Merge pull request #5 from CCBR/docker

Update docker container names for push to nciccbr

.github/pull_request_template.md → .github/PULL_REQUEST_TEMPLATE.md

@@ -1,27 +1,29 @@
----
-name: Pull Request
-about: Create a Pull Request
-title: ''
-labels: ''
-assignees: ''
----
-
 ## Changes
 
+<!--
 Provide a summary of what is included in this Pull Request (PR).
+-->
 
 ## Issues
 
+<!--
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 If this PR fixes any issues, [use a keyword](https://docs.github.com/en/issues/tracking-your-work-with-issues/linking-a-pull-request-to-an-issue#linking-a-pull-request-to-an-issue-using-a-keyword)
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+-->
 
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-## Checklist
+## PR Checklist
 
 (~Strikethrough~ any points that are not applicable.)
 
-- [ ] Write unit tests for any new features or bug fixes.
+- [ ] This comment contains a description of changes with justifications, with any relevant issues linked.
+- ~[ ] Write unit tests for any new features, bug fixes, or other code changes.~ _testing framework not yet implemented_
 - [ ] Update docs if there are any API changes.
-- [ ] Update the changelog with a one-line description of these changes and reference the PR number.
+- [ ] If a new nextflow process is implemented:
+  - [ ] docker container is set in `conf/modules.config`.
+  - [ ] stub is defined.
+- [ ] Update `CHANGELOG.md` with a one-line description of these changes and reference the PR number. Guidelines: https://keepachangelog.com/en/1.1.0/

docker/bagel/Dockerfile

@@ -8,13 +8,16 @@ ENV BUILD_TAG=${BUILD_TAG}
 ARG REPONAME="000000"
 ENV REPONAME=${REPONAME}
 
+# specific tagged version for bagel
+ENV BAGEL_TAG="2.0-115"
+
 # download bagel scripts and install dependencies
 RUN python3 -m pip install --upgrade pip
 RUN pip3 install click numpy scipy scikit-learn
-ADD https://github.com/hart-lab/bagel/archive/refs/tags/v2.0-115.tar.gz /opt2
+ADD https://github.com/hart-lab/bagel/archive/refs/tags/v${BAGEL_TAG}.tar.gz /opt2
 WORKDIR /opt2
-RUN tar -xzvf v2.0-115.tar.gz && rm -f v2.0-115.tar.gz
-ENV PATH="${PATH}:/opt2/bagel-2.0-115"
+RUN tar -xzvf v${BAGEL_TAG}.tar.gz && rm -f v${BAGEL_TAG}.tar.gz
+ENV PATH="${PATH}:/opt2/bagel-${BAGEL_TAG}"
 
 # cleanup etc
 # Save Dockerfile in the docker

docker/bagel/README.md

@@ -1 +1,5 @@
-# Container for bagel processes in CRUISE
+# bagel
+
+Container for bagel processes in CRUISE
+
+<https://hub.docker.com/r/nciccbr/cruise_bagel_2.0>

docker/bagel/meta.yml

@@ -1,4 +1,4 @@
-dockerhub_namespace: kellysovacool
-image_name: bagel
-version: test
+dockerhub_namespace: nciccbr
+image_name: cruise_bagel_2.0
+version: 0.1.0
 container: "$(dockerhub_namespace)/$(image_name):$(version)"

docker/drugz/Dockerfile

@@ -8,14 +8,18 @@ ENV BUILD_TAG=${BUILD_TAG}
 ARG REPONAME="000000"
 ENV REPONAME=${REPONAME}
 
+# specific commit to download from github because drugZ doesn't use tags/versions/releases
+ENV DRUGZ_COMMIT="eb15d34e4dd172965e618d5bb662c053066da799"
+
 # download drugz script and install dependencies
 RUN python3 -m pip install --upgrade pip
 RUN pip3 install six numpy pandas scipy argparse
-ADD https://github.com/hart-lab/drugz/archive/refs/heads/master.zip /opt2
+ADD https://github.com/hart-lab/drugz/archive/${DRUGZ_COMMIT}.zip /opt2
 WORKDIR /opt2
-RUN ls
-RUN unzip master.zip && rm -f master.zip
-ENV PATH="${PATH}:/opt2/drugz-master"
+RUN unzip ${DRUGZ_COMMIT}.zip && rm -f ${DRUGZ_COMMIT}.zip
+RUN mv drugz-${DRUGZ_COMMIT}/ drugZ/
+RUN chmod a+rx /opt2/drugZ/drugz.py
+ENV PATH="${PATH}:/opt2/drugZ"
 
 # cleanup etc
 # Save Dockerfile in the docker

docker/drugz/README.md

@@ -1,3 +1,5 @@
-# drugz
+# drugZ
 
-Container for drugz processes in CRUISE
+Container for drugZ processes in CRUISE
+
+<https://hub.docker.com/r/nciccbr/cruise_drugz>

docker/drugz/meta.yml

@@ -1,4 +1,4 @@
-dockerhub_namespace: kellysovacool
-image_name: drugz
-version: test
+dockerhub_namespace: nciccbr
+image_name: cruise_drugz
+version: 0.1.0
 container: "$(dockerhub_namespace)/$(image_name):$(version)"