Merge pull request #92 from mksanger/add_exodus_actions

Bundle irods clients

.github/workflows/create-release.yml

@@ -5,10 +5,14 @@ on:
     tags:
       - "*"
 
+env:
+  BUNDLE_NAME: bundle-ub-16.04-irods-clients-4.2.7.tgz
+
 jobs:
-  release:
+
+  release_variables:
     runs-on: ubuntu-latest
-    
+
     defaults:
       run:
         shell: bash -l -e -o pipefail {0}
@@ -24,32 +28,27 @@ jobs:
         run: |
           # Avoid git exiting when Actions runs
           git config --global --add safe.directory "$PWD"
-          
+
           git fetch --tags --force
 
       - name: "Get release variables"
         run: |
           echo 'RELEASE_VERSION='$(git describe --always --tags) >> $GITHUB_ENV
           echo 'MASTER_SHA='$(git rev-parse origin/master) >> $GITHUB_ENV
 
-      - name: "Create Release"
-        uses: ncipollo/release-action@v1.12.0
-        with:
-          name: ${{ env.RELEASE_VERSION }}
-          prerelease: ${{ !(github.sha == env.MASTER_SHA) }}
-          generateReleaseNotes: true
-
     outputs:
       isRelease: ${{ github.sha == env.MASTER_SHA }}
+      preRelease: ${{ !(github.sha == env.MASTER_SHA) }}
+      releaseVersion: ${{ env.RELEASE_VERSION }}
 
   deploy:
     runs-on: ubuntu-latest
 
-    needs: release
+    needs: release_variables
 
     # Workaround for https://github.com/actions/runner/issues/1483
     # Actions coerces boolean to string
-    if: needs.release.outputs.isRelease == 'true'
+    if: needs.release_variables.outputs.isRelease == 'true'
 
     steps:
       - name: "Free disk space on the runner"
@@ -103,3 +102,59 @@ jobs:
             docker images
 
             make push GITHUB_ACTIONS=${GITHUB_ACTIONS} GITHUB_REPOSITORY_OWNER=${{ github.repository_owner }}
+
+  bundle:
+    runs-on: ubuntu-latest
+    container: "ghcr.io/wtsi-npg/ub-16.04-irods-clients-4.2.7:latest"
+
+    needs: deploy
+
+    if: always()
+
+    steps:
+    - name: "Install exodus"
+      run: |
+        apt-get update
+        apt-get install -q -y python3-pip
+        pip3 install exodus-bundler
+
+    - name: "Bundle clients"
+
+      run: exodus --tarball --add /usr/lib/irods/plugins/ --add /lib/x86_64-linux-gnu/ --output $BUNDLE_NAME /usr/local/bin/baton-* /usr/bin/ils /usr/bin/iinit /usr/bin/imeta
+
+    - name: "Upload bundle"
+      uses: actions/upload-artifact@v3
+      with:
+        name: client_bundle
+        path: ${{ env.BUNDLE_NAME }}
+
+  release:
+    runs-on: ubuntu-latest
+
+    needs: [release_variables, bundle]
+
+    if: always()
+
+    defaults:
+      run:
+        shell: bash -l -e -o pipefail {0}
+
+    steps:
+
+      - name: "Download artifact"
+        uses: actions/download-artifact@v3
+        with:
+          name: client_bundle
+
+      - name: "Create Release"
+        uses: ncipollo/release-action@v1.12.0
+        with:
+          name: ${{ env.NAME }}
+          prerelease: ${{ env.PRERELEASE }}
+          artifacts: ${{ env.BUNDLE_NAME }}
+          removeArtifacts: true
+          artifactErrorsFailBuild: true
+          generateReleaseNotes: true
+        env:
+          NAME: ${{ needs.release_variables.outputs.releaseVersion }}
+          PRERELEASE: ${{ needs.release_variables.outputs.preRelease }}

README.md

@@ -73,6 +73,22 @@ e.g. Install wrappers to $PREFIX/bin:
     ...
     -rwxr-xr-x 1 kdj staff 409 Apr 12 15:47 samtools
 
+# iRODS Client Bundle
+
+The release contains irods 4.2.7 clients bundled from
+`ub-16.04-irods-clients-4.2.7` to be used on ONT machines, where we
+cannot run containers.  Given the complexity of the iRODS clients'
+dependency chain, the location of the plugins must be provided in the
+iRODS environment file using the `irods_plugins_home` key. Some
+dependencies for these plugins must also be preloaded to avoid local
+system libraries from being pulled in, e.g.:
+
+    $ LD_PRELOAD=path/libarchive.so.16:path/libcrypto.so.1.0.0:path/libssl.so.1.0.0:path/libxml2.so.2:path/libicuuc.so.55:path/libicudata.so.55 \
+        ./exodus/bin/iinit
+
+A script to do this is set up by the ansible used to set up the instruments
+(https://gitlab.internal.sanger.ac.uk/npg/oxford_nanopore_instruments).
+
 
 ## Author