npfzdk/job_working_directory/000/49/outputs/dataset_26f09d54-6733-4b4f-9110-58b7422f6584.dat'", "command_version": "", "copied_from_job_id": null, - "create_time": "2025-05-19T13:46:57.146002", + "create_time": "2025-05-21T14:50:16.787614", "dependencies": [ { "cacheable": false, @@ -1199,41 +1502,76 @@ } ], "exit_code": 0, - "external_id": "247581", + "external_id": "320811", "galaxy_version": "24.2", "handler": null, - "history_id": "e550d863bf084702", - "id": "15b1f0554a03958d", + "history_id": "d10d7a9bf6c42600", + "id": "056fda651c637916", "inputs": { "assembly_csv": { - "id": "e7b347ef21d63fab", + "id": "79581be26281c6bb", + "src": "hda", + "uuid": "8ccb55a4-733f-4671-a12c-c89cee5a694b" + }, + "domesticated_input1": { + "id": "85db74d9c0951b21", + "src": "hda", + "uuid": "a32d019a-ef10-42b8-92d3-b1a89149114e" + }, + "domesticated_input2": { + "id": "1088aa990b0f6a3e", "src": "hda", - "uuid": "976f7d99-07e5-4d5c-ab79-a96ae42760d4" + "uuid": "34ca3b9a-6d8e-4790-8e04-946f777aaa2f" + }, + "domesticated_input3": { + "id": "0adf69845d3170b2", + "src": "hda", + "uuid": "7d434fd6-3da6-4a35-a935-6262c2be3b95" + }, + "domesticated_input4": { + "id": "f38cba32d894e055", + "src": "hda", + "uuid": "50a304a8-ff94-4efc-8d3c-9dd5714d0ab9" + }, + "domesticated_input5": { + "id": "d03e2be198c26beb", + "src": "hda", + "uuid": "d476b171-9eb3-4fcb-9e16-1d4631b211ae" }, "genbank_files1": { - "id": "0d1c6bc715df133f", + "id": "7f005c8d8137335e", "src": "hda", - "uuid": "6e0453c4-6edd-4d76-9504-4cc4941610f6" + "uuid": "586fc714-17c7-4356-a812-a25593d0b941" }, "genbank_files2": { - "id": "7d9d065fa6859d88", + "id": "2893678ebcfeac31", "src": "hda", - "uuid": "6d3c24e5-73cd-4bed-95aa-d1c361c74180" + "uuid": "f75d3cb4-8d11-4da3-99ae-56a96adeb45c" }, "genbank_files3": { - "id": "28aa4b1f3fb7d62b", + "id": "eebf6b53a0733527", "src": "hda", - "uuid": "7793541b-18cc-4f7d-a9df-12396807c368" + "uuid": "0f2c03d7-84e9-4908-8cc2-ce94b456ad1d" }, "genbank_files4": { - "id": "7423dfb808ef4761", + "id": "056fda651c637916", "src": "hda", - "uuid": "ae1611ed-a5e2-46e8-b975-613ada1bb8db" + "uuid": "616f4db3-1967-47c9-b869-b02bcebad7c0" }, "genbank_files5": { - "id": "175236d72b015bf8", + "id": "554aac66b6b91c95", + "src": "hda", + "uuid": "5b4d9931-2f94-469f-8fbb-dddd1b4f23fe" + }, + "genbank_files6": { + "id": "e0b55cd244232b92", "src": "hda", - "uuid": "9adfafe3-b0ad-449b-8555-286ca83e65a4" + "uuid": "1c9febe8-b1ff-4f7e-a395-fbd671fdbf0a" + }, + "genbank_files7": { + "id": "5de07666a9f74c14", + "src": "hda", + "uuid": "156ffebe-1d63-442a-822e-94c26612aebb" } }, "job_messages": [], @@ -1244,85 +1582,86 @@ "model_class": "Job", "output_collections": { "construct_gb": { - "id": "171b3bd3b2ffa75e", + "id": "acd1a5e1ec1673bf", "src": "hdca" } }, "outputs": { - "__new_primary_file_construct_gb|C1_prom_barcode__": { - "id": "2607809b86839f90", + "__new_primary_file_construct_gb|construct_1__": { + "id": "bee5eb96186aeef0", "src": "hda", - "uuid": "4e873fda-e181-4d71-b03b-61441dad6432" + "uuid": "e0540e16-fb06-474f-9574-a0f8c8f44fae" + }, + "__new_primary_file_construct_gb|construct_2__": { + "id": "19dda9511f29e82d", + "src": "hda", + "uuid": "3de1208e-5fa3-4899-b496-f1e4b8a69e8e" }, - "__new_primary_file_construct_gb|C2_gfp_term__": { - "id": "d61271ad2bd59452", + "__new_primary_file_construct_gb|construct_3__": { + "id": "75d4ef21ebceb84b", "src": "hda", - "uuid": "1c217e77-9cfa-48b2-aabb-ccdcd23275ca" + "uuid": "39adc107-3c51-4ceb-a401-d1e85b10d36c" }, - "__new_primary_file_construct_gb|C3_final__": { - "id": "cdfae6a044106877", + "__new_primary_file_construct_gb|construct_4__": { + "id": "7d27617ebf2a7ca2", "src": "hda", - "uuid": "54b8bb86-f05d-4ec1-b551-7ed8ca22aedd" + "uuid": "5ff68ddd-6e45-47d3-877e-f0874370d1d7" }, "output_zip": { - "id": "451b6ce8fd13ed5c", + "id": "aff3a7c3a5e84c2e", "src": "hda", - "uuid": "deeb975f-4ae8-44d3-9c3c-51dc05e74f05" + "uuid": "26f09d54-6733-4b4f-9110-58b7422f6584" } }, "params": { "__input_ext": "\"input\"", "adv": "{\"enzyme\": \"auto\", \"use_file_names_as_ids\": true}", - "assembly_plan_name": "\"BioBrickStandardAssembly\"", - "chromInfo": "\"/tmp/tmpay0tme4v/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", + "assembly_plan_name": "\"Type2sRestrictionAssembly\"", + "chromInfo": "\"/tmp/tmpo3npfzdk/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", "dbkey": "\"?\"", - "domesticated_input": null, - "genbank_files": "{\"values\": [{\"id\": 9, \"src\": \"hdca\"}]}", + "domesticated_input": "{\"values\": [{\"id\": 11, \"src\": \"hdca\"}]}", + "genbank_files": "{\"values\": [{\"id\": 12, \"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, 1.74it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 3/3 [00:02<00:00, 1.43it/s, now=None]\r \r", - "stdout": "Simulating assembly plan assambly...\n{'cancelled_assemblies': 0, 'errored_assemblies': 0, 'valid_assemblies': 3}\nGenerating assemblies reports...\n", + "stderr": "\rassembly: 0%| | 0/4 [00:00<?, ?it/s, now=None]\r \r\rassembly: 0%| | 0/4 [00:00<?, ?it/s, now=None]\rassembly: 50%|\u2588\u2588\u2588\u2588\u2588 | 2/4 [00:00<00:00, 2.41it/s, now=None]\rassembly: 75%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u258c | 3/4 [00:01<00:00, 2.20it/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%| | 0/3 [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, 1.74it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 3/3 [00:02<00:00, 1.43it/s, now=None]\r \r", - "tool_stdout": "Simulating assembly plan assambly...\n{'cancelled_assemblies': 0, 'errored_assemblies': 0, 'valid_assemblies': 3}\nGenerating assemblies reports...\n", - "update_time": "2025-05-19T13:47:10.784667", + "tool_stderr": "\rassembly: 0%| | 0/4 [00:00<?, ?it/s, now=None]\r \r\rassembly: 0%| | 0/4 [00:00<?, ?it/s, now=None]\rassembly: 50%|\u2588\u2588\u2588\u2588\u2588 | 2/4 [00:00<00:00, 2.41it/s, now=None]\rassembly: 75%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u258c | 3/4 [00:01<00:00, 2.20it/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": "2025-05-21T14:50:29.418254", "user_email": "planemo@galaxyproject.org", - "user_id": "fd8809ceca5b90d8" + "user_id": "9f2c11a06c2c8bb2" }, "status": "success", - "test_index": 4, - "time_seconds": 35.92383527755737, + "test_index": 5, + "time_seconds": 52.95538687705994, "tool_id": "cloning_simulation", "tool_version": "0.1.0+galaxy0" }, "has_data": true, - "id": "cloning_simulation-4" + "id": "cloning_simulation-5" }, { "data": { "inputs": { "adv|use_file_names_as_ids": true, "assembly_csv": { - "id": "8970dbe72f491b25", + "id": "1cfd8c9510cd79b8", "src": "hda" }, "assembly_plan_name": "Type2sRestrictionAssembly", "domesticated_input": { - "id": "ec7f951857c74506", - "src": "hdca" - }, - "genbank_files": { - "id": "8c74660869d2dd19", + "id": "18479e206f3c823f", "src": "hdca" }, "topology": "circular" }, "job": { - "command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmpay0tme4v/files/1/9/3/dataset_193cbd10-4b76-46d9-b377-a7f06471d4d4.dat,/tmp/tmpay0tme4v/files/f/a/3/dataset_fa31c5f5-e678-471e-b1a3-4f8a168bbee1.dat,/tmp/tmpay0tme4v/files/6/9/7/dataset_697c83fe-168b-4319-a6e5-3db90c504c8b.dat,/tmp/tmpay0tme4v/files/0/6/d/dataset_06d4dd94-5f33-4ce0-ab0a-e6efe96ca222.dat,/tmp/tmpay0tme4v/files/7/0/1/dataset_701b72c6-ec2e-4435-b0d5-8f419811a4dd.dat,/tmp/tmpay0tme4v/files/5/a/0/dataset_5a07f059-f6f9-49de-b0fc-3cded157f44b.dat,/tmp/tmpay0tme4v/files/7/5/3/dataset_753f0297-4bff-49c8-b22a-1377e43a81f6.dat' --domesticated_seq '/tmp/tmpay0tme4v/files/f/6/d/dataset_f6d602b9-7772-4a93-969d-f0dcdad98c6a.dat,/tmp/tmpay0tme4v/files/d/4/d/dataset_d4dc3ecb-77ff-4b28-a55a-7b263416c6c7.dat,/tmp/tmpay0tme4v/files/7/d/4/dataset_7d489dbd-161e-4f04-a3df-ef5b989ad1e0.dat,/tmp/tmpay0tme4v/files/4/c/a/dataset_4ca3c222-672a-4806-b60c-081f1b7b64cb.dat,/tmp/tmpay0tme4v/files/9/0/6/dataset_906707db-b3cf-40f9-af0b-1ffc143f91e8.dat' --assembly_csv '/tmp/tmpay0tme4v/files/9/c/8/dataset_9c8ec693-02f9-4cc7-b7e3-8bfb0a4dd1dc.dat' --assembly_plan_name 'Type2sRestrictionAssembly' --file_name_mapping '/tmp/tmpay0tme4v/files/1/9/3/dataset_193cbd10-4b76-46d9-b377-a7f06471d4d4.dat:part_A.gb,/tmp/tmpay0tme4v/files/f/a/3/dataset_fa31c5f5-e678-471e-b1a3-4f8a168bbee1.dat:part_B.gb,/tmp/tmpay0tme4v/files/6/9/7/dataset_697c83fe-168b-4319-a6e5-3db90c504c8b.dat:part_C.gb,/tmp/tmpay0tme4v/files/0/6/d/dataset_06d4dd94-5f33-4ce0-ab0a-e6efe96ca222.dat:part_D.gb,/tmp/tmpay0tme4v/files/7/0/1/dataset_701b72c6-ec2e-4435-b0d5-8f419811a4dd.dat:part_E.gb,/tmp/tmpay0tme4v/files/5/a/0/dataset_5a07f059-f6f9-49de-b0fc-3cded157f44b.dat:part_F.gb,/tmp/tmpay0tme4v/files/7/5/3/dataset_753f0297-4bff-49c8-b22a-1377e43a81f6.dat:part_G.gb' --file_name_mapping_dom '/tmp/tmpay0tme4v/files/f/6/d/dataset_f6d602b9-7772-4a93-969d-f0dcdad98c6a.dat:part_H.gb,/tmp/tmpay0tme4v/files/d/4/d/dataset_d4dc3ecb-77ff-4b28-a55a-7b263416c6c7.dat:part_I.gb,/tmp/tmpay0tme4v/files/7/d/4/dataset_7d489dbd-161e-4f04-a3df-ef5b989ad1e0.dat:part_J.gb,/tmp/tmpay0tme4v/files/4/c/a/dataset_4ca3c222-672a-4806-b60c-081f1b7b64cb.dat:part_K.gb,/tmp/tmpay0tme4v/files/9/0/6/dataset_906707db-b3cf-40f9-af0b-1ffc143f91e8.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/tmpay0tme4v/job_working_directory/000/49/outputs/dataset_800320dc-d181-40bf-b1cb-541f43a838c3.dat'", + "command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && cp '/tmp/tmpo3npfzdk/files/8/6/8/dataset_868edfc6-e59e-4522-bd0c-287140d27bcf.dat' 'assembly_csv.csv' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmpo3npfzdk/files/4/c/7/dataset_4c7c671b-5fc3-4e96-b7f2-7e309d53588d.dat,/tmp/tmpo3npfzdk/files/4/c/6/dataset_4c6b4c02-8f84-4314-8a13-682a855005e0.dat,/tmp/tmpo3npfzdk/files/2/9/c/dataset_29c207fc-3958-40b7-8d3a-29486ebe729e.dat,/tmp/tmpo3npfzdk/files/c/6/e/dataset_c6e14abc-4cc3-4027-bb1b-cf87b4df2e4c.dat,/tmp/tmpo3npfzdk/files/c/b/9/dataset_cb90c0ec-c5d5-4a0c-a2a8-82bdf58a4dcd.dat,/tmp/tmpo3npfzdk/files/e/b/6/dataset_eb6733f2-ea91-4ce2-878c-0bca789bfe95.dat,/tmp/tmpo3npfzdk/files/d/e/a/dataset_dea7a300-b098-41a1-863d-ec55e3b78bda.dat,/tmp/tmpo3npfzdk/files/1/3/3/dataset_13300353-8b8d-4bd4-9d25-88dceda7594b.dat,/tmp/tmpo3npfzdk/files/6/1/f/dataset_61ffb7d6-856a-4e4a-9da3-48a419455e92.dat,/tmp/tmpo3npfzdk/files/e/6/4/dataset_e6431634-077e-451e-afa3-b12c08fc5c7c.dat,/tmp/tmpo3npfzdk/files/7/5/8/dataset_758b4a45-c17d-4d1a-a289-79d3b2dfe524.dat,/tmp/tmpo3npfzdk/files/2/2/6/dataset_226889a1-0543-4052-9d94-3276acdbd8ad.dat' --domesticated_seq '/tmp/tmpo3npfzdk/files/4/c/7/dataset_4c7c671b-5fc3-4e96-b7f2-7e309d53588d.dat,/tmp/tmpo3npfzdk/files/4/c/6/dataset_4c6b4c02-8f84-4314-8a13-682a855005e0.dat,/tmp/tmpo3npfzdk/files/2/9/c/dataset_29c207fc-3958-40b7-8d3a-29486ebe729e.dat,/tmp/tmpo3npfzdk/files/c/6/e/dataset_c6e14abc-4cc3-4027-bb1b-cf87b4df2e4c.dat,/tmp/tmpo3npfzdk/files/c/b/9/dataset_cb90c0ec-c5d5-4a0c-a2a8-82bdf58a4dcd.dat,/tmp/tmpo3npfzdk/files/e/b/6/dataset_eb6733f2-ea91-4ce2-878c-0bca789bfe95.dat,/tmp/tmpo3npfzdk/files/d/e/a/dataset_dea7a300-b098-41a1-863d-ec55e3b78bda.dat,/tmp/tmpo3npfzdk/files/1/3/3/dataset_13300353-8b8d-4bd4-9d25-88dceda7594b.dat,/tmp/tmpo3npfzdk/files/6/1/f/dataset_61ffb7d6-856a-4e4a-9da3-48a419455e92.dat,/tmp/tmpo3npfzdk/files/e/6/4/dataset_e6431634-077e-451e-afa3-b12c08fc5c7c.dat,/tmp/tmpo3npfzdk/files/7/5/8/dataset_758b4a45-c17d-4d1a-a289-79d3b2dfe524.dat,/tmp/tmpo3npfzdk/files/2/2/6/dataset_226889a1-0543-4052-9d94-3276acdbd8ad.dat' --assembly_csv 'assembly_csv.csv' --assembly_plan_name 'Type2sRestrictionAssembly' --file_name_mapping '/tmp/tmpo3npfzdk/files/4/c/7/dataset_4c7c671b-5fc3-4e96-b7f2-7e309d53588d.dat:part_A.gb,/tmp/tmpo3npfzdk/files/4/c/6/dataset_4c6b4c02-8f84-4314-8a13-682a855005e0.dat:part_B.gb,/tmp/tmpo3npfzdk/files/2/9/c/dataset_29c207fc-3958-40b7-8d3a-29486ebe729e.dat:part_C.gb,/tmp/tmpo3npfzdk/files/c/6/e/dataset_c6e14abc-4cc3-4027-bb1b-cf87b4df2e4c.dat:part_D.gb,/tmp/tmpo3npfzdk/files/c/b/9/dataset_cb90c0ec-c5d5-4a0c-a2a8-82bdf58a4dcd.dat:part_E.gb,/tmp/tmpo3npfzdk/files/e/b/6/dataset_eb6733f2-ea91-4ce2-878c-0bca789bfe95.dat:part_F.gb,/tmp/tmpo3npfzdk/files/d/e/a/dataset_dea7a300-b098-41a1-863d-ec55e3b78bda.dat:part_G.gb,/tmp/tmpo3npfzdk/files/1/3/3/dataset_13300353-8b8d-4bd4-9d25-88dceda7594b.dat:part_H.gb,/tmp/tmpo3npfzdk/files/6/1/f/dataset_61ffb7d6-856a-4e4a-9da3-48a419455e92.dat:part_I.gb,/tmp/tmpo3npfzdk/files/e/6/4/dataset_e6431634-077e-451e-afa3-b12c08fc5c7c.dat:part_J.gb,/tmp/tmpo3npfzdk/files/7/5/8/dataset_758b4a45-c17d-4d1a-a289-79d3b2dfe524.dat:part_K.gb,/tmp/tmpo3npfzdk/files/2/2/6/dataset_226889a1-0543-4052-9d94-3276acdbd8ad.dat:part_L.gb' --file_name_mapping_dom '/tmp/tmpo3npfzdk/files/4/c/7/dataset_4c7c671b-5fc3-4e96-b7f2-7e309d53588d.dat:part_A.gb,/tmp/tmpo3npfzdk/files/4/c/6/dataset_4c6b4c02-8f84-4314-8a13-682a855005e0.dat:part_B.gb,/tmp/tmpo3npfzdk/files/2/9/c/dataset_29c207fc-3958-40b7-8d3a-29486ebe729e.dat:part_C.gb,/tmp/tmpo3npfzdk/files/c/6/e/dataset_c6e14abc-4cc3-4027-bb1b-cf87b4df2e4c.dat:part_D.gb,/tmp/tmpo3npfzdk/files/c/b/9/dataset_cb90c0ec-c5d5-4a0c-a2a8-82bdf58a4dcd.dat:part_E.gb,/tmp/tmpo3npfzdk/files/e/b/6/dataset_eb6733f2-ea91-4ce2-878c-0bca789bfe95.dat:part_F.gb,/tmp/tmpo3npfzdk/files/d/e/a/dataset_dea7a300-b098-41a1-863d-ec55e3b78bda.dat:part_G.gb,/tmp/tmpo3npfzdk/files/1/3/3/dataset_13300353-8b8d-4bd4-9d25-88dceda7594b.dat:part_H.gb,/tmp/tmpo3npfzdk/files/6/1/f/dataset_61ffb7d6-856a-4e4a-9da3-48a419455e92.dat:part_I.gb,/tmp/tmpo3npfzdk/files/e/6/4/dataset_e6431634-077e-451e-afa3-b12c08fc5c7c.dat:part_J.gb,/tmp/tmpo3npfzdk/files/7/5/8/dataset_758b4a45-c17d-4d1a-a289-79d3b2dfe524.dat:part_K.gb,/tmp/tmpo3npfzdk/files/2/2/6/dataset_226889a1-0543-4052-9d94-3276acdbd8ad.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/tmpo3npfzdk/job_working_directory/000/63/outputs/dataset_7ec4ccea-6d53-4d2c-b343-476013e8c0d9.dat'", "command_version": "", "copied_from_job_id": null, - "create_time": "2025-05-19T13:47:53.361341", + "create_time": "2025-05-21T14:51:10.356913", "dependencies": [ { "cacheable": false, @@ -1501,80 +1840,148 @@ "version": "3.1.5" } ], - "exit_code": 0, - "external_id": "248775", + "exit_code": 1, + "external_id": "321954", "galaxy_version": "24.2", "handler": null, - "history_id": "6a73e15df176b356", - "id": "95f3db52d6362602", + "history_id": "6f2e93d50b248cee", + "id": "7d27617ebf2a7ca2", "inputs": { "assembly_csv": { - "id": "8970dbe72f491b25", + "id": "1cfd8c9510cd79b8", "src": "hda", - "uuid": "9c8ec693-02f9-4cc7-b7e3-8bfb0a4dd1dc" + "uuid": "868edfc6-e59e-4522-bd0c-287140d27bcf" }, "domesticated_input1": { - "id": "e666d72d584b2f08", + "id": "515ae798a3a66959", + "src": "hda", + "uuid": "4c7c671b-5fc3-4e96-b7f2-7e309d53588d" + }, + "domesticated_input10": { + "id": "ad6435740a2af171", "src": "hda", - "uuid": "f6d602b9-7772-4a93-969d-f0dcdad98c6a" + "uuid": "e6431634-077e-451e-afa3-b12c08fc5c7c" + }, + "domesticated_input11": { + "id": "6d393a4d656a3907", + "src": "hda", + "uuid": "758b4a45-c17d-4d1a-a289-79d3b2dfe524" + }, + "domesticated_input12": { + "id": "b1f9d845e51287f2", + "src": "hda", + "uuid": "226889a1-0543-4052-9d94-3276acdbd8ad" }, "domesticated_input2": { - "id": "55c4a2e28d82e47c", + "id": "24ad2b10f2de1c15", "src": "hda", - "uuid": "d4dc3ecb-77ff-4b28-a55a-7b263416c6c7" + "uuid": "4c6b4c02-8f84-4314-8a13-682a855005e0" }, "domesticated_input3": { - "id": "b7e1b2e4287fecf1", + "id": "6bd3728894d22921", "src": "hda", - "uuid": "7d489dbd-161e-4f04-a3df-ef5b989ad1e0" + "uuid": "29c207fc-3958-40b7-8d3a-29486ebe729e" }, "domesticated_input4": { - "id": "fc5d10a4986179ce", + "id": "a7fb62bdcc25db8f", "src": "hda", - "uuid": "4ca3c222-672a-4806-b60c-081f1b7b64cb" + "uuid": "c6e14abc-4cc3-4027-bb1b-cf87b4df2e4c" }, "domesticated_input5": { - "id": "34217302c7a82039", + "id": "b4c6d612f8337c3c", + "src": "hda", + "uuid": "cb90c0ec-c5d5-4a0c-a2a8-82bdf58a4dcd" + }, + "domesticated_input6": { + "id": "dac5f4fe4fc9d2c5", + "src": "hda", + "uuid": "eb6733f2-ea91-4ce2-878c-0bca789bfe95" + }, + "domesticated_input7": { + "id": "01a8e5946ae7b883", "src": "hda", - "uuid": "906707db-b3cf-40f9-af0b-1ffc143f91e8" + "uuid": "dea7a300-b098-41a1-863d-ec55e3b78bda" + }, + "domesticated_input8": { + "id": "348481ce28d8892f", + "src": "hda", + "uuid": "13300353-8b8d-4bd4-9d25-88dceda7594b" + }, + "domesticated_input9": { + "id": "c53526ace39ecb75", + "src": "hda", + "uuid": "61ffb7d6-856a-4e4a-9da3-48a419455e92" }, "genbank_files1": { - "id": "bb3a8c61045de2bc", + "id": "515ae798a3a66959", + "src": "hda", + "uuid": "4c7c671b-5fc3-4e96-b7f2-7e309d53588d" + }, + "genbank_files10": { + "id": "ad6435740a2af171", "src": "hda", - "uuid": "193cbd10-4b76-46d9-b377-a7f06471d4d4" + "uuid": "e6431634-077e-451e-afa3-b12c08fc5c7c" + }, + "genbank_files11": { + "id": "6d393a4d656a3907", + "src": "hda", + "uuid": "758b4a45-c17d-4d1a-a289-79d3b2dfe524" + }, + "genbank_files12": { + "id": "b1f9d845e51287f2", + "src": "hda", + "uuid": "226889a1-0543-4052-9d94-3276acdbd8ad" }, "genbank_files2": { - "id": "ca37518126b9f794", + "id": "24ad2b10f2de1c15", "src": "hda", - "uuid": "fa31c5f5-e678-471e-b1a3-4f8a168bbee1" + "uuid": "4c6b4c02-8f84-4314-8a13-682a855005e0" }, "genbank_files3": { - "id": "f5318c255dfd98f3", + "id": "6bd3728894d22921", "src": "hda", - "uuid": "697c83fe-168b-4319-a6e5-3db90c504c8b" + "uuid": "29c207fc-3958-40b7-8d3a-29486ebe729e" }, "genbank_files4": { - "id": "95f3db52d6362602", + "id": "a7fb62bdcc25db8f", "src": "hda", - "uuid": "06d4dd94-5f33-4ce0-ab0a-e6efe96ca222" + "uuid": "c6e14abc-4cc3-4027-bb1b-cf87b4df2e4c" }, "genbank_files5": { - "id": "22334014eeb47b8b", + "id": "b4c6d612f8337c3c", "src": "hda", - "uuid": "701b72c6-ec2e-4435-b0d5-8f419811a4dd" + "uuid": "cb90c0ec-c5d5-4a0c-a2a8-82bdf58a4dcd" }, "genbank_files6": { - "id": "aebcfa6b078c848c", + "id": "dac5f4fe4fc9d2c5", "src": "hda", - "uuid": "5a07f059-f6f9-49de-b0fc-3cded157f44b" + "uuid": "eb6733f2-ea91-4ce2-878c-0bca789bfe95" }, "genbank_files7": { - "id": "63b7227f824d465f", + "id": "01a8e5946ae7b883", + "src": "hda", + "uuid": "dea7a300-b098-41a1-863d-ec55e3b78bda" + }, + "genbank_files8": { + "id": "348481ce28d8892f", "src": "hda", - "uuid": "753f0297-4bff-49c8-b22a-1377e43a81f6" + "uuid": "13300353-8b8d-4bd4-9d25-88dceda7594b" + }, + "genbank_files9": { + "id": "c53526ace39ecb75", + "src": "hda", + "uuid": "61ffb7d6-856a-4e4a-9da3-48a419455e92" } }, - "job_messages": [], + "job_messages": [ + { + "code_desc": "", + "desc": "Fatal error: Exit code 1 ()", + "error_level": 3, + "exit_code": 1, + "type": "exit_code" + } + ], "job_metrics": [], "job_runner_name": null, "job_stderr": "", @@ -1582,65 +1989,50 @@ "model_class": "Job", "output_collections": { "construct_gb": { - "id": "40769e0726e5d2f9", + "id": "fae073f924dc0737", "src": "hdca" } }, "outputs": { - "__new_primary_file_construct_gb|construct_1__": { - "id": "00e4fea3ca53d1d5", - "src": "hda", - "uuid": "5cef395a-54ba-474b-b40b-1e5b3b2c4269" - }, - "__new_primary_file_construct_gb|construct_2__": { - "id": "684375afe9650993", + "output_zip": { + "id": "24ef522ceac5a910", "src": "hda", - "uuid": "77cca133-2fb3-4cf3-b4b1-a802a1f09ea3" - }, - "__new_primary_file_construct_gb|construct_3__": { - "id": "45afc15ea654e191", - "src": "hda", - "uuid": "dbd53cde-61b2-4db8-b6bf-f0caaec76ace" - }, - "__new_primary_file_construct_gb|construct_4__": { - "id": "8aa0c494b99ce49f", - "src": "hda", - "uuid": "8ea5339c-3186-4886-8af7-2a2d8134e161" - }, - "output_zip": { - "id": "4d559b2811c6a30e", - "src": "hda", - "uuid": "800320dc-d181-40bf-b1cb-541f43a838c3" + "uuid": "7ec4ccea-6d53-4d2c-b343-476013e8c0d9" } }, "params": { "__input_ext": "\"input\"", "adv": "{\"enzyme\": \"auto\", \"use_file_names_as_ids\": true}", "assembly_plan_name": "\"Type2sRestrictionAssembly\"", - "chromInfo": "\"/tmp/tmpay0tme4v/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", + "chromInfo": "\"/tmp/tmpo3npfzdk/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", "dbkey": "\"?\"", - "domesticated_input": "{\"values\": [{\"id\": 11, \"src\": \"hdca\"}]}", - "genbank_files": "{\"values\": [{\"id\": 12, \"src\": \"hdca\"}]}", + "domesticated_input": "{\"values\": [{\"id\": 14, \"src\": \"hdca\"}]}", + "genbank_files": "{\"values\": [{\"id\": 14, \"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, 2.35it/s, now=None]\rassembly: 75%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u258c | 3/4 [00:01<00:00, 2.13it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 4/4 [00:02<00:00, 1.77it/s, now=None]\r \r", - "stdout": "Simulating assembly plan assambly...\n{'cancelled_assemblies': 0, 'errored_assemblies': 0, 'valid_assemblies': 4}\nGenerating assemblies reports...\n", + "state": "error", + "stderr": "Traceback (most recent call last):\n File \"/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py\", line 165, in <module>\n cloning_simulation(\n ~~~~~~~~~~~~~~~~~~^\n args.parts_files, args.domesticated_seq,\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n ...<3 lines>...\n args.output_simulation, args.enzyme, args.outdir_gb\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n )\n ^\n File \"/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py\", line 22, in cloning_simulation\n repository.import_records(files=domesticated_files,\n ~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^\n use_file_names_as_ids=use_file_names_as_id,\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n topology=topology)\n ^^^^^^^^^^^^^^^^^^\n File \"/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf/lib/python3.13/site-packages/dnacauldron/SequenceRepository.py\", line 170, in import_records\n self.add_records(records, collection=collection)\n ~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n File \"/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf/lib/python3.13/site-packages/dnacauldron/SequenceRepository.py\", line 96, in add_records\n self.add_record(record, collection=collection)\n ~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n File \"/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf/lib/python3.13/site-packages/dnacauldron/SequenceRepository.py\", line 85, in add_record\n raise RepositoryDuplicateError([record.id], repository=self)\ndnacauldron.SequenceRepository.RepositoryDuplicateError: Part ID dataset_4c7c671b-5fc3-4e96-b7f2-7e309d53588d duplicated in in repo\n", + "stdout": "", "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, 2.13it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 4/4 [00:02<00:00, 1.77it/s, now=None]\r \r", - "tool_stdout": "Simulating assembly plan assambly...\n{'cancelled_assemblies': 0, 'errored_assemblies': 0, 'valid_assemblies': 4}\nGenerating assemblies reports...\n", - "update_time": "2025-05-19T13:48:06.412363", + "tool_stderr": "Traceback (most recent call last):\n File \"/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py\", line 165, in <module>\n cloning_simulation(\n ~~~~~~~~~~~~~~~~~~^\n args.parts_files, args.domesticated_seq,\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n ...<3 lines>...\n args.output_simulation, args.enzyme, args.outdir_gb\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n )\n ^\n File \"/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py\", line 22, in cloning_simulation\n repository.import_records(files=domesticated_files,\n ~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^\n use_file_names_as_ids=use_file_names_as_id,\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n topology=topology)\n ^^^^^^^^^^^^^^^^^^\n File \"/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf/lib/python3.13/site-packages/dnacauldron/SequenceRepository.py\", line 170, in import_records\n self.add_records(records, collection=collection)\n ~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n File \"/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf/lib/python3.13/site-packages/dnacauldron/SequenceRepository.py\", line 96, in add_records\n self.add_record(record, collection=collection)\n ~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n File \"/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf/lib/python3.13/site-packages/dnacauldron/SequenceRepository.py\", line 85, in add_record\n raise RepositoryDuplicateError([record.id], repository=self)\ndnacauldron.SequenceRepository.RepositoryDuplicateError: Part ID dataset_4c7c671b-5fc3-4e96-b7f2-7e309d53588d duplicated in in repo\n", + "tool_stdout": "", + "update_time": "2025-05-21T14:51:18.877985", "user_email": "planemo@galaxyproject.org", - "user_id": "fd8809ceca5b90d8" + "user_id": "9f2c11a06c2c8bb2" }, - "status": "success", - "test_index": 5, - "time_seconds": 55.54361414909363, + "output_problems": [ + "Job in error state.. tool_id: cloning_simulation, exit_code: 1, stderr: Traceback (most recent call last):\n File \"/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py\", line 165, in <module>\n cloning_simulation(\n ~~~~~~~~~~~~~~~~~~^\n args.parts_files, args.domesticated_seq,\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n ...<3 lines>...\n args.output_simulation, args.enzyme, args.outdir_gb\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n )\n ^\n File \"/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py\", line 22, in cloning_simulation\n repository.import_records(files=domesticated_files,\n ~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^\n use_file_names_as_ids=use_file_names_as_id,\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n topology=topology)\n ^^^^^^^^^^^^^^^^^^\n File \"/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf/lib/python3.13/site-packages/dnacauldron/SequenceRepository.py\", line 170, in import_records\n self.add_records(records, collection=collection)\n ~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n File \"/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf/lib/python3.13/site-packages/dnacauldron/SequenceRepository.py\", line 96, in add_records\n self.add_record(record, collection=collection)\n ~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n File \"/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf/lib/python3.13/site-packages/dnacauldron/SequenceRepository.py\", line 85, in add_record\n raise RepositoryDuplicateError([record.id], repository=self)\ndnacauldron.SequenceRepository.RepositoryDuplicateError: Part ID dataset_4c7c671b-5fc3-4e96-b7f2-7e309d53588d duplicated in in repo\n.", + "Job in error state.. tool_id: cloning_simulation, exit_code: 1, stderr: Traceback (most recent call last):\n File \"/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py\", line 165, in <module>\n cloning_simulation(\n ~~~~~~~~~~~~~~~~~~^\n args.parts_files, args.domesticated_seq,\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n ...<3 lines>...\n args.output_simulation, args.enzyme, args.outdir_gb\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n )\n ^\n File \"/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py\", line 22, in cloning_simulation\n repository.import_records(files=domesticated_files,\n ~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^\n use_file_names_as_ids=use_file_names_as_id,\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n topology=topology)\n ^^^^^^^^^^^^^^^^^^\n File \"/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf/lib/python3.13/site-packages/dnacauldron/SequenceRepository.py\", line 170, in import_records\n self.add_records(records, collection=collection)\n ~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n File \"/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf/lib/python3.13/site-packages/dnacauldron/SequenceRepository.py\", line 96, in add_records\n self.add_record(record, collection=collection)\n ~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n File \"/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf/lib/python3.13/site-packages/dnacauldron/SequenceRepository.py\", line 85, in add_record\n raise RepositoryDuplicateError([record.id], repository=self)\ndnacauldron.SequenceRepository.RepositoryDuplicateError: Part ID dataset_4c7c671b-5fc3-4e96-b7f2-7e309d53588d duplicated in in repo\n.", + "Output collection 'construct_gb': expected to have 4 elements, but it had 0." + ], + "status": "failure", + "test_index": 6, + "time_seconds": 49.28661274909973, "tool_id": "cloning_simulation", "tool_version": "0.1.0+galaxy0" }, "has_data": true, - "id": "cloning_simulation-5" + "id": "cloning_simulation-6" } ], "version": "0.1"