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Updating anvil-edge README for edge-25-02-19-18-16-1
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reports/anvil-edge/tool-tests/edge-25-02-19-18-16-1/chunk.json
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{ | ||
"5": { | ||
"run1": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-edge/tool-tests/edge-25-02-19-18-16-1/results.html", | ||
"date1": "Wed Feb 19 18:32:37 2025", | ||
"tools": "https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-edge/tool-tests/edge-25-02-19-18-16-1/tools.yml" | ||
} | ||
} |
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reports/anvil-edge/tool-tests/edge-25-02-19-18-16-1/chunk.txt
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-t collapse_collections --tool-version 90981f86000f | ||
-t deeptools_multi_bam_summary --tool-version 78f405266706 | ||
-t fastq_paired_end_deinterlacer --tool-version f3936d0632cb | ||
-t circos --tool-version df7356989ac1 | ||
-t mummer_mummer --tool-version 48823c9635a4 | ||
-t porechop --tool-version 93d623d9979c | ||
-t limma_voom --tool-version 0921444c832d | ||
-t limma_voom --tool-version d6f5fa4ee473 | ||
-t sam2interval --tool-version 75557c0908a9 | ||
-t samtools_flagstat --tool-version 22970df7a40e | ||
-t music_construct_eset --tool-version 282819d09a4f | ||
-t music_construct_eset --tool-version 2cfd0db49bbc | ||
-t raceid_clustering --tool-version a4b734cd253b | ||
-t raceid_clustering --tool-version f911a64454fb | ||
-t scanpy_filter --tool-version b409c2486353 | ||
-t scanpy_normalise_data --tool-version 439f7f939d46 | ||
-t scanpy_normalise_data --tool-version 463d4fa8f5ec | ||
-t annotatemyids --tool-version 44018dd6b447 | ||
-t annotatemyids --tool-version fe3ca740a485 | ||
-t diff --tool-version 156d0908e232 | ||
-t bcftools_consensus --tool-version d6dc477167f8 | ||
-t bcftools_plugin_impute_info --tool-version 776ad0b21536 | ||
-t bcftools_query --tool-version c9c5718edc19 | ||
-t vcfgeno2haplo --tool-version a3dea556218d | ||
-t ivar_trim --tool-version db536ad45f28 |
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reports/anvil-edge/tool-tests/edge-25-02-19-18-16-1/errors/062a9aa59e5affed.json
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{ | ||
"model_class": "Job", | ||
"id": "062a9aa59e5affed", | ||
"history_id": "97b4f5385ce85823", | ||
"tool_id": "upload1", | ||
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"galaxy_version": "24.1", | ||
"external_id": "gxy-j7wvn", | ||
"handler": null, | ||
"job_runner_name": null, | ||
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"files_metadata": "{\"__current_case__\": 708, \"file_type\": \"auto\"}", | ||
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"file_count": "\"auto\"", | ||
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"uuid": "75bbfe93-bc13-4c97-bce9-eb30052d0754" | ||
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} |
45 changes: 45 additions & 0 deletions
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reports/anvil-edge/tool-tests/edge-25-02-19-18-16-1/errors/19b70f02cdcfa66f.json
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{ | ||
"model_class": "Job", | ||
"id": "19b70f02cdcfa66f", | ||
"history_id": "97b4f5385ce85823", | ||
"tool_id": "upload1", | ||
"state": "error", | ||
"exit_code": null, | ||
"create_time": "2025-02-19T19:05:55.123704", | ||
"update_time": "2025-02-19T19:06:05.357229", | ||
"galaxy_version": "24.1", | ||
"external_id": "gxy-98bv6", | ||
"handler": null, | ||
"job_runner_name": null, | ||
"command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/116/registry.xml' '/galaxy/server/database/jobs_directory/000/116/upload_params.json' '156:/galaxy/server/database/objects/9/7/7/dataset_9775611b-556f-47e3-804a-b906242cef47_files:/galaxy/server/database/objects/9/7/7/dataset_9775611b-556f-47e3-804a-b906242cef47.dat'", | ||
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"params": { | ||
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"files_metadata": "{\"__current_case__\": 708, \"file_type\": \"auto\"}", | ||
"dbkey": "\"?\"", | ||
"force_composite": "\"false\"", | ||
"files": "[{\"NAME\": \"matrix.filter.rdat\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_qnb0n7gh\", \"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": "3363b05580e3c8ef", | ||
"src": "hda", | ||
"uuid": "9775611b-556f-47e3-804a-b906242cef47" | ||
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"output_collections": {}, | ||
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"tool_stderr": "", | ||
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"stdout": "", | ||
"stderr": "", | ||
"job_messages": null, | ||
"dependencies": [], | ||
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} |
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reports/anvil-edge/tool-tests/edge-25-02-19-18-16-1/errors/1dae1b560d3e3035.json
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{ | ||
"model_class": "Job", | ||
"id": "1dae1b560d3e3035", | ||
"history_id": "97b4f5385ce85823", | ||
"tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/annotatemyids/annotatemyids/3.5.0.1", | ||
"state": "error", | ||
"exit_code": null, | ||
"create_time": "2025-02-19T19:21:18.401094", | ||
"update_time": "2025-02-19T19:22:14.915188", | ||
"galaxy_version": "24.1", | ||
"external_id": "gxy-ztkgn", | ||
"handler": null, | ||
"job_runner_name": null, | ||
"command_line": "Rscript '/galaxy/server/database/jobs_directory/000/145/configs/tmpu9nw48i0'", | ||
"user_email": "tests@fake.org", | ||
"command_version": null, | ||
"params": { | ||
"__input_ext": "\"tabular\"", | ||
"dbkey": "\"?\"", | ||
"chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", | ||
"rscriptOpt": "false", | ||
"remove_dups": "false", | ||
"output_cols": "[\"ENSEMBL\", \"ENTREZID\", \"SYMBOL\", \"GENENAME\"]", | ||
"id_type": "\"SYMBOL\"", | ||
"organism": "\"Hs\"", | ||
"file_has_header": "false" | ||
}, | ||
"inputs": { | ||
"id_file": { | ||
"id": "a3255d132981d58a", | ||
"src": "hda", | ||
"uuid": "38b7d591-dad5-454d-9b19-3d444b16c891" | ||
} | ||
}, | ||
"outputs": { | ||
"out_tab": { | ||
"id": "af75057cd623ca53", | ||
"src": "hda", | ||
"uuid": "d0d3c342-d265-414a-ad53-70012ac78bb0" | ||
} | ||
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"copied_from_job_id": null, | ||
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"tool_stderr": "Warning message:\nIn Sys.setlocale(\"LC_MESSAGES\", \"en_US.UTF-8\") :\n OS reports request to set locale to \"en_US.UTF-8\" cannot be honored\n'select()' returned 1:1 mapping between keys and columns\n", | ||
"job_stdout": null, | ||
"job_stderr": null, | ||
"stdout": "", | ||
"stderr": "Warning message:\nIn Sys.setlocale(\"LC_MESSAGES\", \"en_US.UTF-8\") :\n OS reports request to set locale to \"en_US.UTF-8\" cannot be honored\n'select()' returned 1:1 mapping between keys and columns\n", | ||
"job_messages": null, | ||
"dependencies": [], | ||
"job_metrics": [] | ||
} |
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reports/anvil-edge/tool-tests/edge-25-02-19-18-16-1/errors/244fff1feed176a5.json
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{ | ||
"model_class": "Job", | ||
"id": "244fff1feed176a5", | ||
"history_id": "97b4f5385ce85823", | ||
"tool_id": "upload1", | ||
"state": "error", | ||
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"create_time": "2025-02-19T18:45:27.950355", | ||
"update_time": "2025-02-19T18:45:43.242611", | ||
"galaxy_version": "24.1", | ||
"external_id": "gxy-97fsb", | ||
"handler": null, | ||
"job_runner_name": null, | ||
"command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/41/registry.xml' '/galaxy/server/database/jobs_directory/000/41/upload_params.json' '54:/galaxy/server/database/objects/1/3/f/dataset_13fbd80c-c7b8-475e-b61b-7b33519641d3_files:/galaxy/server/database/objects/1/3/f/dataset_13fbd80c-c7b8-475e-b61b-7b33519641d3.dat'", | ||
"user_email": "tests@fake.org", | ||
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"files_metadata": "{\"__current_case__\": 708, \"file_type\": \"auto\"}", | ||
"dbkey": "\"?\"", | ||
"force_composite": "\"false\"", | ||
"files": "[{\"NAME\": \"WT1.counts\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_7kf4ydcj\", \"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": "29052f37b76c93bd", | ||
"src": "hda", | ||
"uuid": "13fbd80c-c7b8-475e-b61b-7b33519641d3" | ||
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"stdout": "", | ||
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reports/anvil-edge/tool-tests/edge-25-02-19-18-16-1/errors/317747459383feae.json
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{ | ||
"model_class": "Job", | ||
"id": "317747459383feae", | ||
"history_id": "97b4f5385ce85823", | ||
"tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/sam2interval/sam2interval/1.0.2", | ||
"state": "error", | ||
"exit_code": null, | ||
"create_time": "2025-02-19T19:00:34.102685", | ||
"update_time": "2025-02-19T19:00:39.716527", | ||
"galaxy_version": "24.1", | ||
"external_id": "gxy-9jnll", | ||
"handler": null, | ||
"job_runner_name": null, | ||
"command_line": "python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/devteam/sam2interval/75557c0908a9/sam2interval/sam2interval.py' --input_sam_file='/galaxy/server/database/objects/4/1/3/dataset_41312bde-8487-4a79-b3b2-e5d1f2fe3ed4.dat' > '/galaxy/server/database/objects/a/6/a/dataset_a6aaeba0-4656-4e0c-9682-d809c28376ee.dat'", | ||
"user_email": "tests@fake.org", | ||
"command_version": null, | ||
"params": { | ||
"__input_ext": "\"input\"", | ||
"dbkey": "\"?\"", | ||
"chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", | ||
"print_all": "\"\"" | ||
}, | ||
"inputs": { | ||
"input1": { | ||
"id": "238431a8edc42360", | ||
"src": "hda", | ||
"uuid": "41312bde-8487-4a79-b3b2-e5d1f2fe3ed4" | ||
} | ||
}, | ||
"outputs": { | ||
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"src": "hda", | ||
"uuid": "a6aaeba0-4656-4e0c-9682-d809c28376ee" | ||
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"stdout": "", | ||
"stderr": "", | ||
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} |
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reports/anvil-edge/tool-tests/edge-25-02-19-18-16-1/errors/343ba801387957c7.json
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{ | ||
"model_class": "Job", | ||
"id": "343ba801387957c7", | ||
"history_id": "97b4f5385ce85823", | ||
"tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/3.58.1+galaxy0", | ||
"state": "error", | ||
"exit_code": null, | ||
"create_time": "2025-02-19T18:44:06.542815", | ||
"update_time": "2025-02-19T18:44:31.028645", | ||
"galaxy_version": "24.1", | ||
"external_id": "gxy-9lkf2", | ||
"handler": null, | ||
"job_runner_name": null, | ||
"command_line": "Rscript '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/119b069fc845/limma_voom/limma_voom.R' -R '/galaxy/server/database/objects/a/c/1/dataset_ac15f5df-921b-438d-a619-6da2f8a06823.dat' -o '/galaxy/server/database/objects/a/c/1/dataset_ac15f5df-921b-438d-a619-6da2f8a06823_files' -m '/galaxy/server/database/objects/b/9/3/dataset_b93ae922-6b2b-4665-a936-c6a7aa7b5391.dat' -f '/galaxy/server/database/objects/8/3/2/dataset_832012f4-3eed-4ff6-b8ed-625a4f6b0a4a.dat' -D 'Mut-WT' -P i -l '0.0' -p '0.05' -d 'BH' -G '6' -n 'TMM' -b && mkdir ./output_dir && cp '/galaxy/server/database/objects/a/c/1/dataset_ac15f5df-921b-438d-a619-6da2f8a06823_files'/*tsv output_dir/ && cp -r ./glimma* '/galaxy/server/database/objects/a/c/1/dataset_ac15f5df-921b-438d-a619-6da2f8a06823_files'", | ||
"user_email": "tests@fake.org", | ||
"command_version": null, | ||
"params": { | ||
"__input_ext": "\"input\"", | ||
"dbkey": "\"?\"", | ||
"chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", | ||
"adv": "{\"lfc\": \"0.0\", \"normalisationOption\": \"TMM\", \"pAdjust\": \"BH\", \"pVal\": \"0.05\", \"robOption\": true, \"topgenes\": \"6\", \"treat\": false}", | ||
"out": "{\"filtCounts\": false, \"libinfo\": false, \"normCounts\": false, \"plots\": \"i\", \"rdaOption\": false, \"rscript\": false}", | ||
"f": "{\"filt\": {\"__current_case__\": 1, \"filt_select\": \"no\"}}", | ||
"cont": "{\"__current_case__\": 1, \"cfile\": \"no\", \"rep_contrast\": [{\"__index__\": 0, \"contrast\": \"Mut-WT\"}]}", | ||
"anno": "{\"__current_case__\": 1, \"annoOpt\": \"no\"}", | ||
"input": "{\"__current_case__\": 1, \"counts\": {\"values\": [{\"id\": 40, \"src\": \"hda\"}]}, \"fact\": {\"__current_case__\": 0, \"ffile\": \"yes\", \"finfo\": {\"values\": [{\"id\": 41, \"src\": \"hda\"}]}}, \"format\": \"matrix\"}", | ||
"deMethod": "{\"__current_case__\": 0, \"de_select\": \"voom\", \"weightOption\": false}" | ||
}, | ||
"inputs": { | ||
"input|counts": { | ||
"id": "f0ee13039b83e10d", | ||
"src": "hda", | ||
"uuid": "b93ae922-6b2b-4665-a936-c6a7aa7b5391" | ||
}, | ||
"input|fact|finfo": { | ||
"id": "244fff1feed176a5", | ||
"src": "hda", | ||
"uuid": "832012f4-3eed-4ff6-b8ed-625a4f6b0a4a" | ||
} | ||
}, | ||
"outputs": { | ||
"outReport": { | ||
"id": "49282d4f1f8bc74f", | ||
"src": "hda", | ||
"uuid": "ac15f5df-921b-438d-a619-6da2f8a06823" | ||
} | ||
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"output_collections": { | ||
"outTables": { | ||
"src": "hdca", | ||
"id": "b8d8b32f18b5b554" | ||
} | ||
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"tool_stdout": "Warning message:\nIn Sys.setlocale(\"LC_MESSAGES\", \"en_US.UTF-8\") :\n OS reports request to set locale to \"en_US.UTF-8\" cannot be honored\n[1] \"Extracting counts\"\n[1] \"Generating DGEList object\"\n[1] \"Generating Design\"\n[1] \"Calculating Normalisation Factors\"\n[1] \"Generating Contrasts\"\n[1] \"Generating MDS plot\"\n[1] \"Generating DE results\"\n", | ||
"tool_stderr": "Warning message:\nIn Sys.setlocale(\"LC_MESSAGES\", \"en_US.UTF-8\") :\n OS reports request to set locale to \"en_US.UTF-8\" cannot be honored\n", | ||
"job_stdout": null, | ||
"job_stderr": null, | ||
"stdout": "Warning message:\nIn Sys.setlocale(\"LC_MESSAGES\", \"en_US.UTF-8\") :\n OS reports request to set locale to \"en_US.UTF-8\" cannot be honored\n[1] \"Extracting counts\"\n[1] \"Generating DGEList object\"\n[1] \"Generating Design\"\n[1] \"Calculating Normalisation Factors\"\n[1] \"Generating Contrasts\"\n[1] \"Generating MDS plot\"\n[1] \"Generating DE results\"\n", | ||
"stderr": "Warning message:\nIn Sys.setlocale(\"LC_MESSAGES\", \"en_US.UTF-8\") :\n OS reports request to set locale to \"en_US.UTF-8\" cannot be honored\n", | ||
"job_messages": null, | ||
"dependencies": [], | ||
"job_metrics": [] | ||
} |
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