diff --git a/.github/workflows/test-spras.yml b/.github/workflows/test-spras.yml index f31d7e9f..a4d5886b 100644 --- a/.github/workflows/test-spras.yml +++ b/.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 diff --git a/docker-wrappers/AllPairs/Dockerfile b/docker-wrappers/AllPairs/Dockerfile index d75572e2..8241ad01 100644 --- a/docker-wrappers/AllPairs/Dockerfile +++ b/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 diff --git a/docker-wrappers/AllPairs/README.md b/docker-wrappers/AllPairs/README.md index 0c02a4c4..863b12dc 100644 --- a/docker-wrappers/AllPairs/README.md +++ b/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. diff --git a/spras/allpairs.py b/spras/allpairs.py index 42f1041d..1b016534 100644 --- a/spras/allpairs.py +++ b/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,