Install #26
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| name: Install | |
| on: | |
| push: | |
| branches: analysis3 | |
| workflow_dispatch: | |
| jobs: | |
| install: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v4 | |
| - name: Sync repoisitory to Gadi | |
| uses: up9cloud/action-rsync@v1.3 | |
| env: | |
| HOST: gadi.nci.org.au | |
| TARGET: ${{secrets.GADI_REPO_PATH}} | |
| KEY: ${{secrets.DEPLOY_KEY}} | |
| USER: ${{secrets.GADI_USER}} | |
| - name: Install | |
| uses: appleboy/ssh-action@v0.1.7 | |
| with: | |
| host: gadi.nci.org.au | |
| username: ${{secrets.GADI_USER}} | |
| key: ${{secrets.DEPLOY_KEY}} | |
| command_timeout: 120m | |
| script: | | |
| cd ${{secrets.GADI_REPO_PATH}} | |
| ### Create named pipe | |
| named_pipe=$( mktemp -u ) | |
| mkfifo $named_pipe | |
| exec 10<>$named_pipe | |
| ### Submit job | |
| qsub -N build_miniconda3 -lncpus=1,mem=20GB,walltime=2:00:00,jobfs=50GB,storage=gdata/hh5+scratch/hh5 -P kr06 -q copyq -j oe -Wblock=true install.sh >&10 & | |
| pid=$! | |
| ### Get jobid | |
| read -u 10 jobid | |
| echo $jobid | |
| ### Create a trap that cats job output file on exit | |
| outfile=build_miniconda3.o"${jobid%.*}" | |
| trap "while ! [[ -e ${outfile} ]]; do sleep 1; done; cat ${outfile}; exec 10>&-; rm -f $named_pipe;" EXIT | |
| wait $pid |