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Updating anvil-edge README for edge-25-01-02-06-11-1
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reports/anvil-edge/tool-tests/edge-25-01-02-06-11-1/chunk.json
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{ | ||
"6": { | ||
"run1": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-edge/tool-tests/edge-25-01-02-06-11-1/results.html", | ||
"date1": "Thu Jan 02 06:27:55 2025", | ||
"tools": "https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-edge/tool-tests/edge-25-01-02-06-11-1/tools.yml" | ||
} | ||
} |
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reports/anvil-edge/tool-tests/edge-25-01-02-06-11-1/chunk.txt
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-t split_file_to_collection --tool-version 6cbe2f30c2d7 | ||
-t deeptools_multi_bigwig_summary --tool-version 3c9f0c486cca | ||
-t fastq_paired_end_interlacer --tool-version 2ccb8dcabddc | ||
-t jbrowse --tool-version 4542035c1075 | ||
-t jbrowse --tool-version a6e57ff585c0 | ||
-t mummer_delta_filter --tool-version b3acbb3a6af0 | ||
-t poretools_winner --tool-version 79c1ac92f31b | ||
-t edger --tool-version 334ce9b1bac5 | ||
-t qualimap_multi_bamqc --tool-version e38af83df163 | ||
-t samtools_sort --tool-version e613c1ad4c4c | ||
-t 10x_bamtofastq --tool-version f71fd828c126 | ||
-t raceid_trajectory --tool-version 72979cac22b2 | ||
-t raceid_trajectory --tool-version c92d0f9338c5 | ||
-t scanpy_inspect --tool-version c5d3684f7c4c | ||
-t scanpy_find_variable_genes --tool-version 0edb75c411a4 | ||
-t scanpy_find_variable_genes --tool-version 5c62f39aab8f | ||
-t concatenate_multiple_datasets --tool-version 201c568972c3 | ||
-t snpfreqplot --tool-version e362b3143cde | ||
-t bcftools_gtcheck --tool-version 672b6c02fbc7 | ||
-t bcftools_reheader --tool-version 9ef52d95114b | ||
-t bcftools_plugin_tag2tag --tool-version bdfdf5f6e950 | ||
-t vcfgenotypes --tool-version a60ae8af21a1 | ||
-t ivar_removereads --tool-version ee2beb764a7b |
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reports/anvil-edge/tool-tests/edge-25-01-02-06-11-1/errors/039e98ef7e07fc36.json
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{ | ||
"model_class": "Job", | ||
"id": "039e98ef7e07fc36", | ||
"history_id": "417947348fdacb2d", | ||
"tool_id": "upload1", | ||
"state": "error", | ||
"exit_code": null, | ||
"create_time": "2025-01-02T06:44:25.858843", | ||
"update_time": "2025-01-02T06:44:39.170620", | ||
"galaxy_version": "24.1", | ||
"external_id": "gxy-vfs2j", | ||
"handler": null, | ||
"job_runner_name": null, | ||
"command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/66/registry.xml' '/galaxy/server/database/jobs_directory/000/66/upload_params.json' '111:/galaxy/server/database/objects/6/f/d/dataset_6fdb4ae0-d4b9-4455-8267-26504b1c3a4e_files:/galaxy/server/database/objects/6/f/d/dataset_6fdb4ae0-d4b9-4455-8267-26504b1c3a4e.dat'", | ||
"user_email": "tests@fake.org", | ||
"command_version": null, | ||
"params": { | ||
"paramfile": "\"/galaxy/server/database/tmp/upload_params_oyf3asmn\"", | ||
"files_metadata": "{\"__current_case__\": 708, \"file_type\": \"auto\"}", | ||
"dbkey": "\"?\"", | ||
"force_composite": "\"false\"", | ||
"files": "[{\"NAME\": \"A.gff\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_c871qbon\", \"file_type\": \"\", \"ftp_files\": null, \"space_to_tab\": null, \"to_posix_lines\": \"Yes\", \"url_paste\": null, \"uuid\": null}]", | ||
"file_count": "\"auto\"", | ||
"file_type": "\"auto\"" | ||
}, | ||
"inputs": {}, | ||
"outputs": { | ||
"output0": { | ||
"id": "7e10eda76b933a67", | ||
"src": "hda", | ||
"uuid": "6fdb4ae0-d4b9-4455-8267-26504b1c3a4e" | ||
} | ||
}, | ||
"copied_from_job_id": null, | ||
"output_collections": {}, | ||
"tool_stdout": "", | ||
"tool_stderr": "", | ||
"job_stdout": null, | ||
"job_stderr": null, | ||
"stdout": "", | ||
"stderr": "", | ||
"job_messages": null, | ||
"dependencies": [], | ||
"job_metrics": [] | ||
} |
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reports/anvil-edge/tool-tests/edge-25-01-02-06-11-1/errors/24611f45b2c6f4c6.json
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{ | ||
"model_class": "Job", | ||
"id": "24611f45b2c6f4c6", | ||
"history_id": "417947348fdacb2d", | ||
"tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1", | ||
"state": "error", | ||
"exit_code": null, | ||
"create_time": "2025-01-02T06:43:40.627763", | ||
"update_time": "2025-01-02T06:43:46.594588", | ||
"galaxy_version": "24.1", | ||
"external_id": "gxy-vgq6z", | ||
"handler": null, | ||
"job_runner_name": null, | ||
"command_line": "mkdir -p /galaxy/server/database/objects/d/1/b/dataset_d1bb7e69-77ec-4295-853d-fa8a94c59224_files && cp /galaxy/server/database/jobs_directory/000/60/configs/tmprwvpsk2e /galaxy/server/database/objects/d/1/b/dataset_d1bb7e69-77ec-4295-853d-fa8a94c59224_files/galaxy.xml && export JBROWSE_SOURCE_DIR=$(dirname $(which prepare-refseqs.pl))/../opt/jbrowse && python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/a6e57ff585c0/jbrowse/jbrowse.py' --jbrowse ${JBROWSE_SOURCE_DIR} --standalone 'data' --outdir /galaxy/server/database/objects/d/1/b/dataset_d1bb7e69-77ec-4295-853d-fa8a94c59224_files /galaxy/server/database/jobs_directory/000/60/configs/tmprwvpsk2e && cp /galaxy/server/database/jobs_directory/000/60/configs/tmpghdqxa_n /galaxy/server/database/objects/d/1/b/dataset_d1bb7e69-77ec-4295-853d-fa8a94c59224.dat; cp /galaxy/server/database/jobs_directory/000/60/configs/tmprwvpsk2e /galaxy/server/database/objects/d/1/b/dataset_d1bb7e69-77ec-4295-853d-fa8a94c59224.dat", | ||
"user_email": "tests@fake.org", | ||
"command_version": null, | ||
"params": { | ||
"__input_ext": "\"fasta\"", | ||
"dbkey": "\"?\"", | ||
"chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", | ||
"uglyTestingHack": "\"enabled\"", | ||
"plugins": "{\"BlastView\": true, \"ComboTrackSelector\": false, \"GCContent\": false}", | ||
"jbgen": "{\"aboutDescription\": \"\", \"defaultLocation\": \"\", \"hideGenomeOptions\": false, \"shareLink\": true, \"show_menu\": true, \"show_nav\": true, \"show_overview\": true, \"show_tracklist\": true, \"trackPadding\": \"20\"}", | ||
"track_groups": "[]", | ||
"action": "{\"__current_case__\": 0, \"action_select\": \"create\"}", | ||
"gencode": "\"11\"", | ||
"standalone": "\"data\"", | ||
"reference_genome": "{\"__current_case__\": 1, \"genome\": {\"values\": [{\"id\": 104, \"src\": \"hda\"}]}, \"genome_type_select\": \"history\"}" | ||
}, | ||
"inputs": { | ||
"reference_genome|genome": { | ||
"id": "59e7f7bb0c0090a3", | ||
"src": "hda", | ||
"uuid": "f078e412-c1c9-4650-be7b-e5e1e28f0ac9" | ||
} | ||
}, | ||
"outputs": { | ||
"output": { | ||
"id": "86e3335ea84ed5fd", | ||
"src": "hda", | ||
"uuid": "d1bb7e69-77ec-4295-853d-fa8a94c59224" | ||
} | ||
}, | ||
"copied_from_job_id": null, | ||
"output_collections": {}, | ||
"tool_stdout": "", | ||
"tool_stderr": "WARNING: No feature names found for indexing, only reference sequence names will be indexed.\n", | ||
"job_stdout": null, | ||
"job_stderr": null, | ||
"stdout": "", | ||
"stderr": "WARNING: No feature names found for indexing, only reference sequence names will be indexed.\n", | ||
"job_messages": null, | ||
"dependencies": [], | ||
"job_metrics": [] | ||
} |
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reports/anvil-edge/tool-tests/edge-25-01-02-06-11-1/errors/2737299cf0223786.json
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{ | ||
"model_class": "Job", | ||
"id": "2737299cf0223786", | ||
"history_id": "417947348fdacb2d", | ||
"tool_id": "upload1", | ||
"state": "error", | ||
"exit_code": null, | ||
"create_time": "2025-01-02T07:28:48.509281", | ||
"update_time": "2025-01-02T07:29:00.317303", | ||
"galaxy_version": "24.1", | ||
"external_id": "gxy-9mg8g", | ||
"handler": null, | ||
"job_runner_name": null, | ||
"command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/252/registry.xml' '/galaxy/server/database/jobs_directory/000/252/upload_params.json' '330:/galaxy/server/database/objects/8/7/e/dataset_87ebc466-7379-4a64-a05c-66c208fc7c0b_files:/galaxy/server/database/objects/8/7/e/dataset_87ebc466-7379-4a64-a05c-66c208fc7c0b.dat'", | ||
"user_email": "tests@fake.org", | ||
"command_version": null, | ||
"params": { | ||
"paramfile": "\"/galaxy/server/database/tmp/upload_params_wa0ac7yr\"", | ||
"files_metadata": "{\"__current_case__\": 325, \"file_type\": \"tabular\"}", | ||
"dbkey": "\"?\"", | ||
"force_composite": "\"false\"", | ||
"files": "[{\"NAME\": \"input436.tabular\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_d496aotr\", \"file_type\": \"\", \"ftp_files\": null, \"space_to_tab\": null, \"to_posix_lines\": \"Yes\", \"url_paste\": null, \"uuid\": null}]", | ||
"file_count": "\"auto\"", | ||
"file_type": "\"tabular\"" | ||
}, | ||
"inputs": {}, | ||
"outputs": { | ||
"output0": { | ||
"id": "1bb67360a25de827", | ||
"src": "hda", | ||
"uuid": "87ebc466-7379-4a64-a05c-66c208fc7c0b" | ||
} | ||
}, | ||
"copied_from_job_id": null, | ||
"output_collections": {}, | ||
"tool_stdout": "", | ||
"tool_stderr": "", | ||
"job_stdout": null, | ||
"job_stderr": null, | ||
"stdout": "", | ||
"stderr": "", | ||
"job_messages": null, | ||
"dependencies": [], | ||
"job_metrics": [] | ||
} |
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reports/anvil-edge/tool-tests/edge-25-01-02-06-11-1/errors/27d5e95f2f20c64a.json
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{ | ||
"model_class": "Job", | ||
"id": "27d5e95f2f20c64a", | ||
"history_id": "417947348fdacb2d", | ||
"tool_id": "upload1", | ||
"state": "error", | ||
"exit_code": null, | ||
"create_time": "2025-01-02T07:24:22.286949", | ||
"update_time": "2025-01-02T07:24:33.096654", | ||
"galaxy_version": "24.1", | ||
"external_id": "gxy-shj2j", | ||
"handler": null, | ||
"job_runner_name": null, | ||
"command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/228/registry.xml' '/galaxy/server/database/jobs_directory/000/228/upload_params.json' '304:/galaxy/server/database/objects/0/d/a/dataset_0da8bf9d-0629-434d-b81c-8712e4bfcc87_files:/galaxy/server/database/objects/0/d/a/dataset_0da8bf9d-0629-434d-b81c-8712e4bfcc87.dat'", | ||
"user_email": "tests@fake.org", | ||
"command_version": null, | ||
"params": { | ||
"paramfile": "\"/galaxy/server/database/tmp/upload_params_uvmau3b2\"", | ||
"files_metadata": "{\"__current_case__\": 708, \"file_type\": \"auto\"}", | ||
"dbkey": "\"?\"", | ||
"force_composite": "\"false\"", | ||
"files": "[{\"NAME\": \"krumsiek11.h5ad\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_7qyzzj7r\", \"file_type\": \"\", \"ftp_files\": null, \"space_to_tab\": null, \"to_posix_lines\": \"Yes\", \"url_paste\": null, \"uuid\": null}]", | ||
"file_count": "\"auto\"", | ||
"file_type": "\"auto\"" | ||
}, | ||
"inputs": {}, | ||
"outputs": { | ||
"output0": { | ||
"id": "8688d9f2b42bcb18", | ||
"src": "hda", | ||
"uuid": "0da8bf9d-0629-434d-b81c-8712e4bfcc87" | ||
} | ||
}, | ||
"copied_from_job_id": null, | ||
"output_collections": {}, | ||
"tool_stdout": "", | ||
"tool_stderr": "", | ||
"job_stdout": null, | ||
"job_stderr": null, | ||
"stdout": "", | ||
"stderr": "", | ||
"job_messages": null, | ||
"dependencies": [], | ||
"job_metrics": [] | ||
} |
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reports/anvil-edge/tool-tests/edge-25-01-02-06-11-1/errors/313ab96f9d8f8251.json
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{ | ||
"model_class": "Job", | ||
"id": "313ab96f9d8f8251", | ||
"history_id": "417947348fdacb2d", | ||
"tool_id": "upload1", | ||
"state": "error", | ||
"exit_code": null, | ||
"create_time": "2025-01-02T06:44:26.074855", | ||
"update_time": "2025-01-02T06:44:39.404990", | ||
"galaxy_version": "24.1", | ||
"external_id": "gxy-nl8rl", | ||
"handler": null, | ||
"job_runner_name": null, | ||
"command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/67/registry.xml' '/galaxy/server/database/jobs_directory/000/67/upload_params.json' '112:/galaxy/server/database/objects/c/0/a/dataset_c0a39b3d-1a79-4cbc-b3aa-f58d3711a5e4_files:/galaxy/server/database/objects/c/0/a/dataset_c0a39b3d-1a79-4cbc-b3aa-f58d3711a5e4.dat'", | ||
"user_email": "tests@fake.org", | ||
"command_version": null, | ||
"params": { | ||
"paramfile": "\"/galaxy/server/database/tmp/upload_params_9bks87yq\"", | ||
"files_metadata": "{\"__current_case__\": 708, \"file_type\": \"auto\"}", | ||
"dbkey": "\"?\"", | ||
"force_composite": "\"false\"", | ||
"files": "[{\"NAME\": \"B.gff\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_d7avqvm1\", \"file_type\": \"\", \"ftp_files\": null, \"space_to_tab\": null, \"to_posix_lines\": \"Yes\", \"url_paste\": null, \"uuid\": null}]", | ||
"file_count": "\"auto\"", | ||
"file_type": "\"auto\"" | ||
}, | ||
"inputs": {}, | ||
"outputs": { | ||
"output0": { | ||
"id": "bb2cdd97a30e285f", | ||
"src": "hda", | ||
"uuid": "c0a39b3d-1a79-4cbc-b3aa-f58d3711a5e4" | ||
} | ||
}, | ||
"copied_from_job_id": null, | ||
"output_collections": {}, | ||
"tool_stdout": "", | ||
"tool_stderr": "", | ||
"job_stdout": null, | ||
"job_stderr": null, | ||
"stdout": "", | ||
"stderr": "", | ||
"job_messages": null, | ||
"dependencies": [], | ||
"job_metrics": [] | ||
} |
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reports/anvil-edge/tool-tests/edge-25-01-02-06-11-1/errors/3e8cd1fa93a54128.json
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{ | ||
"model_class": "Job", | ||
"id": "3e8cd1fa93a54128", | ||
"history_id": "417947348fdacb2d", | ||
"tool_id": "upload1", | ||
"state": "error", | ||
"exit_code": null, | ||
"create_time": "2025-01-02T06:44:26.989906", | ||
"update_time": "2025-01-02T06:44:55.079112", | ||
"galaxy_version": "24.1", | ||
"external_id": "gxy-2jvcs", | ||
"handler": null, | ||
"job_runner_name": null, | ||
"command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/71/registry.xml' '/galaxy/server/database/jobs_directory/000/71/upload_params.json' '116:/galaxy/server/database/objects/d/6/0/dataset_d604e90e-77f3-472a-9043-73f2ce850a5c_files:/galaxy/server/database/objects/d/6/0/dataset_d604e90e-77f3-472a-9043-73f2ce850a5c.dat'", | ||
"user_email": "tests@fake.org", | ||
"command_version": null, | ||
"params": { | ||
"paramfile": "\"/galaxy/server/database/tmp/upload_params_nk3htj2u\"", | ||
"files_metadata": "{\"__current_case__\": 708, \"file_type\": \"auto\"}", | ||
"dbkey": "\"?\"", | ||
"force_composite": "\"false\"", | ||
"files": "[{\"NAME\": \"interpro.gff\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_7xtcn_br\", \"file_type\": \"\", \"ftp_files\": null, \"space_to_tab\": null, \"to_posix_lines\": \"Yes\", \"url_paste\": null, \"uuid\": null}]", | ||
"file_count": "\"auto\"", | ||
"file_type": "\"auto\"" | ||
}, | ||
"inputs": {}, | ||
"outputs": { | ||
"output0": { | ||
"id": "4963a0f517e742b4", | ||
"src": "hda", | ||
"uuid": "d604e90e-77f3-472a-9043-73f2ce850a5c" | ||
} | ||
}, | ||
"copied_from_job_id": null, | ||
"output_collections": {}, | ||
"tool_stdout": "", | ||
"tool_stderr": "", | ||
"job_stdout": null, | ||
"job_stderr": null, | ||
"stdout": "", | ||
"stderr": "", | ||
"job_messages": null, | ||
"dependencies": [], | ||
"job_metrics": [] | ||
} |
45 changes: 45 additions & 0 deletions
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reports/anvil-edge/tool-tests/edge-25-01-02-06-11-1/errors/52803ce717ec40bb.json
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{ | ||
"model_class": "Job", | ||
"id": "52803ce717ec40bb", | ||
"history_id": "417947348fdacb2d", | ||
"tool_id": "upload1", | ||
"state": "error", | ||
"exit_code": null, | ||
"create_time": "2025-01-02T06:37:44.318341", | ||
"update_time": "2025-01-02T06:37:54.371100", | ||
"galaxy_version": "24.1", | ||
"external_id": "gxy-cj5vn", | ||
"handler": null, | ||
"job_runner_name": null, | ||
"command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/34/registry.xml' '/galaxy/server/database/jobs_directory/000/34/upload_params.json' '72:/galaxy/server/database/objects/8/c/0/dataset_8c031b9d-2c7d-4fc8-b8ea-f13f7170c690_files:/galaxy/server/database/objects/8/c/0/dataset_8c031b9d-2c7d-4fc8-b8ea-f13f7170c690.dat'", | ||
"user_email": "tests@fake.org", | ||
"command_version": null, | ||
"params": { | ||
"paramfile": "\"/galaxy/server/database/tmp/upload_params_qddtf6b0\"", | ||
"files_metadata": "{\"__current_case__\": 542, \"file_type\": \"sdf\"}", | ||
"dbkey": "\"?\"", | ||
"force_composite": "\"false\"", | ||
"files": "[{\"NAME\": \"3_molecules.sdf\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_i8a5i9k0\", \"file_type\": \"\", \"ftp_files\": null, \"space_to_tab\": null, \"to_posix_lines\": \"Yes\", \"url_paste\": null, \"uuid\": null}]", | ||
"file_count": "\"auto\"", | ||
"file_type": "\"sdf\"" | ||
}, | ||
"inputs": {}, | ||
"outputs": { | ||
"output0": { | ||
"id": "808d25e5c3af11a1", | ||
"src": "hda", | ||
"uuid": "8c031b9d-2c7d-4fc8-b8ea-f13f7170c690" | ||
} | ||
}, | ||
"copied_from_job_id": null, | ||
"output_collections": {}, | ||
"tool_stdout": "", | ||
"tool_stderr": "", | ||
"job_stdout": null, | ||
"job_stderr": null, | ||
"stdout": "", | ||
"stderr": "", | ||
"job_messages": null, | ||
"dependencies": [], | ||
"job_metrics": [] | ||
} |
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