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Updating anvil-edge README for edge-24-09-22-18-15-1
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7 changes: 7 additions & 0 deletions
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reports/anvil-edge/tool-tests/edge-24-09-22-18-15-1/chunk.json
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,7 @@ | ||
| { | ||
| "13": { | ||
| "run1": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-edge/tool-tests/edge-24-09-22-18-15-1/results.html", | ||
| "date1": "Sun Sep 22 18:31:24 2024", | ||
| "tools": "https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-edge/tool-tests/edge-24-09-22-18-15-1/tools.yml" | ||
| } | ||
| } |
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reports/anvil-edge/tool-tests/edge-24-09-22-18-15-1/chunk.txt
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,25 @@ | ||
| -t deeptools_plot_heatmap --tool-version a4dfb122e52b | ||
| -t deeptools_plot_profile --tool-version c361b12d207a | ||
| -t fastp --tool-version dbf9c561ef29 | ||
| -t rgrnastar --tool-version c772497b2c32 | ||
| -t rgrnastar --tool-version 2055c2667eb3 | ||
| -t rgrnastar --tool-version 980d2a2e1180 | ||
| -t poretools_events --tool-version 28d7819c312f | ||
| -t pharmcat --tool-version d67642a21a1d | ||
| -t qualimap_bamqc --tool-version 19ece8afbaab | ||
| -t samtools_stats --tool-version 145f6d74ff5e | ||
| -t samtools_stats --tool-version 24c5d43cb545 | ||
| -t filter_on_md --tool-version ac70bfaf1224 | ||
| -t dropletutils --tool-version a9caad671439 | ||
| -t dropletutils --tool-version 2c1200fba922 | ||
| -t scater_filter --tool-version 652923ce664f | ||
| -t scater_filter --tool-version b7ea9f09c02f | ||
| -t sceasy_convert --tool-version f62bc418173f | ||
| -t scanpy_find_markers --tool-version eb01a7e59e9a | ||
| -t scanpy_find_markers --tool-version f04dd4e5b6a7 | ||
| -t reshape2_cast --tool-version d3b66a3a08ca | ||
| -t snpsift_genesets --tool-version d12a810c837e | ||
| -t bcftools_plugin_setgt --tool-version 8abfcd1a6949 | ||
| -t bcftools_call --tool-version 072f606e2e69 | ||
| -t vcfbreakcreatemulti --tool-version 9fd5d91eb91b | ||
| -t vcfselectsamples --tool-version 2ba3b87f904f |
60 changes: 60 additions & 0 deletions
60
reports/anvil-edge/tool-tests/edge-24-09-22-18-15-1/errors/00bf5e33f5f60a84.json
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,60 @@ | ||
| { | ||
| "model_class": "Job", | ||
| "id": "00bf5e33f5f60a84", | ||
| "history_id": "b2116f9eb07476cf", | ||
| "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/dropletutils/dropletutils/1.10.0+galaxy2", | ||
| "state": "error", | ||
| "exit_code": null, | ||
| "create_time": "2024-09-22T19:16:09.360909", | ||
| "update_time": "2024-09-22T19:16:29.622402", | ||
| "galaxy_version": "24.1", | ||
| "external_id": "gxy-r4m44", | ||
| "handler": null, | ||
| "job_runner_name": null, | ||
| "command_line": "Rscript '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/dropletutils/a9caad671439/dropletutils/scripts/dropletutils.Rscript' '/galaxy/server/database/jobs_directory/000/157/configs/tmpfdt0g2xt'", | ||
| "user_email": "tests@fake.org", | ||
| "command_version": null, | ||
| "params": { | ||
| "__input_ext": "\"h5\"", | ||
| "dbkey": "\"?\"", | ||
| "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", | ||
| "seed": "\"100\"", | ||
| "operation": "{\"__current_case__\": 0, \"method\": {\"__current_case__\": 1, \"fdr_thresh\": \"0.02\", \"lower\": \"150\", \"use\": \"emptydrops\"}, \"outformat\": \"h5\", \"use\": \"filter\"}", | ||
| "tenx_format": "{\"__current_case__\": 1, \"input\": {\"values\": [{\"id\": 239, \"src\": \"hda\"}]}, \"use\": \"h5\"}" | ||
| }, | ||
| "inputs": { | ||
| "tenx_format|input": { | ||
| "id": "2e82e628690af495", | ||
| "src": "hda", | ||
| "uuid": "55edb90b-5bb7-4496-a18a-d9fa3f535a94" | ||
| } | ||
| }, | ||
| "outputs": { | ||
| "fileout_h5": { | ||
| "id": "24cc1dc6eaa8876f", | ||
| "src": "hda", | ||
| "uuid": "22598fa7-3f7c-4764-842e-089622eb9d10" | ||
| }, | ||
| "plot": { | ||
| "id": "807bfe01e9a68c8e", | ||
| "src": "hda", | ||
| "uuid": "7906c188-bd71-4f7a-9151-2df05203f29e" | ||
| }, | ||
| "table": { | ||
| "id": "a9e73c1f2c590fd8", | ||
| "src": "hda", | ||
| "uuid": "c5d79519-4992-4643-bfff-73421ab8e541" | ||
| } | ||
| }, | ||
| "copied_from_job_id": null, | ||
| "output_collections": {}, | ||
| "tool_stdout": "[1] \"Cell Library Size Distribution:\"\n Min. 1st Qu. Median Mean 3rd Qu. Max. \n 0.0 8.0 20.0 114.3 46.0 2347.0 \n", | ||
| "tool_stderr": "Error in print.default(ifelse(is.na(y), NA_character_, sQuote(y)), quote = FALSE, : \n ignoring SIGPIPE signal\nCalls: <Anonymous> -> print.numeric_version -> print -> print.default\nExecution halted\nCells: 954\nCells and Limited: 85\n", | ||
| "job_stdout": null, | ||
| "job_stderr": null, | ||
| "stdout": "[1] \"Cell Library Size Distribution:\"\n Min. 1st Qu. Median Mean 3rd Qu. Max. \n 0.0 8.0 20.0 114.3 46.0 2347.0 \n", | ||
| "stderr": "Error in print.default(ifelse(is.na(y), NA_character_, sQuote(y)), quote = FALSE, : \n ignoring SIGPIPE signal\nCalls: <Anonymous> -> print.numeric_version -> print -> print.default\nExecution halted\nCells: 954\nCells and Limited: 85\n", | ||
| "job_messages": null, | ||
| "dependencies": [], | ||
| "job_metrics": [] | ||
| } |
45 changes: 45 additions & 0 deletions
45
reports/anvil-edge/tool-tests/edge-24-09-22-18-15-1/errors/23fa96fce5eed89f.json
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,45 @@ | ||
| { | ||
| "model_class": "Job", | ||
| "id": "23fa96fce5eed89f", | ||
| "history_id": "b2116f9eb07476cf", | ||
| "tool_id": "upload1", | ||
| "state": "error", | ||
| "exit_code": null, | ||
| "create_time": "2024-09-22T19:28:21.683999", | ||
| "update_time": "2024-09-22T19:28:34.511928", | ||
| "galaxy_version": "24.1", | ||
| "external_id": "gxy-jmt8r", | ||
| "handler": null, | ||
| "job_runner_name": null, | ||
| "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/197/registry.xml' '/galaxy/server/database/jobs_directory/000/197/upload_params.json' '288:/galaxy/server/database/objects/b/4/4/dataset_b44f93e4-bfca-464d-a379-27ceddc4acca_files:/galaxy/server/database/objects/b/4/4/dataset_b44f93e4-bfca-464d-a379-27ceddc4acca.dat'", | ||
| "user_email": "tests@fake.org", | ||
| "command_version": null, | ||
| "params": { | ||
| "paramfile": "\"/galaxy/server/database/tmp/upload_params_0nlfp5ye\"", | ||
| "files_metadata": "{\"__current_case__\": 342, \"file_type\": \"vcf\"}", | ||
| "dbkey": "\"?\"", | ||
| "force_composite": "\"false\"", | ||
| "files": "[{\"NAME\": \"mpileup.X.vcf\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_jayzma20\", \"file_type\": \"\", \"ftp_files\": null, \"space_to_tab\": null, \"to_posix_lines\": \"Yes\", \"url_paste\": null, \"uuid\": null}]", | ||
| "file_count": "\"auto\"", | ||
| "file_type": "\"vcf\"" | ||
| }, | ||
| "inputs": {}, | ||
| "outputs": { | ||
| "output0": { | ||
| "id": "13ba1acd5cd466b0", | ||
| "src": "hda", | ||
| "uuid": "b44f93e4-bfca-464d-a379-27ceddc4acca" | ||
| } | ||
| }, | ||
| "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": [] | ||
| } |
48 changes: 48 additions & 0 deletions
48
reports/anvil-edge/tool-tests/edge-24-09-22-18-15-1/errors/3497a43a628aa539.json
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,48 @@ | ||
| { | ||
| "model_class": "Job", | ||
| "id": "3497a43a628aa539", | ||
| "history_id": "b2116f9eb07476cf", | ||
| "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/vcfbreakcreatemulti/vcfbreakcreatemulti/1.0.0_rc3+galaxy0", | ||
| "state": "error", | ||
| "exit_code": null, | ||
| "create_time": "2024-09-22T19:32:02.592388", | ||
| "update_time": "2024-09-22T19:32:07.528710", | ||
| "galaxy_version": "24.1", | ||
| "external_id": "gxy-wfclp", | ||
| "handler": null, | ||
| "job_runner_name": null, | ||
| "command_line": "vcfcreatemulti '/galaxy/server/database/objects/d/9/9/dataset_d99e1928-6dab-496e-8e1b-ba71ca77232c.dat' > '/galaxy/server/database/objects/f/8/2/dataset_f8217004-c37e-4cd0-8d89-f5b32de01fb7.dat'", | ||
| "user_email": "tests@fake.org", | ||
| "command_version": null, | ||
| "params": { | ||
| "__input_ext": "\"vcf\"", | ||
| "dbkey": "\"?\"", | ||
| "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", | ||
| "break_or_create": "\"create\"" | ||
| }, | ||
| "inputs": { | ||
| "input1": { | ||
| "id": "d06e50ccbd12ddff", | ||
| "src": "hda", | ||
| "uuid": "d99e1928-6dab-496e-8e1b-ba71ca77232c" | ||
| } | ||
| }, | ||
| "outputs": { | ||
| "out_file1": { | ||
| "id": "ead3b0e6133fe849", | ||
| "src": "hda", | ||
| "uuid": "f8217004-c37e-4cd0-8d89-f5b32de01fb7" | ||
| } | ||
| }, | ||
| "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": [] | ||
| } |
60 changes: 60 additions & 0 deletions
60
reports/anvil-edge/tool-tests/edge-24-09-22-18-15-1/errors/35041e98d94fab80.json
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,60 @@ | ||
| { | ||
| "model_class": "Job", | ||
| "id": "35041e98d94fab80", | ||
| "history_id": "b2116f9eb07476cf", | ||
| "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/dropletutils/dropletutils/1.10.0+galaxy2", | ||
| "state": "error", | ||
| "exit_code": null, | ||
| "create_time": "2024-09-22T19:12:07.837952", | ||
| "update_time": "2024-09-22T19:12:51.758939", | ||
| "galaxy_version": "24.1", | ||
| "external_id": "gxy-8zwzq", | ||
| "handler": null, | ||
| "job_runner_name": null, | ||
| "command_line": "mkdir 'tenx.input' && ln -s '/galaxy/server/database/objects/3/f/3/dataset_3f3a1e79-ddd2-4a3b-8a0c-255a2b3dc762.dat' 'tenx.input/matrix.mtx' && ln -s '/galaxy/server/database/objects/f/b/e/dataset_fbe12ec9-a2ac-4d4c-acf6-dc88ad69cfea.dat' 'tenx.input/genes.tsv' && ln -s '/galaxy/server/database/objects/5/1/4/dataset_5147fd90-efd6-45df-8967-a3ae5d8fa9bf.dat' 'tenx.input/barcodes.tsv' && Rscript '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/dropletutils/a9caad671439/dropletutils/scripts/dropletutils.Rscript' '/galaxy/server/database/jobs_directory/000/143/configs/tmppyne47_7'", | ||
| "user_email": "tests@fake.org", | ||
| "command_version": null, | ||
| "params": { | ||
| "__input_ext": "\"mtx\"", | ||
| "dbkey": "\"?\"", | ||
| "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", | ||
| "seed": "\"100\"", | ||
| "operation": "{\"__current_case__\": 0, \"method\": {\"__current_case__\": 0, \"expected\": \"3000\", \"lowerprop\": \"0.1\", \"upperquant\": \"0.99\", \"use\": \"defaultdrops\"}, \"outformat\": \"h5\", \"use\": \"filter\"}", | ||
| "tenx_format": "{\"__current_case__\": 0, \"input\": {\"values\": [{\"id\": 221, \"src\": \"hda\"}]}, \"input_barcodes\": {\"values\": [{\"id\": 223, \"src\": \"hda\"}]}, \"input_genes\": {\"values\": [{\"id\": 222, \"src\": \"hda\"}]}, \"use\": \"directory\"}" | ||
| }, | ||
| "inputs": { | ||
| "tenx_format|input": { | ||
| "id": "b8141cadd821f42c", | ||
| "src": "hda", | ||
| "uuid": "3f3a1e79-ddd2-4a3b-8a0c-255a2b3dc762" | ||
| }, | ||
| "tenx_format|input_genes": { | ||
| "id": "986bd4ea81b0e86b", | ||
| "src": "hda", | ||
| "uuid": "fbe12ec9-a2ac-4d4c-acf6-dc88ad69cfea" | ||
| }, | ||
| "tenx_format|input_barcodes": { | ||
| "id": "4caf66e9bcb59cbb", | ||
| "src": "hda", | ||
| "uuid": "5147fd90-efd6-45df-8967-a3ae5d8fa9bf" | ||
| } | ||
| }, | ||
| "outputs": { | ||
| "fileout_h5": { | ||
| "id": "115df72712751f2b", | ||
| "src": "hda", | ||
| "uuid": "0d63ccd2-01ba-4bef-a871-82ed36507abc" | ||
| } | ||
| }, | ||
| "copied_from_job_id": null, | ||
| "output_collections": {}, | ||
| "tool_stdout": "", | ||
| "tool_stderr": "Error in print.default(ifelse(is.na(y), NA_character_, sQuote(y)), quote = FALSE, : \n ignoring SIGPIPE signal\nCalls: <Anonymous> -> print.numeric_version -> print -> print.default\nExecution halted\nCells: 1025\n", | ||
| "job_stdout": null, | ||
| "job_stderr": null, | ||
| "stdout": "", | ||
| "stderr": "Error in print.default(ifelse(is.na(y), NA_character_, sQuote(y)), quote = FALSE, : \n ignoring SIGPIPE signal\nCalls: <Anonymous> -> print.numeric_version -> print -> print.default\nExecution halted\nCells: 1025\n", | ||
| "job_messages": null, | ||
| "dependencies": [], | ||
| "job_metrics": [] | ||
| } |
45 changes: 45 additions & 0 deletions
45
reports/anvil-edge/tool-tests/edge-24-09-22-18-15-1/errors/3a1ae83738ad2097.json
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,45 @@ | ||
| { | ||
| "model_class": "Job", | ||
| "id": "3a1ae83738ad2097", | ||
| "history_id": "b2116f9eb07476cf", | ||
| "tool_id": "upload1", | ||
| "state": "error", | ||
| "exit_code": null, | ||
| "create_time": "2024-09-22T19:18:18.442121", | ||
| "update_time": "2024-09-22T19:18:32.113800", | ||
| "galaxy_version": "24.1", | ||
| "external_id": "gxy-7mrp9", | ||
| "handler": null, | ||
| "job_runner_name": null, | ||
| "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/164/registry.xml' '/galaxy/server/database/jobs_directory/000/164/upload_params.json' '251:/galaxy/server/database/objects/6/5/3/dataset_65383493-7b0c-4fec-8619-3b08c0acb31e_files:/galaxy/server/database/objects/6/5/3/dataset_65383493-7b0c-4fec-8619-3b08c0acb31e.dat'", | ||
| "user_email": "tests@fake.org", | ||
| "command_version": null, | ||
| "params": { | ||
| "paramfile": "\"/galaxy/server/database/tmp/upload_params_1c3mi3iw\"", | ||
| "files_metadata": "{\"__current_case__\": 708, \"file_type\": \"auto\"}", | ||
| "dbkey": "\"?\"", | ||
| "force_composite": "\"false\"", | ||
| "files": "[{\"NAME\": \"in_matrix.mtx\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_rqb29y5m\", \"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": "a8832ac7c6c647b7", | ||
| "src": "hda", | ||
| "uuid": "65383493-7b0c-4fec-8619-3b08c0acb31e" | ||
| } | ||
| }, | ||
| "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
45
reports/anvil-edge/tool-tests/edge-24-09-22-18-15-1/errors/3c44190b9eacecba.json
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,45 @@ | ||
| { | ||
| "model_class": "Job", | ||
| "id": "3c44190b9eacecba", | ||
| "history_id": "b2116f9eb07476cf", | ||
| "tool_id": "upload1", | ||
| "state": "error", | ||
| "exit_code": null, | ||
| "create_time": "2024-09-22T19:26:01.127709", | ||
| "update_time": "2024-09-22T19:26:13.923825", | ||
| "galaxy_version": "24.1", | ||
| "external_id": "gxy-8rp2r", | ||
| "handler": null, | ||
| "job_runner_name": null, | ||
| "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/188/registry.xml' '/galaxy/server/database/jobs_directory/000/188/upload_params.json' '279:/galaxy/server/database/objects/8/d/b/dataset_8dbed0ac-d5d0-4501-a8c7-08ec7d986fe9_files:/galaxy/server/database/objects/8/d/b/dataset_8dbed0ac-d5d0-4501-a8c7-08ec7d986fe9.dat'", | ||
| "user_email": "tests@fake.org", | ||
| "command_version": null, | ||
| "params": { | ||
| "paramfile": "\"/galaxy/server/database/tmp/upload_params_wbkakvms\"", | ||
| "files_metadata": "{\"__current_case__\": 342, \"file_type\": \"vcf\"}", | ||
| "dbkey": "\"?\"", | ||
| "force_composite": "\"false\"", | ||
| "files": "[{\"NAME\": \"plugin1.vcf\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_rz57e17f\", \"file_type\": \"\", \"ftp_files\": null, \"space_to_tab\": null, \"to_posix_lines\": \"Yes\", \"url_paste\": null, \"uuid\": null}]", | ||
| "file_count": "\"auto\"", | ||
| "file_type": "\"vcf\"" | ||
| }, | ||
| "inputs": {}, | ||
| "outputs": { | ||
| "output0": { | ||
| "id": "de9f71eaa45f3b0d", | ||
| "src": "hda", | ||
| "uuid": "8dbed0ac-d5d0-4501-a8c7-08ec7d986fe9" | ||
| } | ||
| }, | ||
| "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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