Update docs for Nirvana reference disk [VS-796] [VS-531] #8170
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## ah_var_store #8170 +/- ##
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| Note: this Nirvana reference image was not available in time for it to be used to create the Delta VAT. The | ||
| `GvsCreateVATfromVDS` WDL has been speculatively updated to take advantage of references loaded from an attached |
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I think this could be a teeny bit more aggressive ("hey, make sure you run this on a test set before Echo, dummy!") haha
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Yeah this dummy will be testing his changes with Quickstart data as soon as the WX-910 fixes hit production, hopefully early next week with the monolith release.
I have not, I'd certainly be interested in some pairing / mobbing to do that. Also this requires the Cromwell shell escape fixes to be available in production. I hope to merge that soon but I'm not sure these days how long after merge to Cromwell develop before code goes to production. |
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Here's an example run on a quickstart: https://app.terra.bio/#workspaces/gvs-dev/GVS%20Quickstart%20v3%20ggrant/job_history/4b83a498-5bd8-4f42-b312-1d0efcf55cfc - The ancestry file really should be installed in the quickstart storage if it is not there already, and the sites-only-vcf I generated using the hail code (a while ago). |
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| Note: this Nirvana reference image was not available in time for it to be used to create the Delta VAT. The | ||
| `GvsCreateVATfromVDS` WDL has been speculatively updated to take advantage of references loaded from an attached |
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I think this could be a teeny bit more aggressive ("hey, make sure you run this on a test set before Echo, dummy!") haha
| mkdir datasources_dir | ||
| tar zxvf ~{nirvana_data_tar} -C datasources_dir ## --strip-components 2 | ||
| DATA_SOURCES_FOLDER="$PWD/datasources_dir/references" | ||
| DATA_SOURCES_FOLDER="/cromwell_root/broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1" |
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this is the only line I'm at all worried about
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| REFERENCE_DISK_MOUNT_POINT=$(lsblk | sed -E -n 's!.*(/mnt/[a-f0-9]+).*!\1!p') | ||
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| # Find this one particular reference under the mount path: | ||
| GRCH38_PATH=$(find ${REFERENCE_DISK_MOUNT_POINT} -name Homo_sapiens.GRCh38.Nirvana.dat) |
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see if this fails if the file is not found
| # version of the Nirvana reference image is deployed into Terra. | ||
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| # Find where the reference disk has been mounted on this VM: | ||
| REFERENCE_DISK_MOUNT_POINT=$(lsblk | sed -E -n 's!.*(/mnt/[a-f0-9]+).*!\1!p') |
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see that this fails clearly if reference volume is not found (like 'Use reference disks' was not checked)
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