Skip to content

Commit

Permalink
Updating anvil-production README for prod-25-01-04-00-34-1
Browse files Browse the repository at this point in the history
  • Loading branch information
actions-user committed Jan 4, 2025
1 parent 332411b commit ca846cb
Show file tree
Hide file tree
Showing 24 changed files with 22,075 additions and 6 deletions.
2 changes: 1 addition & 1 deletion reports/anvil-production/README.md

Large diffs are not rendered by default.

10 changes: 5 additions & 5 deletions reports/anvil-production/tool-tests/chunks.json
Original file line number Diff line number Diff line change
Expand Up @@ -7,11 +7,11 @@
"date2": "Thu Dec 26 00:49:58 2024"
},
"10": {
"run1": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-production/tool-tests/prod-24-12-28-00-34-1/results.html",
"date1": "Sat Dec 28 00:50:11 2024",
"tools": "https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-production/tool-tests/prod-24-12-28-00-34-1/tools.yml",
"run2": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-production/tool-tests/prod-24-12-21-00-35-1/results.html",
"date2": "Sat Dec 21 00:51:11 2024"
"run1": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-production/tool-tests/prod-25-01-04-00-34-1/results.html",
"date1": "Sat Jan 04 00:53:57 2025",
"tools": "https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-production/tool-tests/prod-25-01-04-00-34-1/tools.yml",
"run2": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-production/tool-tests/prod-24-12-28-00-34-1/results.html",
"date2": "Sat Dec 28 00:50:11 2024"
},
"11": {
"run1": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-production/tool-tests/prod-24-12-28-12-32-1/results.html",
Expand Down
Original file line number Diff line number Diff line change
@@ -0,0 +1,7 @@
{
"10": {
"run1": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-production/tool-tests/prod-25-01-04-00-34-1/results.html",
"date1": "Sat Jan 04 00:53:57 2025",
"tools": "https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-production/tool-tests/prod-25-01-04-00-34-1/tools.yml"
}
}
Original file line number Diff line number Diff line change
@@ -0,0 +1,15 @@
-t annotatemyids --tool-version 44018dd6b447
-t datamash_reverse --tool-version 0f1724dd59d2
-t trimmomatic --tool-version d94aff5ee623
-t samtools_fixmate --tool-version bc0cc7bfbfe9
-t sam_to_bam --tool-version cf1ffd88f895
-t bcftools_plugin_setgt --tool-version 8abfcd1a6949
-t bcftools_call --tool-version 072f606e2e69
-t vcfbreakcreatemulti --tool-version 9fd5d91eb91b
-t vcfselectsamples --tool-version 2ba3b87f904f
-t poretools_occupancy --tool-version 338d15b8d6fb
-t deeptools_plot_heatmap --tool-version a4dfb122e52b
-t deeptools_plot_profile --tool-version c361b12d207a
-t lofreq_filter --tool-version 7dfca164d2e3
-t salmon --tool-version cc05793bb896
-t mummer_mummerplot --tool-version ebe3b0f84de9
Original file line number Diff line number Diff line change
@@ -0,0 +1,44 @@
{
"model_class": "Job",
"id": "1808197a8973047c",
"state": "error",
"exit_code": null,
"update_time": "2025-01-04T01:02:44.775747",
"create_time": "2025-01-04T01:02:35.250575",
"galaxy_version": "23.1",
"command_version": null,
"copied_from_job_id": null,
"tool_id": "upload1",
"history_id": "fc16d5ed9abfd51d",
"external_id": "gxy-j4smt",
"command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/32/registry.xml' '/galaxy/server/database/jobs_directory/000/32/upload_params.json' '47:/galaxy/server/database/objects/6/a/d/dataset_6add4177-cda6-4c30-b17c-de310ca1a20c_files:/galaxy/server/database/objects/6/a/d/dataset_6add4177-cda6-4c30-b17c-de310ca1a20c.dat'",
"traceback": null,
"params": {
"paramfile": "\"/galaxy/server/database/tmp/upload_params_5q080t2x\"",
"files_metadata": "{\"__current_case__\": 82, \"file_type\": \"fastqsanger.gz\"}",
"dbkey": "\"?\"",
"force_composite": "\"false\"",
"files": "[{\"NAME\": \"Illumina_SG_R2.fastq.gz\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_fho1h2m5\", \"file_type\": \"\", \"ftp_files\": null, \"space_to_tab\": null, \"to_posix_lines\": \"Yes\", \"url_paste\": null, \"uuid\": null}]",
"file_count": "\"auto\"",
"file_type": "\"fastqsanger.gz\""
},
"inputs": {},
"outputs": {
"output0": {
"id": "4e4774aad94d9f51",
"src": "hda",
"uuid": "6add4177-cda6-4c30-b17c-de310ca1a20c"
}
},
"output_collections": {},
"tool_stdout": "",
"tool_stderr": "",
"job_stdout": null,
"job_stderr": null,
"stderr": "",
"stdout": "",
"job_messages": null,
"dependencies": [],
"user_email": "tests@fake.org",
"job_metrics": []
}
Original file line number Diff line number Diff line change
@@ -0,0 +1,58 @@
{
"model_class": "Job",
"id": "2466d705e4bff954",
"state": "error",
"exit_code": null,
"update_time": "2025-01-04T01:20:47.362319",
"create_time": "2025-01-04T01:20:42.287058",
"galaxy_version": "23.1",
"command_version": null,
"copied_from_job_id": null,
"tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/salmon/salmon/1.3.0+galaxy1",
"history_id": "fc16d5ed9abfd51d",
"external_id": "gxy-x94d5",
"command_line": "mkdir ./index && mkdir ./output && salmon index -i ./index --kmerLen '31' --gencode --transcripts '/galaxy/server/database/objects/0/1/2/dataset_012edd49-7e08-4f70-ba8c-5b73c3579c91.dat' && ln -s /galaxy/server/database/objects/0/1/2/dataset_012edd49-7e08-4f70-ba8c-5b73c3579c91.dat ./single.fasta && salmon quant --index './index' --libType U --unmatedReads ./single.fasta --threads \"${GALAXY_SLOTS:-4}\" --incompatPrior '0.0' --biasSpeedSamp '5' --fldMax '1000' --fldMean '250' --fldSD '25' --forgettingFactor '0.65' --maxReadOcc '100' --numBiasSamples '2000000' --numAuxModelSamples '5000000' --numPreAuxModelSamples '5000' --numGibbsSamples '0' --numBootstraps '0' --thinningFactor '16' --sigDigits '3' --vbPrior '1e-05' -o ./output",
"traceback": null,
"params": {
"__input_ext": "\"fasta\"",
"dbkey": "\"?\"",
"chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"",
"adv": "{\"biasSpeedSamp\": \"5\", \"bootstrapReproject\": false, \"dumpEq\": false, \"dumpEqWeights\": false, \"fldMax\": \"1000\", \"fldMean\": \"250\", \"fldSD\": \"25\", \"forgettingFactor\": \"0.65\", \"initUniform\": false, \"maxReadOcc\": \"100\", \"minAssignedFrags\": \"\", \"noBiasLengthThreshold\": false, \"noEffectiveLengthCorrection\": false, \"noFragLengthDist\": false, \"noGammaDraw\": false, \"noLengthCorrection\": false, \"numAuxModelSamples\": \"5000000\", \"numBiasSamples\": \"2000000\", \"numBootstraps\": \"0\", \"numGibbsSamples\": \"0\", \"numPreAuxModelSamples\": \"5000\", \"perTranscriptPrior\": false, \"rangeFactorizationBins\": \"0\", \"sigDigits\": \"3\", \"skipQuant\": false, \"thinningFactor\": \"16\", \"useEM\": false, \"vbPrior\": \"1e-05\", \"writeOrphanLinks\": false, \"writeUnmappedNames\": false}",
"meta": "false",
"incompatPrior": "\"0.0\"",
"gcBias": "false",
"seqBias": "false",
"geneMap": null,
"quant_type": "{\"__current_case__\": 0, \"consensusSlack\": \"0\", \"consistentHits\": false, \"discardOrphansQuasi\": false, \"dovetail\": false, \"input\": {\"single_or_paired\": {\"__current_case__\": 0, \"input_singles\": {\"values\": [{\"id\": 139, \"src\": \"hda\"}]}, \"single_or_paired_opts\": \"single\", \"strandedness\": \"U\"}}, \"qtype\": \"reads\", \"quasiCoverage\": \"\", \"recoverOrphans\": false, \"refTranscriptSource\": {\"TranscriptSource\": \"history\", \"__current_case__\": 1, \"s_index\": {\"fasta\": {\"values\": [{\"id\": 139, \"src\": \"hda\"}]}, \"kmer\": \"31\", \"phash\": false}}, \"type\": \"quasi\", \"validmap\": {\"__current_case__\": 1, \"validateMappings\": false}, \"writeMappings\": false}"
},
"inputs": {
"quant_type|refTranscriptSource|s_index|fasta": {
"id": "7e9522e6f1b53186",
"src": "hda",
"uuid": "012edd49-7e08-4f70-ba8c-5b73c3579c91"
},
"quant_type|input|single_or_paired|input_singles": {
"id": "7e9522e6f1b53186",
"src": "hda",
"uuid": "012edd49-7e08-4f70-ba8c-5b73c3579c91"
}
},
"outputs": {
"output_quant": {
"id": "8ba88500ae8f7ffa",
"src": "hda",
"uuid": "5c1bc533-fdd7-4eab-ae31-b1f32045e89f"
}
},
"output_collections": {},
"tool_stdout": "",
"tool_stderr": "",
"job_stdout": null,
"job_stderr": null,
"stderr": "",
"stdout": "",
"job_messages": null,
"dependencies": [],
"user_email": "tests@fake.org",
"job_metrics": []
}
Original file line number Diff line number Diff line change
@@ -0,0 +1,44 @@
{
"model_class": "Job",
"id": "36b346e7b07077f3",
"state": "error",
"exit_code": null,
"update_time": "2025-01-04T01:03:52.960827",
"create_time": "2025-01-04T01:03:43.447355",
"galaxy_version": "23.1",
"command_version": null,
"copied_from_job_id": null,
"tool_id": "upload1",
"history_id": "fc16d5ed9abfd51d",
"external_id": "gxy-w8wdm",
"command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/37/registry.xml' '/galaxy/server/database/jobs_directory/000/37/upload_params.json' '52:/galaxy/server/database/objects/f/c/8/dataset_fc87b07b-4c0c-4ee2-8e19-255735b88d31_files:/galaxy/server/database/objects/f/c/8/dataset_fc87b07b-4c0c-4ee2-8e19-255735b88d31.dat'",
"traceback": null,
"params": {
"paramfile": "\"/galaxy/server/database/tmp/upload_params_2horgkvh\"",
"files_metadata": "{\"__current_case__\": 81, \"file_type\": \"fastqsanger\"}",
"dbkey": "\"?\"",
"force_composite": "\"false\"",
"files": "[{\"NAME\": \"Illumina_SG_R1.fastq\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_h_gysq4i\", \"file_type\": \"\", \"ftp_files\": null, \"space_to_tab\": null, \"to_posix_lines\": \"Yes\", \"url_paste\": null, \"uuid\": null}]",
"file_count": "\"auto\"",
"file_type": "\"fastqsanger\""
},
"inputs": {},
"outputs": {
"output0": {
"id": "eeb9a5a272936e62",
"src": "hda",
"uuid": "fc87b07b-4c0c-4ee2-8e19-255735b88d31"
}
},
"output_collections": {},
"tool_stdout": "",
"tool_stderr": "",
"job_stdout": null,
"job_stderr": null,
"stderr": "",
"stdout": "",
"job_messages": null,
"dependencies": [],
"user_email": "tests@fake.org",
"job_metrics": []
}
Original file line number Diff line number Diff line change
@@ -0,0 +1,44 @@
{
"model_class": "Job",
"id": "53c2f3b9a9da7164",
"state": "error",
"exit_code": null,
"update_time": "2025-01-04T01:14:52.226722",
"create_time": "2025-01-04T01:14:43.955102",
"galaxy_version": "23.1",
"command_version": null,
"copied_from_job_id": null,
"tool_id": "upload1",
"history_id": "fc16d5ed9abfd51d",
"external_id": "gxy-ddbh7",
"command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/96/registry.xml' '/galaxy/server/database/jobs_directory/000/96/upload_params.json' '116:/galaxy/server/database/objects/8/4/f/dataset_84fbedd5-14e9-4764-aff3-ba5c1b4cfca4_files:/galaxy/server/database/objects/8/4/f/dataset_84fbedd5-14e9-4764-aff3-ba5c1b4cfca4.dat'",
"traceback": null,
"params": {
"paramfile": "\"/galaxy/server/database/tmp/upload_params_7iigk7id\"",
"files_metadata": "{\"__current_case__\": 240, \"file_type\": \"fast5.tar\"}",
"dbkey": "\"?\"",
"force_composite": "\"false\"",
"files": "[{\"NAME\": \"poretools-in1.tar.bz2\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_acecy4ck\", \"file_type\": \"\", \"ftp_files\": null, \"space_to_tab\": null, \"to_posix_lines\": \"Yes\", \"url_paste\": null, \"uuid\": null}]",
"file_count": "\"auto\"",
"file_type": "\"fast5.tar\""
},
"inputs": {},
"outputs": {
"output0": {
"id": "b4c001f459224de7",
"src": "hda",
"uuid": "84fbedd5-14e9-4764-aff3-ba5c1b4cfca4"
}
},
"output_collections": {},
"tool_stdout": "",
"tool_stderr": "",
"job_stdout": null,
"job_stderr": null,
"stderr": "",
"stdout": "",
"job_messages": null,
"dependencies": [],
"user_email": "tests@fake.org",
"job_metrics": []
}
Original file line number Diff line number Diff line change
@@ -0,0 +1,44 @@
{
"model_class": "Job",
"id": "5f7e521540777467",
"state": "error",
"exit_code": null,
"update_time": "2025-01-04T01:01:43.466586",
"create_time": "2025-01-04T01:01:34.051616",
"galaxy_version": "23.1",
"command_version": null,
"copied_from_job_id": null,
"tool_id": "upload1",
"history_id": "fc16d5ed9abfd51d",
"external_id": "gxy-98w6t",
"command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/24/registry.xml' '/galaxy/server/database/jobs_directory/000/24/upload_params.json' '36:/galaxy/server/database/objects/a/c/a/dataset_acae293f-069f-4491-9e6a-d80c74df0e9b_files:/galaxy/server/database/objects/a/c/a/dataset_acae293f-069f-4491-9e6a-d80c74df0e9b.dat'",
"traceback": null,
"params": {
"paramfile": "\"/galaxy/server/database/tmp/upload_params_fyifb5ci\"",
"files_metadata": "{\"__current_case__\": 84, \"file_type\": \"fastqsolexa\"}",
"dbkey": "\"?\"",
"force_composite": "\"false\"",
"files": "[{\"NAME\": \"Illumina_SG_R1.fastqsolexa\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_wh5t4ey2\", \"file_type\": \"\", \"ftp_files\": null, \"space_to_tab\": null, \"to_posix_lines\": \"Yes\", \"url_paste\": null, \"uuid\": null}]",
"file_count": "\"auto\"",
"file_type": "\"fastqsolexa\""
},
"inputs": {},
"outputs": {
"output0": {
"id": "48117b37c6fc4855",
"src": "hda",
"uuid": "acae293f-069f-4491-9e6a-d80c74df0e9b"
}
},
"output_collections": {},
"tool_stdout": "",
"tool_stderr": "",
"job_stdout": null,
"job_stderr": null,
"stderr": "",
"stdout": "",
"job_messages": null,
"dependencies": [],
"user_email": "tests@fake.org",
"job_metrics": []
}
Original file line number Diff line number Diff line change
@@ -0,0 +1,44 @@
{
"model_class": "Job",
"id": "6cb69cf4d30d5f53",
"state": "error",
"exit_code": null,
"update_time": "2025-01-04T01:01:43.616468",
"create_time": "2025-01-04T01:01:34.298435",
"galaxy_version": "23.1",
"command_version": null,
"copied_from_job_id": null,
"tool_id": "upload1",
"history_id": "fc16d5ed9abfd51d",
"external_id": "gxy-m4crj",
"command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/25/registry.xml' '/galaxy/server/database/jobs_directory/000/25/upload_params.json' '37:/galaxy/server/database/objects/a/b/0/dataset_ab0c3d1d-2f05-4a81-8111-134f470ef0d8_files:/galaxy/server/database/objects/a/b/0/dataset_ab0c3d1d-2f05-4a81-8111-134f470ef0d8.dat'",
"traceback": null,
"params": {
"paramfile": "\"/galaxy/server/database/tmp/upload_params_5ccypvzj\"",
"files_metadata": "{\"__current_case__\": 84, \"file_type\": \"fastqsolexa\"}",
"dbkey": "\"?\"",
"force_composite": "\"false\"",
"files": "[{\"NAME\": \"Illumina_SG_R2.fastqsolexa\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_gn3fqhe5\", \"file_type\": \"\", \"ftp_files\": null, \"space_to_tab\": null, \"to_posix_lines\": \"Yes\", \"url_paste\": null, \"uuid\": null}]",
"file_count": "\"auto\"",
"file_type": "\"fastqsolexa\""
},
"inputs": {},
"outputs": {
"output0": {
"id": "36b346e7b07077f3",
"src": "hda",
"uuid": "ab0c3d1d-2f05-4a81-8111-134f470ef0d8"
}
},
"output_collections": {},
"tool_stdout": "",
"tool_stderr": "",
"job_stdout": null,
"job_stderr": null,
"stderr": "",
"stdout": "",
"job_messages": null,
"dependencies": [],
"user_email": "tests@fake.org",
"job_metrics": []
}
Original file line number Diff line number Diff line change
@@ -0,0 +1,44 @@
{
"model_class": "Job",
"id": "9f01be9dcb05c5f5",
"state": "error",
"exit_code": null,
"update_time": "2025-01-04T01:09:13.051173",
"create_time": "2025-01-04T01:09:03.536960",
"galaxy_version": "23.1",
"command_version": null,
"copied_from_job_id": null,
"tool_id": "upload1",
"history_id": "fc16d5ed9abfd51d",
"external_id": "gxy-clxx4",
"command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/65/registry.xml' '/galaxy/server/database/jobs_directory/000/65/upload_params.json' '85:/galaxy/server/database/objects/c/6/d/dataset_c6d322df-914e-4dfe-9371-b496d605f764_files:/galaxy/server/database/objects/c/6/d/dataset_c6d322df-914e-4dfe-9371-b496d605f764.dat'",
"traceback": null,
"params": {
"paramfile": "\"/galaxy/server/database/tmp/upload_params_odctmkkz\"",
"files_metadata": "{\"__current_case__\": 300, \"file_type\": \"sam\"}",
"dbkey": "\"?\"",
"force_composite": "\"false\"",
"files": "[{\"NAME\": \"sam_to_bam_noheader_in2.sam\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_pmdyx3i0\", \"file_type\": \"\", \"ftp_files\": null, \"space_to_tab\": null, \"to_posix_lines\": \"Yes\", \"url_paste\": null, \"uuid\": null}]",
"file_count": "\"auto\"",
"file_type": "\"sam\""
},
"inputs": {},
"outputs": {
"output0": {
"id": "2e07ec7d7382b3a6",
"src": "hda",
"uuid": "c6d322df-914e-4dfe-9371-b496d605f764"
}
},
"output_collections": {},
"tool_stdout": "",
"tool_stderr": "",
"job_stdout": null,
"job_stderr": null,
"stderr": "",
"stdout": "",
"job_messages": null,
"dependencies": [],
"user_email": "tests@fake.org",
"job_metrics": []
}
Loading

0 comments on commit ca846cb

Please sign in to comment.