Cleanup staging server #4
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| name: Cleanup staging server | |
| on: | |
| schedule: | |
| - cron: '13 9 * * MON' | |
| workflow_dispatch: null | |
| jobs: | |
| deploy: | |
| name: Cleanup | |
| runs-on: ubuntu-latest | |
| environment: staging | |
| steps: | |
| - name: Check out | |
| uses: actions/checkout@v4 | |
| - name: Configure AWS credentials | |
| uses: aws-actions/configure-aws-credentials@v4 | |
| with: | |
| aws-access-key-id: ${{ secrets.AWS_ACCESS_KEY_ID }} | |
| aws-secret-access-key: ${{ secrets.AWS_SECRET_ACCESS_KEY }} | |
| aws-region: us-east-1 | |
| - name: Get instance address | |
| id: ec2-describe-instances | |
| run: | | |
| INSTANCE_ADDRESS=$(aws ec2 describe-instances \ | |
| --instance-ids ${{ vars.INSTANCE_ID }} \ | |
| --query "Reservations[*].Instances[*].[PublicDnsName]" \ | |
| --output text) | |
| echo "INSTANCE_ADDRESS=$INSTANCE_ADDRESS" >> "$GITHUB_OUTPUT" | |
| - name: Set up SSH | |
| run: | | |
| mkdir --parents ~/.ssh | |
| echo "${{ secrets.SSH_PRIVATE_KEY }}" > ~/.ssh/staging | |
| chmod 600 ~/.ssh/staging | |
| cat >>~/.ssh/config <<END | |
| Host staging | |
| HostName ${{ steps.ec2-describe-instances.outputs.INSTANCE_ADDRESS }} | |
| User ec2-user | |
| IdentityFile ~/.ssh/staging | |
| END | |
| ssh-keyscan -H ${{ steps.ec2-describe-instances.outputs.INSTANCE_ADDRESS }} >> ~/.ssh/known_hosts | |
| - name: Test ssh | |
| run: | | |
| xid=`date +"%Y-%m-%dT%H-%M-%S"` | |
| cat <<'EOF' > cleanup_apollo.$xid.sh | |
| set -e | |
| set -u | |
| set -o pipefail | |
| set -x | |
| demoDataDir=${{ '${HOME}' }}/dario/demoData | |
| rm -rf $demoDataDir | |
| mkdir -p $demoDataDir | |
| cd $demoDataDir | |
| wormbase='https://ftp.ebi.ac.uk/pub/databases/wormbase/parasite/releases/WBPS19/species' | |
| curl -O -s -L $wormbase/schistosoma_haematobium/TD2_PRJEB44434/schistosoma_haematobium.TD2_PRJEB44434.WBPS19.genomic.fa.gz | |
| curl -O -s -L $wormbase/schistosoma_mansoni/PRJEA36577/schistosoma_mansoni.PRJEA36577.WBPS19.genomic.fa.gz | |
| curl -O -s -L $wormbase/schistosoma_haematobium/TD2_PRJEB44434/schistosoma_haematobium.TD2_PRJEB44434.WBPS19.annotations.gff3.gz | |
| curl -O -s -L $wormbase/schistosoma_mansoni/PRJEA36577/schistosoma_mansoni.PRJEA36577.WBPS19.annotations.gff3.gz | |
| gunzip *.gz | |
| cd ${{ '${HOME}' }}/Apollo3/packages/apollo-cli | |
| export APOLLO_PROFILE=auto | |
| function apollo () { | |
| yarn node bin/run.js "$@" | |
| } | |
| apollo config address http://localhost | |
| apollo config accessType root | |
| apollo config rootCredentials.username ${{ secrets.ROOT_USER_NAME }} | |
| apollo config rootCredentials.password ${{ secrets.ROOT_USER_PASSWORD }} | |
| apollo login | |
| echo "apollo assembly get | apollo assembly delete -v -a -" | |
| apollo assembly add-fasta -i $demoDataDir/schistosoma_haematobium.TD2_PRJEB44434.WBPS19.genomic.fa -a schistosoma_haematobium -f | |
| apollo assembly add-fasta -i $demoDataDir/schistosoma_mansoni.PRJEA36577.WBPS19.genomic.fa -a schistosoma_mansoni -f | |
| apollo feature import -i $demoDataDir/schistosoma_haematobium.TD2_PRJEB44434.WBPS19.annotations.gff3 -a schistosoma_haematobium -d | |
| apollo feature import -i $demoDataDir/schistosoma_mansoni.PRJEA36577.WBPS19.annotations.gff3 -a schistosoma_mansoni -d | |
| EOF | |
| rsync -av cleanup_apollo.$xid.sh staging:dario/ | |
| ssh staging -f "bash dario/cleanup_apollo.$xid.sh > dario/cleanup_apollo.$xid.out 2> dario/cleanup_apollo.$xid.err; echo 'Exit code:' $? >> dario/cleanup_apollo.$xid.err && rm dario/cleanup_apollo.$xid.sh" |