Add bash to PathLinker and bump to v2

Push v2 to DockerHub
Reed-CompBio · Jun 21, 2024 · bbc217e · bbc217e
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commit bbc217e
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Showing 4 changed files with 7 additions and 4 deletions.
diff --git a/.github/workflows/test-spras.yml b/.github/workflows/test-spras.yml
@@ -78,11 +78,12 @@ jobs:
       run: |
         docker pull reedcompbio/omics-integrator-1:latest
         docker pull reedcompbio/omics-integrator-2:v2
-        docker pull reedcompbio/pathlinker:latest
+        docker pull reedcompbio/pathlinker:v2
         docker pull reedcompbio/meo:latest
         docker pull reedcompbio/mincostflow:latest
         docker pull reedcompbio/allpairs:latest
         docker pull reedcompbio/domino:latest
+        docker pull reedcompbio/py4cytoscape:v2
     - name: Build Omics Integrator 1 Docker image
       uses: docker/build-push-action@v1
       with:
@@ -108,7 +109,7 @@ jobs:
         dockerfile: docker-wrappers/PathLinker/Dockerfile
         repository: reedcompbio/pathlinker
         tags: latest
-        cache_froms: reedcompbio/pathlinker:latest
+        cache_froms: reedcompbio/pathlinker:v2
         push: false
     - name: Build Maximum Edge Orientation Docker image
       uses: docker/build-push-action@v1

diff --git a/docker-wrappers/PathLinker/Dockerfile b/docker-wrappers/PathLinker/Dockerfile
@@ -4,7 +4,8 @@ FROM python:3.5.10-alpine
 
 # gettext is required for the envsubst command
 # See https://github.com/haskell/cabal/issues/6126 regarding wget
-RUN apk add --no-cache ca-certificates gettext wget
+# bash is required for dsub in the All of Us cloud environment
+RUN apk add --no-cache ca-certificates gettext wget bash
 
 WORKDIR /PathLinker
 COPY pathlinker-files.txt .

diff --git a/docker-wrappers/PathLinker/README.md b/docker-wrappers/PathLinker/README.md
@@ -29,6 +29,7 @@ Windows users may need to escape the absolute paths so that `/data` becomes `//d
 
 ## Versions:
 - v1: Initial version. Copies PathLinker source files from GitHub and pip installs packages from requirements file.
+- v2: Add bash, which is not available in Alpine Linux.
 
 ## TODO
 - Attribute https://github.com/Murali-group/PathLinker

diff --git a/spras/pathlinker.py b/spras/pathlinker.py
@@ -115,7 +115,7 @@ def run(nodetypes=None, network=None, output_file=None, k=None, container_framew
 
         print('Running PathLinker with arguments: {}'.format(' '.join(command)), flush=True)
 
-        container_suffix = "pathlinker"
+        container_suffix = "pathlinker:v2"
         out = run_container(container_framework,
                             container_suffix,
                             command,