Merge branch 'develop' into dependabot/pip/3rd-party-tools/subread/bl…

…ack-24.3.0

3rd-party-tools/snapatac2/Dockerfile

@@ -5,14 +5,16 @@ ENV TERM=xterm-256color \
         TINI_VERSION=v0.19.0\
         PATH=$PATH:/usr/gitc
 
-ARG SNAPATAC2_VERSION=2.3.1
+ARG SNAPATAC2_VERSION=2.6.3
 
 LABEL MAINTAINER="Broad Institute DSDE <[email protected]" \
         SNAPATAC2_VERSION=${SNAPATAC2_VERSION}
 
 WORKDIR /usr/gitc
 
-RUN pip install cmake; \
+RUN apt-get update; \
+    apt-get install -y tabix; \
+    pip install cmake; \
     curl https://sh.rustup.rs -sSf | sh -s -- -y; \
     source "$HOME/.cargo/env"; \
     pip install snapatac2==${SNAPATAC2_VERSION}; \
@@ -23,6 +25,5 @@ RUN pip install cmake; \
     chmod +x /sbin/tini; \
     rm -r /usr/gitc/temp;
 
-
 # Set tini as default entrypoint
 ENTRYPOINT [ "/sbin/tini", "--" ]

3rd-party-tools/snapatac2/docker_build.sh

@@ -2,7 +2,9 @@
 set -e
 
 # Update version when changes to Dockerfile are made
-DOCKER_IMAGE_VERSION=1.0.3
+
+DOCKER_IMAGE_VERSION=1.0.9
+
 TIMESTAMP=$(date +"%s")
 DIR=$(cd $(dirname $0) && pwd)
 
@@ -11,7 +13,7 @@ GCR_URL="us.gcr.io/broad-gotc-prod/"
 QUAY_URL="quay.io/broadinstitute/gotc-prod-snapatac2/"
 
 # SnapATAC2 version
-SNAPATAC2_VERSION="2.3.1"
+SNAPATAC2_VERSION="2.6.3"
 
 # Necessary tools and help text
 TOOLS=(docker gcloud)

3rd-party-tools/snapatac2/docker_versions.tsv

@@ -1,2 +1,9 @@
 us.gcr.io/broad-gotc-prod/snapatac2:1.0.2-2.2.0-1679678908
 us.gcr.io/broad-gotc-prod/snapatac2:1.0.3-2.3.0-1682089891
+us.gcr.io/broad-gotc-prod/snapatac2:1.0.4-2.3.1-1700590229
+us.gcr.io/broad-gotc-prod/snapatac2:1.0.4-2.6.0-1714058747
+us.gcr.io/broad-gotc-prod/snapatac2:1.0.5-2.6.0-1714070943
+us.gcr.io/broad-gotc-prod/snapatac2:1.0.6-2.6.1-1714757147
+us.gcr.io/broad-gotc-prod/snapatac2:1.0.7-2.6.2-1715265458
+us.gcr.io/broad-gotc-prod/snapatac2:1.0.8-2.6.2-1715613634
+us.gcr.io/broad-gotc-prod/snapatac2:1.0.9-2.6.3-1715865353