Merge branch 'feat-annonars-fe' into feat-annonars-decipher-hi

varfish-org · Nov 22, 2023 · d44194c · d44194c
2 parents 294ef08 + 79f2207
commit d44194c
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Showing 13 changed files with 28 additions and 19 deletions.
diff --git a/README.md b/README.md
@@ -112,6 +112,18 @@ The known URLs are managed in `download_urls.yml`.
 # terraform apply
 ```
 
+### Uploading Data to S3
+
+For example, as follows
+
+```
+# s5cmd --dry-run --profile ext-varfish-public \
+    --endpoint-url https://ceph-s3-ext.cubi.bihealth.org \
+    sync \
+    'output/full/mehari/genes-txs-grch3*' \
+    s3://varfish-public/public/
+```
+
 ### Semantic Commits
 
 Generally, follow [Semantic Commits v1](https://www.conventionalcommits.org/en/v1.0.0/#specification), also see [examples](https://www.conventionalcommits.org/en/v1.0.0/#examples).

diff --git a/download_urls.yml b/download_urls.yml
@@ -87,11 +87,11 @@
     strategy: no-excerpt
     count: null
 
-- url: https://github.com/bihealth/mehari-data-tx/releases/download/v0.2.2/mehari-data-txs-grch37-0.2.2.bin.zst
+- url: https://github.com/bihealth/mehari-data-tx/releases/download/v0.3.0/mehari-data-txs-grch37-0.3.0.bin.zst
   excerpt_strategy:
     strategy: no-excerpt
     count: null
-- url: https://github.com/bihealth/mehari-data-tx/releases/download/v0.2.2/mehari-data-txs-grch38-0.2.2.bin.zst
+- url: https://github.com/bihealth/mehari-data-tx/releases/download/v0.3.0/mehari-data-txs-grch38-0.3.0.bin.zst
   excerpt_strategy:
     strategy: no-excerpt
     count: null

diff --git a/environment.yml b/environment.yml
@@ -43,7 +43,7 @@ dependencies:
   # Varfish related
   - annonars =0.28.0
   - viguno =0.1.6
-  - mehari =0.6.2
+  - mehari =0.18.1
   - varfish-server-worker =0.10.1
   # S3 uploads
   - s5cmd =2.1.0
diff --git a/excerpt-data/7f3ada74ad5a5b89/mehari-data-txs-grch38-0.2.2.bin.zst b/excerpt-data/7f3ada74ad5a5b89/mehari-data-txs-grch38-0.2.2.bin.zst
diff --git a/excerpt-data/7f3ada74ad5a5b89/url.txt b/excerpt-data/7f3ada74ad5a5b89/url.txt
diff --git a/excerpt-data/988e607a52814735/mehari-data-txs-grch37-0.3.0.bin.zst b/excerpt-data/988e607a52814735/mehari-data-txs-grch37-0.3.0.bin.zst
diff --git a/excerpt-data/988e607a52814735/url.txt b/excerpt-data/988e607a52814735/url.txt
diff --git a/excerpt-data/a35f53fe452560ef/mehari-data-txs-grch38-0.3.0.bin.zst b/excerpt-data/a35f53fe452560ef/mehari-data-txs-grch38-0.3.0.bin.zst
diff --git a/excerpt-data/a35f53fe452560ef/url.txt b/excerpt-data/a35f53fe452560ef/url.txt
diff --git a/excerpt-data/b1bd50fe7ab9da7a/mehari-data-txs-grch37-0.2.2.bin.zst b/excerpt-data/b1bd50fe7ab9da7a/mehari-data-txs-grch37-0.2.2.bin.zst
diff --git a/excerpt-data/b1bd50fe7ab9da7a/url.txt b/excerpt-data/b1bd50fe7ab9da7a/url.txt
diff --git a/rules/output/annonars/genes.smk b/rules/output/annonars/genes.smk
@@ -34,9 +34,6 @@ rule output_annonars_genes:  # -- build annonars genes RocksDB file
         v_annonars=RE_VERSION,
     shell:
         r"""
-        export TMPDIR=$(mktemp -d)
-        trap "rm -rf $TMPDIR" EXIT
-
         annonars gene import \
             --path-out-rocksdb $(dirname {output.rocksdb_identity}) \
             --path-in-acmg {input.acmg_sf} \

diff --git a/varfish_db_downloader/versions.py b/varfish_db_downloader/versions.py
@@ -158,7 +158,7 @@ class DataVersions:
     hpo="20230606",
     orphapacket="10.1",
     patho_mms="20220730",
-    mehari_tx="0.2.2",
+    mehari_tx="0.3.0",
     clinvar_release=CLINVAR_RELEASE,
     clinvar_version=CLINVAR_VERSION,
     tracks="0",