diff --git a/HISTORY.rst b/HISTORY.rst index 23fc79f97..d1dfd6d14 100644 --- a/HISTORY.rst +++ b/HISTORY.rst @@ -26,7 +26,8 @@ End-User Summary - Switching scoring to MutationTaster 85 interface, added back MT 85 link-out alongside MT 2021 link-out (#509). - Made flag filter and flag form nomenclature consistent (#297) - Improved developer setup documentation and added Windows installation instructions (#533). -- Fixed broken VariantValidator query (#523) +- Fixed broken VariantValidator query (#523). +- Adjusting path to new varfish-annotator db download (#546). Full Change List ================ @@ -51,7 +52,8 @@ Full Change List - Updating ``utility/*.sh`` scripts from "upstream" sodar-server (#531). - Improved developer setup documentation and added Windows installation instructions (#533). - Skip commit trailer checks for dependabot (#537). -- Fixed broken VariantValidator query (#523) +- Fixed broken VariantValidator query (#523). +- Adjusting path to new varfish-annotator db download (#546). ------ v1.2.0 diff --git a/docs_manual/admin_ingest.rst b/docs_manual/admin_ingest.rst index f1a363094..e2637bcd1 100644 --- a/docs_manual/admin_ingest.rst +++ b/docs_manual/admin_ingest.rst @@ -48,19 +48,19 @@ The downloaded archive has a size of ~10 GB while the extracted data has a size .. code-block:: bash $ GENOME=grch37 # alternatively use grch38 - $ RELEASE=20210728 - $ mkdir varfish-annotator-20210728-$GENOME - $ cd varfish-annotator-20210728-$GENOME + $ RELEASE=20210728b + $ mkdir varfish-annotator-$RELEASE-$GENOME + $ cd varfish-annotator-$RELEASE-$GENOME $ wget --no-check-certificate \ https://file-public.cubi.bihealth.org/transient/varfish/anthenea/varfish-annotator-db-$RELEASE-$GENOME.h2.db.gz{,.sha256} \ https://file-public.cubi.bihealth.org/transient/varfish/anthenea/jannovar-db-$RELEASE-$GENOME.tar.gz{,.sha256} $ sha256sum --check varfish-annotator-db-$RELEASE-$GENOME.h2.db.gz.sha256 - varfish-annotator-db-20210728-grch37.h2.db.gz: OK + varfish-annotator-db-$RELEASE-grch37.h2.db.gz: OK $ sha256sum --check jannovar-db-$RELEASE-$GENOME.tar.gz.sha256 - jannovar-db-20210728-grch37.tar.gz: OK + jannovar-db-$RELEASE-grch37.tar.gz: OK $ gzip -d varfish-annotator-db-$RELEASE-$GENOME.h2.db.gz $ tar xf jannovar-db-$RELEASE-$GENOME.tar.gz - $ rm jannovar-db-20210728-$RELEASE.tar.gz{,.sha256} \ + $ rm jannovar-db-$RELEASE-$RELEASE.tar.gz{,.sha256} \ varfish-annotator-db-$RELEASE-$GENOME.h2.db.gz.sha256 $ mv jannovar-db-$RELEASE-$GENOME/* . $ rmdir jannovar-db-$RELEASE-$GENOME @@ -100,9 +100,9 @@ You must provide an bgzip-compressed VCF file ``INPUT.vcf.gz`` -XX:MaxHeapSize=10g \ -XX:+UseConcMarkSweepGC \ annotate \ - --db-path varfish-annotator-20210728-$GENOME/varfish-annotator-db-$RELEASE-$GENOME.h2.db \ - --ensembl-ser-path varfish-annotator-20210728-$GENOME/ensembl*.ser \ - --refseq-ser-path varfish-annotator-20210728-$GENOME/refseq_curated*.ser \ + --db-path varfish-annotator-$RELEASE-$GENOME/varfish-annotator-db-$RELEASE-$GENOME.h2.db \ + --ensembl-ser-path varfish-annotator-$RELEASE-$GENOME/ensembl*.ser \ + --refseq-ser-path varfish-annotator-$RELEASE-$GENOME/refseq_curated*.ser \ --ref-path $REFERENCE \ --input-vcf "INPUT.vcf.gz" \ --release "$GENOME" \ @@ -132,9 +132,9 @@ While only release GRCh37/hg19 is supported, using a file with UCSC-style chromo :lineno-start: 4 :dedent: 0 - --db-path varfish-annotator-20210728-$GENOME/varfish-annotator-db-$RELEASE-$GENOME.h2.db \ - --ensembl-ser-path varfish-annotator-20210728-$GENOME/ensembl*.ser \ - --refseq-ser-path varfish-annotator-20210728-$GENOME/refseq_curated*.ser \ + --db-path varfish-annotator-$RELEASE-$GENOME/varfish-annotator-db-$RELEASE-$GENOME.h2.db \ + --ensembl-ser-path varfish-annotator-$RELEASE-$GENOME/ensembl*.ser \ + --refseq-ser-path varfish-annotator-$RELEASE-$GENOME/refseq_curated*.ser \ --ref-path $REFERENCE \ The following lines provide the path to the input VCF file, specify the release name (must be ``GRCh37``) and the name of the case as written out. @@ -221,9 +221,9 @@ Structural variants can be annotated as follows. --default-sv-method=YOURCALLERvVERSION" --release $GENOME \ \ - --db-path varfish-annotator-20210728-$GENOME/varfish-annotator-db-$RELEASE-$GENOME.h2.db \ - --ensembl-ser-path varfish-annotator-20210728-$GENOME/ensembl*.ser \ - --refseq-ser-path varfish-annotator-20210728-$GENOME/refseq_curated*.ser \ + --db-path varfish-annotator-$RELEASE-$GENOME/varfish-annotator-db-$RELEASE-$GENOME.h2.db \ + --ensembl-ser-path varfish-annotator-$RELEASE-$GENOME/ensembl*.ser \ + --refseq-ser-path varfish-annotator-$RELEASE-$GENOME/refseq_curated*.ser \ \ --input-vcf FAM_sv_calls.vcf.gz \ --output-db-info FAM_sv_calls.db-info.tsv \ diff --git a/docs_manual/admin_install.rst b/docs_manual/admin_install.rst index c302f1a2a..9d9bdc1f2 100644 --- a/docs_manual/admin_install.rst +++ b/docs_manual/admin_install.rst @@ -84,9 +84,9 @@ We currently only provide prebuilt databases for either GRCh37 or GRCh38. .. code-block:: bash - $ wget --no-check-certificate https://file-public.cubi.bihealth.org/transient/varfish/anthenea/varfish-site-data-v1-20210728-grch37.tar.gz{,.sha256} - $ sha256sum --check varfish-site-data-v1-20210728-grch37.tar.gz.sha256 - $ tar xf varfish-site-data-v1-20210728-grch37.tar.gz + $ wget --no-check-certificate https://file-public.cubi.bihealth.org/transient/varfish/anthenea/varfish-site-data-v1-20210728b-grch37.tar.gz{,.sha256} + $ sha256sum --check varfish-site-data-v1-20210728b-grch37.tar.gz.sha256 + $ tar xf varfish-site-data-v1-20210728b-grch37.tar.gz $ ls volumes exomiser jannovar minio postgres redis traefik @@ -219,13 +219,13 @@ Modify the ``docker-compose.yml`` file by finding the following entry:: - varfish restart: unless-stopped volumes: - - "/root/varfish-server-background-db-20210728:/data:ro" + - "/root/varfish-server-background-db-20210728b:/data:ro" [...] And add another volume that maps your directory into the container:: volumes: - - "/root/varfish-server-background-db-20210728:/data:ro" + - "/root/varfish-server-background-db-20210728b:/data:ro" - type: bind source: varfish-db-downloader/ target: /data-db-downloader