diff --git a/README.md b/README.md index b2e440e..a29f6ac 100644 --- a/README.md +++ b/README.md @@ -73,32 +73,61 @@ For this, we have prepared strongly reduced data sets (overall less than 2GB rat Obtain the annonars data: ```bash session -mkdir -p .dev/volumes/varfish-static/data/download -SRC_DST=" -full/annonars/gnomad-mtdna-grch37-3.1+0.12.8/*:annonars/gnomad-mtdna-grch37-3.1+0.12.8 -full/annonars/gnomad-mtdna-grch38-3.1+0.12.8/*:annonars/gnomad-mtdna-grch38-3.1+0.12.8 -full/annonars/helixmtdb-grch37-20200327+0.12.8/*:annonars/helixmtdb-grch37-20200327+0.12.8 -full/annonars/helixmtdb-grch38-20200327+0.12.8/*:annonars/helixmtdb-grch38-20200327+0.12.8 -full/annonars/genes-3.1+2.1.1+4.4+20230606+10.1+20230828+0.19.0/*:annonars/genes-3.1+2.1.1+4.4+20230606+10.1+20230828+0.19.0 -full/mehari/genes-txs-grch37-0.3.0/*:mehari/genes-txs-grch37-0.3.0 -full/mehari/genes-txs-grch38-0.3.0/*:mehari/genes-txs-grch38-0.3.0 -full/mehari/genes-xlink-20230624/*:mehari/genes-xlink-20230624 -full/tracks/*:tracks -full/worker/*:worker -reduced-dev/annonars/*:annonars -reduced-dev/mehari/*:mehari -reduced-dev/viguno/*:viguno -" -(set -x; for src_dst in $SRC_DST; do \ - src=$(echo $src_dst | cut -d : -f 1); \ - dst=$(echo $src_dst | cut -d : -f 2); \ - mkdir -p .dev/volumes/varfish-static/data/download/$dst; \ +cat <<"EOF" >/tmp/tokens.txt +## -- full data ------------------------------------------------------------- +## uncomment the lines and use instead of reduced data for a full installation +# full/annonars/cadd-grch37-1.6+0.29.1 +# full/annonars/cadd-grch38-1.6+0.29.1 +# full/annonars/cons-grch37-20161007+0.29.1 +# full/annonars/cons-grch38-20190906+0.29.1 +# full/annonars/dbnsfp-grch37-4.4a+0.29.1 +# full/annonars/dbnsfp-grch37-4.4c+0.29.1 +# full/annonars/dbnsfp-grch38-4.4a+0.29.1 +# full/annonars/dbnsfp-grch38-4.4c+0.29.1 +# full/annonars/dbscsnv-grch37-1.1+0.29.1 +# full/annonars/dbscsnv-grch38-1.1+0.29.1 +# full/annonars/dbsnp-grch37-b151+0.29.1 +# full/annonars/dbsnp-grch38-b151+0.29.1 +full/annonars/functional-grch37-105.20201022+0.29.1 +full/annonars/functional-grch38-110+0.29.1 +full/annonars/genes-3.1+2.1.1+4.4+20230606+10.1+20231123+0.29.3 +# full/annonars/gnomad-exomes-grch37-2.1.1+0.29.1 +# full/annonars/gnomad-exomes-grch38-2.1.1+0.29.1 +# full/annonars/gnomad-genomes-grch37-2.1.1+0.29.1 +# full/annonars/gnomad-genomes-grch38-3.1.2+0.29.1 +full/annonars/gnomad-mtdna-grch37-3.1+0.29.1 +full/annonars/gnomad-mtdna-grch38-3.1+0.29.1 +full/annonars/gnomad-sv-exomes-grch37-0.3.1+0.29.1 +full/annonars/gnomad-sv-exomes-grch38-4.0+0.29.1 +full/annonars/gnomad-sv-genomes-grch37-2.1.1+0.29.1 +full/annonars/gnomad-sv-genomes-grch38-4.0+0.29.1 +full/annonars/helixmtdb-grch37-20200327+0.29.1 +full/annonars/helixmtdb-grch38-20200327+0.29.1 +full/annonars/regions-grch37-20231122+0.29.3 +full/annonars/regions-grch38-20231122+0.29.3 +# full/mehari/freqs-grch37-2.1.1+2.1.1+3.1+20200327+0.29.1 +# full/mehari/freqs-grch37-2.1.1+2.1.1+3.1+20200327+0.29.1 +full/mehari/genes-xlink-20231122 +full/tracks/* +full/worker/* +# full/viguno/hpo-20230606+0.1.6 +## -- reduced data for dev --------------------------------------------------- +reduced-dev/annonars/* +reduced-dev/mehari/* +reduced-dev/viguno/* +EOF +STATIC=varfish-static +mkdir -p .dev/volumes/$STATIC/data/download +(set -x; for token in $(grep -v ^# /tmp/tokens.txt); do \ + src=$token; \ + dst=$(echo $token | perl -p -e 's|/\*||' | perl -p -e 's#^(full/|reduced-dev/)##'); \ + mkdir -p .dev/volumes/$STATIC/data/download/$dst; \ s5cmd \ --endpoint-url=https://ceph-s3-public.cubi.bihealth.org \ --no-sign-request \ sync \ "s3://varfish-public/$src" \ - ".dev/volumes/varfish-static/data/download/$dst"; \ + ".dev/volumes/$STATIC/data/download/$dst"; \ done) ``` @@ -109,21 +138,22 @@ Setup symlink structure so the data is at the expected location. ## annonars ## -mkdir -p .dev/volumes/varfish-static/data/annonars +STATIC=varfish-static +mkdir -p .dev/volumes/$STATIC/data/annonars -ln -sr .dev/volumes/varfish-static/data/download/annonars/genes-* \ - .dev/volumes/varfish-static/data/annonars/genes +ln -sr .dev/volumes/$STATIC/data/download/annonars/genes-* \ + .dev/volumes/$STATIC/data/annonars/genes names="cadd dbsnp dbnsfp dbscsnv gnomad-mtdna gnomad-genomes gnomad-exomes helixmtdb cons"; \ for genome in grch37 grch38; do \ for name in $names; do \ - mkdir -p .dev/volumes/varfish-static/data/annonars/$genome; \ - test -e .dev/volumes/varfish-static/data/$genome/$name || \ + mkdir -p .dev/volumes/$STATIC/data/annonars/$genome; \ + test -e .dev/volumes/$STATIC/data/$genome/$name || \ ln -sr \ - $(echo .dev/volumes/varfish-static/data/download/annonars/$name-$genome-* \ + $(echo .dev/volumes/$STATIC/data/download/annonars/$name-$genome-* \ | tr ' ' '\n' \ | tail -n 1) \ - .dev/volumes/varfish-static/data/annonars/$genome/$name; \ + .dev/volumes/$STATIC/data/annonars/$genome/$name; \ done; \ done @@ -131,127 +161,166 @@ done ## mehari ## -mkdir -p .dev/volumes/varfish-static/data/mehari/grch3{7,8} +STATIC=varfish-static +mkdir -p .dev/volumes/$STATIC/data/mehari/grch3{7,8} -ln -sr .dev/volumes/varfish-static/data/download/mehari/genes-txs-grch37-*/mehari-data-txs-grch37-*in.zst \ - .dev/volumes/varfish-static/data/mehari/grch37/txs.bin.zst -ln -sr .dev/volumes/varfish-static/data/download/mehari/freqs-grch37-* \ - .dev/volumes/varfish-static/data/mehari/grch37/freqs -ln -sr .dev/volumes/varfish-static/data/download/mehari/genes-txs-grch38-*/mehari-data-txs-grch38-*.bin.zst \ - .dev/volumes/varfish-static/data/mehari/grch38/txs.bin.zst -ln -sr .dev/volumes/varfish-static/data/download/mehari/freqs-grch38-* \ - .dev/volumes/varfish-static/data/mehari/grch38/freqs +rm -f .dev/volumes/$STATIC/data/mehari/grch3?/freqs + +ln -sr .dev/volumes/$STATIC/data/download/mehari/freqs-grch37-* \ + .dev/volumes/$STATIC/data/mehari/grch37/freqs +ln -sr .dev/volumes/$STATIC/data/download/mehari/freqs-grch38-* \ + .dev/volumes/$STATIC/data/mehari/grch38/freqs ## ## viguno ## -ln -sr .dev/volumes/varfish-static/data/download/mehari/genes-xlink-20230624/genes-xlink.tsv \ - .dev/volumes/varfish-static/data/hgnc_xlink.tsv -ln -sr .dev/volumes/varfish-static/data/download/viguno/hpo-20230606+0.1.6 \ - .dev/volumes/varfish-static/data/hpo +STATIC=varfish-static + +rm -f .dev/volumes/$STATIC/data/{hgnc_xlink.tsv,hpo} + +ln -sr .dev/volumes/$STATIC/data/download/mehari/genes-xlink-20231122/genes-xlink.tsv \ + .dev/volumes/$STATIC/data/hgnc_xlink.tsv +ln -sr .dev/volumes/$STATIC/data/download/viguno/hpo-20230606+0.1.6 \ + .dev/volumes/$STATIC/data/hpo ## ## worker ## -mkdir -p .dev/volumes/varfish-static/data/worker/{grch3{7,8}/strucvars/bgdbs,noref/genes} - -ln -sr .dev/volumes/varfish-static/data/download/worker/bgdb-exac-grch37-*/bgdb-exac.bin \ - .dev/volumes/varfish-static/data/worker/grch37/strucvars/bgdbs/exac.bin -ln -sr .dev/volumes/varfish-static/data/download/worker/bgdb-g1k-grch37-phase3v2+0.9.0/bgdb-g1k.bin \ - .dev/volumes/varfish-static/data/worker/grch37/strucvars/bgdbs/g1k.bin -ln -sr .dev/volumes/varfish-static/data/download/worker/bgdb-gnomad-grch37-*/bgdb-gnomad.bin \ - .dev/volumes/varfish-static/data/worker/grch37/strucvars/bgdbs/gnomad.bin -ln -sr .dev/volumes/varfish-static/data/download/worker/bgdb-dbvar-grch37-*/bgdb-dbvar.bin \ - .dev/volumes/varfish-static/data/worker/grch37/strucvars/bgdbs/dbvar.bin -ln -sr .dev/volumes/varfish-static/data/download/worker/bgdb-dbvar-grch38-*/bgdb-dbvar.bin \ - .dev/volumes/varfish-static/data/worker/grch38/strucvars/bgdbs/dbvar.bin -ln -sr .dev/volumes/varfish-static/data/download/worker/bgdb-dgv-grch37-*/bgdb-dgv.bin \ - .dev/volumes/varfish-static/data/worker/grch37/strucvars/bgdbs/dgv.bin -ln -sr .dev/volumes/varfish-static/data/download/worker/bgdb-dgv-grch38-*/bgdb-dgv.bin \ - .dev/volumes/varfish-static/data/worker/grch38/strucvars/bgdbs/dgv.bin -ln -sr .dev/volumes/varfish-static/data/download/worker/bgdb-dgv-gs-grch37-*/bgdb-dgv-gs.bin \ - .dev/volumes/varfish-static/data/worker/grch37/strucvars/bgdbs/dgv-gs.bin -ln -sr .dev/volumes/varfish-static/data/download/worker/bgdb-dgv-gs-grch38-*/bgdb-dgv-gs.bin \ - .dev/volumes/varfish-static/data/worker/grch38/strucvars/bgdbs/dgv-gs.bin - -ln -sr .dev/volumes/varfish-static/data/download/worker/clinvar-strucvars-grch37-*/clinvar-strucvars.bin \ - .dev/volumes/varfish-static/data/worker/grch37/strucvars/clinvar.bin -ln -sr .dev/volumes/varfish-static/data/download/worker/clinvar-strucvars-grch38-*/clinvar-strucvars.bin \ - .dev/volumes/varfish-static/data/worker/grch38/strucvars/clinvar.bin - -ln -sr .dev/volumes/varfish-static/data/download/worker/patho-mms-grch37-*/patho-mms.bed \ - .dev/volumes/varfish-static/data/worker/grch37/strucvars/patho-mms.bed -ln -sr .dev/volumes/varfish-static/data/download/worker/patho-mms-grch38-*/patho-mms.bed \ - .dev/volumes/varfish-static/data/worker/grch38/strucvars/patho-mms.bed - -mkdir -p .dev/volumes/varfish-static/data/worker/grch3{7,8}/tads - -ln -sr .dev/volumes/varfish-static/data/download/worker/tads-grch37-dixon2015/hesc.bed \ - .dev/volumes/varfish-static/data/worker/grch37/tads/hesc.bed -ln -sr .dev/volumes/varfish-static/data/download/worker/tads-grch38-dixon2015/hesc.bed \ - .dev/volumes/varfish-static/data/worker/grch38/tads/hesc.bed - -ln -sr .dev/volumes/varfish-static/data/download/worker/genes-xlink-*/genes-xlink.bin \ - .dev/volumes/varfish-static/data/worker/noref/genes/xlink.bin -ln -sr .dev/volumes/varfish-static/data/download/worker/acmg-sf-*/acmg_sf.tsv \ - .dev/volumes/varfish-static/data/worker/noref/genes/acmg.tsv -ln -sr .dev/volumes/varfish-static/data/download/worker/mim2gene-*/mim2gene.tsv \ - .dev/volumes/varfish-static/data/worker/noref/genes/mime2gene.tsv - -mkdir -p .dev/volumes/varfish-static/data/worker/grch3{7,8}/genes - -ln -sr .dev/volumes/varfish-static/data/download/worker/genes-regions-grch37-*/ensembl_genes.bin \ - .dev/volumes/varfish-static/data/worker/grch37/genes/ensembl_regions.bin -ln -sr .dev/volumes/varfish-static/data/download/worker/genes-regions-grch38-*/ensembl_genes.bin \ - .dev/volumes/varfish-static/data/worker/grch38/genes/ensembl_regions.bin - -ln -sr .dev/volumes/varfish-static/data/download/worker/genes-regions-grch37-*/refseq_genes.bin \ - .dev/volumes/varfish-static/data/worker/grch37/genes/refseq_regions.bin -ln -sr .dev/volumes/varfish-static/data/download/worker/genes-regions-grch38-*/refseq_genes.bin \ - .dev/volumes/varfish-static/data/worker/grch38/genes/refseq_regions.bin - -mkdir -p .dev/volumes/varfish-static/data/worker/grch3{7,8}/features - -ln -sr .dev/volumes/varfish-static/data/download/worker/masked-repeat-grch37-*/masked-repeat.bin \ - .dev/volumes/varfish-static/data/worker/grch37/features/masked_repeat.bin -ln -sr .dev/volumes/varfish-static/data/download/worker/masked-segdup-grch37-*/masked-segdup.bin \ - .dev/volumes/varfish-static/data/worker/grch37/features/masked_seqdup.bin - -ln -sr .dev/volumes/varfish-static/data/download/worker/masked-repeat-grch38-*/masked-repeat.bin \ - .dev/volumes/varfish-static/data/worker/grch38/features/masked_repeat.bin -ln -sr .dev/volumes/varfish-static/data/download/worker/masked-segdup-grch38-*/masked-segdup.bin \ - .dev/volumes/varfish-static/data/worker/grch38/features/masked_seqdup.bin +STATIC=varfish-static +mkdir -p .dev/volumes/$STATIC/data/worker/{grch3{7,8}/strucvars/bgdbs,noref/genes} + +rm -f .dev/volumes/$STATIC/data/worker/grch3?/strucvars/bgdbs/{exac,g1k,gnomad,dbvar,dgv,dgv-gs}.bin + +ln -sr .dev/volumes/$STATIC/data/download/worker/bgdb-exac-grch37-*/bgdb-exac.bin \ + .dev/volumes/$STATIC/data/worker/grch37/strucvars/bgdbs/exac.bin +ln -sr .dev/volumes/$STATIC/data/download/worker/bgdb-g1k-grch37-phase3v2+0.9.0/bgdb-g1k.bin \ + .dev/volumes/$STATIC/data/worker/grch37/strucvars/bgdbs/g1k.bin +ln -sr .dev/volumes/$STATIC/data/download/worker/bgdb-gnomad-grch37-*/bgdb-gnomad.bin \ + .dev/volumes/$STATIC/data/worker/grch37/strucvars/bgdbs/gnomad.bin +ln -sr .dev/volumes/$STATIC/data/download/worker/bgdb-dbvar-grch37-*/bgdb-dbvar.bin \ + .dev/volumes/$STATIC/data/worker/grch37/strucvars/bgdbs/dbvar.bin +ln -sr .dev/volumes/$STATIC/data/download/worker/bgdb-dbvar-grch38-*/bgdb-dbvar.bin \ + .dev/volumes/$STATIC/data/worker/grch38/strucvars/bgdbs/dbvar.bin +ln -sr .dev/volumes/$STATIC/data/download/worker/bgdb-dgv-grch37-*/bgdb-dgv.bin \ + .dev/volumes/$STATIC/data/worker/grch37/strucvars/bgdbs/dgv.bin +ln -sr .dev/volumes/$STATIC/data/download/worker/bgdb-dgv-grch38-*/bgdb-dgv.bin \ + .dev/volumes/$STATIC/data/worker/grch38/strucvars/bgdbs/dgv.bin +ln -sr .dev/volumes/$STATIC/data/download/worker/bgdb-dgv-gs-grch37-*/bgdb-dgv-gs.bin \ + .dev/volumes/$STATIC/data/worker/grch37/strucvars/bgdbs/dgv-gs.bin +ln -sr .dev/volumes/$STATIC/data/download/worker/bgdb-dgv-gs-grch38-*/bgdb-dgv-gs.bin \ + .dev/volumes/$STATIC/data/worker/grch38/strucvars/bgdbs/dgv-gs.bin + +rm -f .dev/volumes/$STATIC/data/worker/grch3?/strucvars/clinvar.bin + +ln -sr .dev/volumes/$STATIC/data/download/worker/clinvar-strucvars-grch37-*/clinvar-strucvars.bin \ + .dev/volumes/$STATIC/data/worker/grch37/strucvars/clinvar.bin +ln -sr .dev/volumes/$STATIC/data/download/worker/clinvar-strucvars-grch38-*/clinvar-strucvars.bin \ + .dev/volumes/$STATIC/data/worker/grch38/strucvars/clinvar.bin + +rm -f .dev/volumes/$STATIC/data/worker/grch3?/strucvars/patho-mms.bin + +ln -sr .dev/volumes/$STATIC/data/download/worker/patho-mms-grch37-*/patho-mms.bed \ + .dev/volumes/$STATIC/data/worker/grch37/strucvars/patho-mms.bed +ln -sr .dev/volumes/$STATIC/data/download/worker/patho-mms-grch38-*/patho-mms.bed \ + .dev/volumes/$STATIC/data/worker/grch38/strucvars/patho-mms.bed + +mkdir -p .dev/volumes/$STATIC/data/worker/grch3{7,8}/tads +rm -f .dev/volumes/$STATIC/data/worker/grch3?/tads/hesc.bed + +ln -sr .dev/volumes/$STATIC/data/download/worker/tads-grch37-dixon2015/hesc.bed \ + .dev/volumes/$STATIC/data/worker/grch37/tads/hesc.bed +ln -sr .dev/volumes/$STATIC/data/download/worker/tads-grch38-dixon2015/hesc.bed \ + .dev/volumes/$STATIC/data/worker/grch38/tads/hesc.bed + +rm -f .dev/volumes/$STATIC/data/worker/noref/genes/{xlink.bin,acmg.tsv,mime2gene.tsv} + +ln -sr .dev/volumes/$STATIC/data/download/worker/genes-xlink-*/genes-xlink.bin \ + .dev/volumes/$STATIC/data/worker/noref/genes/xlink.bin +ln -sr .dev/volumes/$STATIC/data/download/worker/acmg-sf-*/acmg_sf.tsv \ + .dev/volumes/$STATIC/data/worker/noref/genes/acmg.tsv +ln -sr .dev/volumes/$STATIC/data/download/worker/mim2gene-*/mim2gene.tsv \ + .dev/volumes/$STATIC/data/worker/noref/genes/mime2gene.tsv + +mkdir -p .dev/volumes/$STATIC/data/worker/grch3{7,8}/genes +rm -f .dev/volumes/$STATIC/data/worker/grch3?/genes/{ensembl_genes.bin,refseq_genes.bin} + +ln -sr .dev/volumes/$STATIC/data/download/worker/genes-regions-grch37-*/ensembl_genes.bin \ + .dev/volumes/$STATIC/data/worker/grch37/genes/ensembl_regions.bin +ln -sr .dev/volumes/$STATIC/data/download/worker/genes-regions-grch38-*/ensembl_genes.bin \ + .dev/volumes/$STATIC/data/worker/grch38/genes/ensembl_regions.bin + +ln -sr .dev/volumes/$STATIC/data/download/worker/genes-regions-grch37-*/refseq_genes.bin \ + .dev/volumes/$STATIC/data/worker/grch37/genes/refseq_regions.bin +ln -sr .dev/volumes/$STATIC/data/download/worker/genes-regions-grch38-*/refseq_genes.bin \ + .dev/volumes/$STATIC/data/worker/grch38/genes/refseq_regions.bin + +mkdir -p .dev/volumes/$STATIC/data/worker/grch3{7,8}/features +rm -f .dev/volumes/$STATIC/data/worker/grch3?/features/{masked_repeat.bin,masked_seqdup.bin} + +ln -sr .dev/volumes/$STATIC/data/download/worker/masked-repeat-grch37-*/masked-repeat.bin \ + .dev/volumes/$STATIC/data/worker/grch37/features/masked_repeat.bin +ln -sr .dev/volumes/$STATIC/data/download/worker/masked-segdup-grch37-*/masked-segdup.bin \ + .dev/volumes/$STATIC/data/worker/grch37/features/masked_seqdup.bin + +ln -sr .dev/volumes/$STATIC/data/download/worker/masked-repeat-grch38-*/masked-repeat.bin \ + .dev/volumes/$STATIC/data/worker/grch38/features/masked_repeat.bin +ln -sr .dev/volumes/$STATIC/data/download/worker/masked-segdup-grch38-*/masked-segdup.bin \ + .dev/volumes/$STATIC/data/worker/grch38/features/masked_seqdup.bin ## ## tracks ## -mkdir -p .dev/volumes/varfish-static/data/nginx/grch3{7,8} +STATIC=varfish-static +mkdir -p .dev/volumes/$STATIC/data/nginx/grch3{7,8} +rm -f .dev/volumes/$STATIC/data/nginx/grch3?/* -paths_37=$(find .dev/volumes/varfish-static/data/download/tracks/ -type f -name '*.bed' -or -name '*.bed.gz' | sort | grep grch37) +paths_37=$(find .dev/volumes/$STATIC/data/download/tracks/ -type f -name '*.bed' -or -name '*.bed.gz' | sort | grep grch37) for path in $paths_37; do if [[ -e ${path}.tbi ]]; then - ln -sr $path ${path}.tbi .dev/volumes/varfish-static/data/nginx/grch37 + ln -sr $path ${path}.tbi .dev/volumes/$STATIC/data/nginx/grch37 else - ln -sr $path .dev/volumes/varfish-static/data/nginx/grch37 + ln -sr $path .dev/volumes/$STATIC/data/nginx/grch37 fi done -paths_38=$(find .dev/volumes/varfish-static/data/download/tracks/ -type f -name '*.bed' -or -name '*.bed.gz' | sort | grep grch38) +paths_38=$(find .dev/volumes/$STATIC/data/download/tracks/ -type f -name '*.bed' -or -name '*.bed.gz' | sort | grep grch38) for path in $paths_38; do if [[ -e ${path}.tbi ]]; then - ln -sr $path ${path}.tbi .dev/volumes/varfish-static/data/nginx/grch38 + ln -sr $path ${path}.tbi .dev/volumes/$STATIC/data/nginx/grch38 else - ln -sr $path .dev/volumes/varfish-static/data/nginx/grch38 + ln -sr $path .dev/volumes/$STATIC/data/nginx/grch38 fi done ``` +To download Mehari transcripts + +```bash session +STATIC=varfish-static +mkdir -p .dev/volumes/$STATIC/data/download/mehari-data-txs-grch3{7,8} + +for ext in .zst .zst.sha256 .zst.report .zst.report.sha256; do + wget -O .dev/volumes/$STATIC/data/download/mehari-data-txs-grch37/mehari-data-txs-grch37-0.4.1.bin$ext \ + https://github.com/bihealth/mehari-data-tx/releases/download/v0.4.1/mehari-data-txs-grch37-0.4.1.bin$ext + wget -O .dev/volumes/$STATIC/data/download/mehari-data-txs-grch38/mehari-data-txs-grch38-0.4.1.bin$ext \ + https://github.com/bihealth/mehari-data-tx/releases/download/v0.4.1/mehari-data-txs-grch37-0.4.1.bin$ext +done + +rm -f .dev/volumes/$STATIC/data/mehari/grch3?/txs.bin.zst +ln -sr .dev/volumes/$STATIC/data/download/mehari-data-txs-grch37/mehari-data-txs-grch37-0.4.1.bin.zst \ + .dev/volumes/$STATIC/data/mehari/grch37/txs.bin.zst +ln -sr .dev/volumes/$STATIC/data/download/mehari-data-txs-grch38/mehari-data-txs-grch38-0.4.1.bin.zst \ + .dev/volumes/$STATIC/data/mehari/grch38/txs.bin.zst +``` + To create an in-house database: ```bash session +STATIC=varfish-static + varfish-server-worker db mk-inhouse \ --path-output-tsv /tmp/inhouse.tsv \ $(find YOUR_PATH -name '*.gts.tsv.gz' | sort) @@ -259,38 +328,40 @@ varfish-server-worker db mk-inhouse \ varfish-server-worker db to-bin \ --input-type strucvar-inhouse \ --path-input /tmp/inhouse.tsv \ - --path-output-bin .dev/volumes/varfish-static/data/worker/grch37/strucvars/inhouse.bin + --path-output-bin .dev/volumes/$STATIC/data/worker/grch37/strucvars/inhouse.bin ``` To obtain ClinVar Note that this will install the data from November 12, 2023 and you might want to [look here for the latest release](https://github.com/bihealth/annonars-data-clinvar/releases). ```bash session +STATIC=varfish-static + wget -O /tmp/annonars-clinvar-minimal-grch37-20231112+0.25.0.tar.gz \ https://github.com/bihealth/annonars-data-clinvar/releases/download/annonars-data-clinvar-20231112/annonars-clinvar-minimal-grch37-20231112+0.25.0.tar.gz wget -O /tmp/annonars-clinvar-minimal-grch38-20231112+0.25.0.tar.gz \ https://github.com/bihealth/annonars-data-clinvar/releases/download/annonars-data-clinvar-20231112/annonars-clinvar-minimal-grch38-20231112+0.25.0.tar.gz -tar -C .dev/volumes/varfish-static/data/download/annonars/ \ +tar -C .dev/volumes/$STATIC/data/download/annonars/ \ -xf /tmp/annonars-clinvar-minimal-grch37-20231112+0.25.0.tar.gz -tar -C .dev/volumes/varfish-static/data/download/annonars \ +tar -C .dev/volumes/$STATIC/data/download/annonars \ -xf /tmp/annonars-clinvar-minimal-grch38-20231112+0.25.0.tar.gz -rm -f .dev/volumes/varfish-static/data/annonars/grch37/clinvar -ln -sr .dev/volumes/varfish-static/data/download/annonars/annonars-clinvar-minimal-grch37-20231112+0.25.0 \ - .dev/volumes/varfish-static/data/annonars/grch37/clinvar -rm -f .dev/volumes/varfish-static/data/annonars/grch38/clinvar -ln -sr .dev/volumes/varfish-static/data/download/annonars/annonars-clinvar-minimal-grch38-20231112+0.25.0 \ - .dev/volumes/varfish-static/data/annonars/grch38/clinvar +rm -f .dev/volumes/$STATIC/data/annonars/grch37/clinvar +ln -sr .dev/volumes/$STATIC/data/download/annonars/annonars-clinvar-minimal-grch37-20231112+0.25.0 \ + .dev/volumes/$STATIC/data/annonars/grch37/clinvar +rm -f .dev/volumes/$STATIC/data/annonars/grch38/clinvar +ln -sr .dev/volumes/$STATIC/data/download/annonars/annonars-clinvar-minimal-grch38-20231112+0.25.0 \ + .dev/volumes/$STATIC/data/annonars/grch38/clinvar wget -O /tmp/annonars-clinvar-genes-20231112+0.25.0.tar.gz \ https://github.com/bihealth/annonars-data-clinvar/releases/download/annonars-data-clinvar-20231112/annonars-clinvar-genes-20231112+0.25.0.tar.gz -tar -C .dev/volumes/varfish-static/data/download/annonars \ +tar -C .dev/volumes/$STATIC/data/download/annonars \ -xf /tmp/annonars-clinvar-genes-20231112+0.25.0.tar.gz -rm -f .dev/volumes/varfish-static/data/annonars/clinvar-genes -ln -sr .dev/volumes/varfish-static/data/download/annonars/annonars-clinvar-genes-20231112+0.25.0 \ - .dev/volumes/varfish-static/data/annonars/clinvar-genes +rm -f .dev/volumes/$STATIC/data/annonars/clinvar-genes +ln -sr .dev/volumes/$STATIC/data/download/annonars/annonars-clinvar-genes-20231112+0.25.0 \ + .dev/volumes/$STATIC/data/annonars/clinvar-genes ```