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Updating anvil-edge README for edge-24-09-01-06-11-1
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7 changes: 7 additions & 0 deletions
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reports/anvil-edge/tool-tests/edge-24-09-01-06-11-1/chunk.json
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,7 @@ | ||
| { | ||
| "12": { | ||
| "run1": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-edge/tool-tests/edge-24-09-01-06-11-1/results.html", | ||
| "date1": "Sun Sep 01 06:26:20 2024", | ||
| "tools": "https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-edge/tool-tests/edge-24-09-01-06-11-1/tools.yml" | ||
| } | ||
| } |
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reports/anvil-edge/tool-tests/edge-24-09-01-06-11-1/chunk.txt
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,23 @@ | ||
| -t deeptools_compute_matrix --tool-version 514fa53b5efb | ||
| -t deeptools_bam_coverage --tool-version bb1e4f63e0e6 | ||
| -t multiqc --tool-version 75c93c70d094 | ||
| -t multiqc --tool-version 9a913cdee30e | ||
| -t multiqc --tool-version df99138d2776 | ||
| -t lastz --tool-version e7f19d6a9af8 | ||
| -t nanoplot --tool-version edbb6c5028f5 | ||
| -t poretools_extract --tool-version 7e4f1ed70187 | ||
| -t pileup_interval --tool-version 9c1c0b947e46 | ||
| -t samtools_depth --tool-version 44de678a44c4 | ||
| -t samtools_rmdup --tool-version 586f9e1cdb2b | ||
| -t modify_loom --tool-version 05631436cdf1 | ||
| -t scater_plot_tsne --tool-version 99f912d5af9f | ||
| -t salmon_kallisto_mtx_to_10x --tool-version 88f5a0a6a818 | ||
| -t salmon_kallisto_mtx_to_10x --tool-version e42c217a450f | ||
| -t scanpy_find_cluster --tool-version 35caf3c27c91 | ||
| -t scanpy_find_cluster --tool-version 9e4f79e40b84 | ||
| -t reshape2_melt --tool-version 317ed0ee8bf2 | ||
| -t freebayes --tool-version ef2c525bd8cd | ||
| -t bcftools_cnv --tool-version 01d6b7d6365e | ||
| -t bcftools_roh --tool-version b76adb2f1c51 | ||
| -t vcfbedintersect --tool-version aea8e90ad788 | ||
| -t vcfvcfintersect --tool-version 166c4f50525f |
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45
reports/anvil-edge/tool-tests/edge-24-09-01-06-11-1/errors/0819d429057bf8a0.json
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,45 @@ | ||
| { | ||
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45 changes: 45 additions & 0 deletions
45
reports/anvil-edge/tool-tests/edge-24-09-01-06-11-1/errors/0fdb98639d6d499e.json
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,45 @@ | ||
| { | ||
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45 changes: 45 additions & 0 deletions
45
reports/anvil-edge/tool-tests/edge-24-09-01-06-11-1/errors/15b628f3a8b45d2c.json
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,45 @@ | ||
| { | ||
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| "id": "15b628f3a8b45d2c", | ||
| "history_id": "0f5f5d39c9be041a", | ||
| "tool_id": "upload1", | ||
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| "create_time": "2024-09-01T06:52:17.979200", | ||
| "update_time": "2024-09-01T06:55:00.198902", | ||
| "galaxy_version": "24.1", | ||
| "external_id": "gxy-jwpk2", | ||
| "handler": null, | ||
| "job_runner_name": null, | ||
| "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/201/registry.xml' '/galaxy/server/database/jobs_directory/000/201/upload_params.json' '266:/galaxy/server/database/objects/a/c/1/dataset_ac145c97-0ccc-4734-af6b-7098b1ca253c_files:/galaxy/server/database/objects/a/c/1/dataset_ac145c97-0ccc-4734-af6b-7098b1ca253c.dat'", | ||
| "user_email": "tests@fake.org", | ||
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45 changes: 45 additions & 0 deletions
45
reports/anvil-edge/tool-tests/edge-24-09-01-06-11-1/errors/17b9af32bdd92c3c.json
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,45 @@ | ||
| { | ||
| "model_class": "Job", | ||
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| "history_id": "0f5f5d39c9be041a", | ||
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| "create_time": "2024-09-01T06:43:40.568049", | ||
| "update_time": "2024-09-01T06:45:24.125923", | ||
| "galaxy_version": "24.1", | ||
| "external_id": "gxy-b5r4g", | ||
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| "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/109/registry.xml' '/galaxy/server/database/jobs_directory/000/109/upload_params.json' '162:/galaxy/server/database/objects/8/4/3/dataset_8437b923-4ebe-4dff-ae17-b6dd10e8ed7c_files:/galaxy/server/database/objects/8/4/3/dataset_8437b923-4ebe-4dff-ae17-b6dd10e8ed7c.dat'", | ||
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45 changes: 45 additions & 0 deletions
45
reports/anvil-edge/tool-tests/edge-24-09-01-06-11-1/errors/1e422eebd2ee4ea3.json
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,45 @@ | ||
| { | ||
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45 changes: 45 additions & 0 deletions
45
reports/anvil-edge/tool-tests/edge-24-09-01-06-11-1/errors/1ed84d616d66eb3e.json
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,45 @@ | ||
| { | ||
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56 changes: 56 additions & 0 deletions
56
reports/anvil-edge/tool-tests/edge-24-09-01-06-11-1/errors/28e6fe619e9e1c2d.json
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| Original file line number | Diff line number | Diff line change |
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| "handler": null, | ||
| "job_runner_name": null, | ||
| "command_line": "ln -s -f '/galaxy/server/database/objects/5/4/0/dataset_54058f86-0e55-4242-8e7c-69e29d989e47.dat' 'localref.fa' && samtools faidx 'localref.fa' 2>&1 || echo \"Error running samtools faidx for FreeBayes\" >&2 && ln -s -f '/galaxy/server/database/objects/9/1/9/dataset_9196fc04-b291-4934-9ca7-95edcbf7aa6d.dat' 'b_0.bam' && ln -s -f '/galaxy/server/database/objects/_metadata_files/0/8/c/metadata_08ceb78f-5a73-48fa-a0a1-d6361e1ca94b.dat' 'b_0.bam.bai' && samtools view -H b_0.bam| grep '^@SQ' | cut -f 2- | awk '{ gsub(\"^SN:\",\"\",$1); gsub(\"^LN:\",\"\",$2); print $1\"\\t0\\t\"$2; }' >> regions_all.bed && sort -u regions_all.bed > regions_uniq.bed && mkdir vcf_output failed_alleles trace && for i in `cat regions_uniq.bed | awk '{print $1\":\"$2\"..\"$3}'`; do echo \" freebayes --region '$i' --bam 'b_0.bam' --fasta-reference 'localref.fa' --vcf './vcf_output/part_$i.vcf' --min-coverage 14 --skip-coverage 0 --limit-coverage 0 --haplotype-length 0 --min-alternate-count 1 --min-alternate-fraction 0.05 --pooled-continuous --report-monomorphic --standard-filters \"; done > freebayes_commands.sh && cat freebayes_commands.sh | parallel --will-cite -j ${GALAXY_SLOTS:-1} && grep \"^#\" \"./vcf_output/part_$i.vcf\" > header.txt && for i in `cat regions_uniq.bed | awk '{print $1\":\"$2\"..\"$3}'`; do cat \"./vcf_output/part_$i.vcf\" | grep -v \"^#\" || true ; done | sort -k1,1 -k2,2n -k5,5 -u | cat header.txt - > '/galaxy/server/database/objects/1/3/1/dataset_13188573-d0df-4046-b4a6-2da6796dbc9f.dat'", | ||
| "user_email": "tests@fake.org", | ||
| "command_version": null, | ||
| "params": { | ||
| "__input_ext": "\"bam\"", | ||
| "dbkey": "\"?\"", | ||
| "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", | ||
| "options_type": "{\"__current_case__\": 4, \"options_type_selector\": \"naive_w_filters\"}", | ||
| "coverage_options": "{\"__current_case__\": 0, \"coverage_options_selector\": \"set\", \"limit_coverage\": \"0\", \"min_coverage\": \"14\", \"skip_coverage\": \"0\"}", | ||
| "target_limit_type": "{\"__current_case__\": 0, \"target_limit_type_selector\": \"do_not_limit\"}", | ||
| "reference_source": "{\"__current_case__\": 1, \"batchmode\": {\"__current_case__\": 0, \"input_bams\": {\"values\": [{\"id\": 345, \"src\": \"hda\"}]}, \"processmode\": \"individual\"}, \"ref_file\": {\"values\": [{\"id\": 346, \"src\": \"hda\"}]}, \"reference_source_selector\": \"history\"}" | ||
| }, | ||
| "inputs": { | ||
| "reference_source|ref_file": { | ||
| "id": "77e464c82d2dd442", | ||
| "src": "hda", | ||
| "uuid": "54058f86-0e55-4242-8e7c-69e29d989e47" | ||
| }, | ||
| "reference_source|batchmode|input_bams": { | ||
| "id": "cd7534d53f3302d3", | ||
| "src": "hda", | ||
| "uuid": "9196fc04-b291-4934-9ca7-95edcbf7aa6d" | ||
| } | ||
| }, | ||
| "outputs": { | ||
| "output_vcf": { | ||
| "id": "0d42b19d3e5ce231", | ||
| "src": "hda", | ||
| "uuid": "13188573-d0df-4046-b4a6-2da6796dbc9f" | ||
| } | ||
| }, | ||
| "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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