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Update step names to match name convention
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Make bundle name more descriptive

Add some documentation for how the bundle is used
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mksanger committed Jan 18, 2024
1 parent 608795f commit c8dfae7
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13 changes: 7 additions & 6 deletions .github/workflows/create-release.yml
Original file line number Diff line number Diff line change
Expand Up @@ -15,6 +15,7 @@ jobs:
run: |
echo 'RELEASE_VERSION='$(git describe --always --tags) >> $GITHUB_ENV
echo 'MASTER_SHA='$(git rev-parse origin/master) >> $GITHUB_ENV
echo 'BUNDLE_NAME'=bundle-ub-16.04-irods-clients-4.2.7.tgz' >> $GITHUB_ENV
outputs:
isRelease: ${{ github.sha == env.MASTER_SHA }}
Expand Down Expand Up @@ -90,21 +91,21 @@ jobs:
if: always()

steps:
- name: install exodus
- name: "Install exodus"
run: |
apt-get update
apt-get install -q -y python3-pip
pip3 install exodus-bundler
- name: bundle clients
- name: "Bundle clients"

run: exodus --tarball --add /usr/lib/irods/plugins/ --add /lib/x86_64-linux-gnu/ --output client_bundle.tgz /usr/local/bin/baton-* /usr/bin/ils /usr/bin/iinit /usr/bin/imeta
run: exodus --tarball --add /usr/lib/irods/plugins/ --add /lib/x86_64-linux-gnu/ --output ${{ env.BUNDLE_NAME }} /usr/local/bin/baton-* /usr/bin/ils /usr/bin/iinit /usr/bin/imeta

- name: upload bundle
- name: "Upload bundle"
uses: actions/upload-artifact@v3
with:
name: client_bundle
path: "client_bundle.tgz"
path: ${{ env.BUNDLE_NAME }}

release:
runs-on: ubuntu-latest
Expand Down Expand Up @@ -141,7 +142,7 @@ jobs:
with:
name: ${{ env.RELEASE_VERSION }}
prerelease: ${{ !(github.sha == env.MASTER_SHA) }}
artifacts: "client_bundle.tgz"
artifacts: ${{ env.BUNDLE_NAME}}
removeArtifacts: true
artifactErrorsFailBuild: true
generateReleaseNotes: true
16 changes: 16 additions & 0 deletions README.md
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Expand Up @@ -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

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