Add bash to AllPairs v2 Docker image and push

.github/workflows/test-spras.yml

@@ -81,7 +81,7 @@ jobs:
         docker pull reedcompbio/pathlinker:v2
         docker pull reedcompbio/meo:latest
         docker pull reedcompbio/mincostflow:latest
-        docker pull reedcompbio/allpairs:latest
+        docker pull reedcompbio/allpairs:v2
         docker pull reedcompbio/domino:latest
         docker pull reedcompbio/py4cytoscape:v2
     - name: Build Omics Integrator 1 Docker image
@@ -135,7 +135,7 @@ jobs:
         path: docker-wrappers/AllPairs/.
         dockerfile: docker-wrappers/AllPairs/Dockerfile
         repository: reedcompbio/allpairs
-        tags: latest
+        tags: v2
         cache_froms: reedcompbio/allpairs:latest
         push: false
     - name: Build DOMINO Docker image

docker-wrappers/AllPairs/Dockerfile

@@ -1,6 +1,9 @@
 # AllPairs wrapper
 FROM python:3.9-alpine3.16
 
+# bash is required for dsub in the All of Us cloud environment
+RUN apk add --no-cache bash
+
 WORKDIR /AllPairs
 
 RUN pip install networkx==2.6.3

docker-wrappers/AllPairs/README.md

@@ -29,3 +29,4 @@ The Docker wrapper can be tested with `pytest -k test_ap.py` from the root of th
 
 ## Versions:
 - v1: Initial version. Copies source file from SPRAS repository.
+- v2: Add bash, which is not available in Alpine Linux.

spras/allpairs.py

@@ -94,8 +94,7 @@ def run(nodetypes=None, network=None, output_file=None, container_framework="doc
 
         print('Running All Pairs Shortest Paths with arguments: {}'.format(' '.join(command)), flush=True)
 
-        container_suffix = "allpairs"
-
+        container_suffix = "allpairs:v2"
         out = run_container(
                             container_framework,
                             container_suffix,