Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

docs: instructions how to setup with dated worker #40

Merged
merged 1 commit into from
Nov 29, 2023
Merged

docs: instructions how to setup with dated worker #40

Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
22 changes: 21 additions & 1 deletion README.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -219,12 +219,17 @@ ln -sr .dev/volumes/$STATIC/data/download/worker/clinvar-strucvars-grch37-*/clin
ln -sr .dev/volumes/$STATIC/data/download/worker/clinvar-strucvars-grch38-*/clinvar-strucvars.bin \
.dev/volumes/$STATIC/data/worker/grch38/strucvars/clinvar.bin

rm -f .dev/volumes/$STATIC/data/worker/grch3?/strucvars/patho-mms.bin
rm -f .dev/volumes/$STATIC/data/worker/grch3?/strucvars/patho-mms.{bin,bed}

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
# TODO: here, we need to remove the legacy *.bin file in the future
ln -sr .dev/volumes/$STATIC/data/download/worker/patho-mms-grch37-*/patho-mms.bed \
.dev/volumes/$STATIC/data/worker/grch37/strucvars/patho-mms.bin
ln -sr .dev/volumes/$STATIC/data/download/worker/patho-mms-grch38-*/patho-mms.bed \
.dev/volumes/$STATIC/data/worker/grch38/strucvars/patho-mms.bin

mkdir -p .dev/volumes/$STATIC/data/worker/grch3{7,8}/tads
rm -f .dev/volumes/$STATIC/data/worker/grch3?/tads/hesc.bed
Expand All @@ -242,6 +247,10 @@ 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
# TODO: get rid of legacy omim.tsv
ln -sr .dev/volumes/$STATIC/data/download/worker/mim2gene-*/mim2gene.tsv \
.dev/volumes/$STATIC/data/worker/noref/genes/omim.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}
Expand Down Expand Up @@ -269,6 +278,17 @@ ln -sr .dev/volumes/$STATIC/data/download/worker/masked-repeat-grch38-*/masked-r
ln -sr .dev/volumes/$STATIC/data/download/worker/masked-segdup-grch38-*/masked-segdup.bin \
.dev/volumes/$STATIC/data/worker/grch38/features/masked_seqdup.bin

## create legacy dataset for the dated worker (v0.10.2)
## TODO: later get rid of this

mkdir -p .dev/volumes/$STATIC/data/worker-data-0.10.2/mehari/{grch37,grch38}
ln -sr .dev/volumes/$STATIC/data/worker \
.dev/volumes/$STATIC/data/worker-data-0.10.2
wget -O .dev/volumes/$STATIC/data/worker-data-0.10.2/mehari/grch37/txs.bin.zst \
https://github.com/bihealth/mehari-data-tx/releases/download/v0.2.2/mehari-data-txs-grch37-0.2.2.bin.zst
wget -O .dev/volumes/$STATIC/data/worker-data-0.10.2/mehari/grch38/txs.bin.zst \
https://github.com/bihealth/mehari-data-tx/releases/download/v0.2.2/mehari-data-txs-grch38-0.2.2.bin.zst

##
## tracks
##
Expand Down
Loading