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Updating anvil-edge README for edge-25-02-19-18-16-1
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actions-user committed Feb 19, 2025
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2 changes: 1 addition & 1 deletion reports/anvil-edge/README.md

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10 changes: 5 additions & 5 deletions reports/anvil-edge/tool-tests/chunks.json
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"date2": "Wed Feb 12 06:28:31 2025"
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"date1": "Wed Feb 12 18:35:02 2025",
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"date2": "Wed Feb 05 18:34:20 2025"
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"date1": "Wed Feb 19 18:32:37 2025",
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"date2": "Wed Feb 12 18:35:02 2025"
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"6": {
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{
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"date1": "Wed Feb 19 18:32:37 2025",
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}
25 changes: 25 additions & 0 deletions reports/anvil-edge/tool-tests/edge-25-02-19-18-16-1/chunk.txt
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@@ -0,0 +1,25 @@
-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
Original file line number Diff line number Diff line change
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Original file line number Diff line number Diff line change
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Original file line number Diff line number Diff line change
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{
"model_class": "Job",
"id": "1dae1b560d3e3035",
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"tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/annotatemyids/annotatemyids/3.5.0.1",
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"create_time": "2025-02-19T19:21:18.401094",
"update_time": "2025-02-19T19:22:14.915188",
"galaxy_version": "24.1",
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"chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"",
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"output_cols": "[\"ENSEMBL\", \"ENTREZID\", \"SYMBOL\", \"GENENAME\"]",
"id_type": "\"SYMBOL\"",
"organism": "\"Hs\"",
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"id": "a3255d132981d58a",
"src": "hda",
"uuid": "38b7d591-dad5-454d-9b19-3d444b16c891"
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},
"outputs": {
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"src": "hda",
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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,
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"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",
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Original file line number Diff line number Diff line change
@@ -0,0 +1,45 @@
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"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'",
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"command_version": null,
"params": {
"paramfile": "\"/galaxy/server/database/tmp/upload_params_vqub0pww\"",
"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\"",
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"job_stderr": null,
"stdout": "",
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"job_messages": null,
"dependencies": [],
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}
Original file line number Diff line number Diff line change
@@ -0,0 +1,48 @@
{
"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": {
"out_file1": {
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"src": "hda",
"uuid": "a6aaeba0-4656-4e0c-9682-d809c28376ee"
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"job_stderr": null,
"stdout": "",
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"job_messages": null,
"dependencies": [],
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}
Original file line number Diff line number Diff line change
@@ -0,0 +1,64 @@
{
"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",
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"create_time": "2025-02-19T18:44:06.542815",
"update_time": "2025-02-19T18:44:31.028645",
"galaxy_version": "24.1",
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"handler": null,
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"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'",
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"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": {
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"src": "hda",
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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",
"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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