Merge branch 'fk-compare-gtfs' of github.com:broadinstitute/warp-tool…

…s into fk-compare-gtfs
broadinstitute · Dec 13, 2024 · 789f2cf · 789f2cf
2 parents 8d30f93 + 76a2443
commit 789f2cf
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Showing 3 changed files with 26 additions and 25 deletions.
diff --git a/.github/workflows/build-snapatac2.yml b/.github/workflows/build-snapatac2.yml
@@ -59,27 +59,27 @@ jobs:
     - name: Push image
       run: "docker push ${DOCKER_REGISTRY}/${GCR_PATH}:${TAG}"
 
-  build-for-acr:
-    runs-on: ubuntu-latest
-    defaults:
-      run:
-        working-directory: 3rd-party-tools/snapatac2
-    steps:
-      # checkout the repo
-      - name: 'Checkout GitHub Action'
-        uses: actions/checkout@v3
+  # build-for-acr:
+  #   runs-on: ubuntu-latest
+  #   defaults:
+  #     run:
+  #       working-directory: 3rd-party-tools/snapatac2
+  #   steps:
+  #     # checkout the repo
+  #     - name: 'Checkout GitHub Action'
+  #       uses: actions/checkout@v3
 
-      - name: 'Login via Azure CLI'
-        uses: azure/login@v1
-        with:
-          creds: ${{ secrets.AZURE_CREDENTIALS }}
+  #     - name: 'Login via Azure CLI'
+  #       uses: azure/login@v1
+  #       with:
+  #         creds: ${{ secrets.AZURE_CREDENTIALS }}
 
-      - name: 'Build and push image'
-        uses: azure/docker-login@v1
-        with:
-          login-server: ${{ secrets.REGISTRY_LOGIN_SERVER }}
-          username: ${{ secrets.REGISTRY_USERNAME }}
-          password: ${{ secrets.REGISTRY_PASSWORD }}
-      - run: |
-          docker build . -t ${{ secrets.REGISTRY_LOGIN_SERVER }}/${ACR_PATH}:${TAG}
-          docker push ${{ secrets.REGISTRY_LOGIN_SERVER }}/${ACR_PATH}:${TAG}
+  #     - name: 'Build and push image'
+  #       uses: azure/docker-login@v1
+  #       with:
+  #         login-server: ${{ secrets.REGISTRY_LOGIN_SERVER }}
+  #         username: ${{ secrets.REGISTRY_USERNAME }}
+  #         password: ${{ secrets.REGISTRY_PASSWORD }}
+  #     - run: |
+  #         docker build . -t ${{ secrets.REGISTRY_LOGIN_SERVER }}/${ACR_PATH}:${TAG}
+  #         docker push ${{ secrets.REGISTRY_LOGIN_SERVER }}/${ACR_PATH}:${TAG}
diff --git a/3rd-party-tools/snapatac2/Dockerfile b/3rd-party-tools/snapatac2/Dockerfile
@@ -5,7 +5,7 @@ ENV TERM=xterm-256color \
         TINI_VERSION=v0.19.0\
         PATH=$PATH:/usr/gitc
 
-ARG SNAPATAC2_VERSION=2.7.0
+ARG SNAPATAC2_VERSION=2.7.1
 
 LABEL MAINTAINER="Broad Institute DSDE <[email protected]" \
         SNAPATAC2_VERSION=${SNAPATAC2_VERSION}
@@ -18,6 +18,7 @@ RUN apt-get update; \
     curl https://sh.rustup.rs -sSf | sh -s -- -y; \
     source "$HOME/.cargo/env"; \
     pip install snapatac2==${SNAPATAC2_VERSION}; \
+    pip install scanpy; \
     # Install TINI
     mkdir temp; \
     cd temp; \

diff --git a/3rd-party-tools/snapatac2/docker_build.sh b/3rd-party-tools/snapatac2/docker_build.sh
@@ -3,7 +3,7 @@ set -e
 
 # Update version when changes to Dockerfile are made
 
-DOCKER_IMAGE_VERSION=1.0.9
+DOCKER_IMAGE_VERSION=1.0.10
 
 TIMESTAMP=$(date +"%s")
 DIR=$(cd $(dirname $0) && pwd)
@@ -13,7 +13,7 @@ GCR_URL="us.gcr.io/broad-gotc-prod/"
 QUAY_URL="quay.io/broadinstitute/gotc-prod-snapatac2/"
 
 # SnapATAC2 version
-SNAPATAC2_VERSION="2.6.3"
+SNAPATAC2_VERSION="2.7.1"
 
 # Necessary tools and help text
 TOOLS=(docker gcloud)