Reload data on a demo server #41
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| name: Reload data on a demo server | |
| on: | |
| workflow_call: | |
| inputs: | |
| environment: | |
| description: Environment in which to reload data | |
| type: string | |
| required: true | |
| workflow_dispatch: | |
| inputs: | |
| environment: | |
| description: Environment in which to reload data | |
| type: environment | |
| required: true | |
| jobs: | |
| reload: | |
| name: Clean up ${{ inputs.environment }} demo server | |
| runs-on: ubuntu-latest | |
| environment: ${{ inputs.environment }} | |
| 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 | |
| ServerAliveInterval 60 | |
| ServerAliveCountMax 10 | |
| END | |
| ssh-keyscan -H ${{ steps.ec2-describe-instances.outputs.INSTANCE_ADDRESS }} >> ~/.ssh/known_hosts | |
| - name: Create Docker context | |
| run: | | |
| docker context create staging \ | |
| --docker host=ssh://staging \ | |
| --description "Staging server" | |
| - name: Load data | |
| run: | | |
| # docker --context staging pull ghcr.io/gmod/apollo-cli:${{ vars.DOCKER_TAG }} | |
| function apollo() { | |
| docker \ | |
| --context staging \ | |
| run \ | |
| --rm \ | |
| --interactive \ | |
| --add-host host.docker.internal=host-gateway \ | |
| --volume /home/ec2-user/.config/apollo-cli:/root/.config/apollo-cli \ | |
| --volume /home/ec2-user/data:/data \ | |
| --env APOLLO_PROFILE=auto \ | |
| ghcr.io/gmod/apollo-cli:${{ vars.DOCKER_TAG }} \ | |
| "$@" | |
| } | |
| set -x | |
| apollo config address http://host.docker.internal/apollo | |
| apollo config accessType root | |
| apollo config rootCredentials.username ${{ secrets.ROOT_USER_NAME }} | |
| apollo config rootCredentials.password ${{ secrets.ROOT_USER_PASSWORD }} | |
| apollo login --force | |
| apollo jbrowse set-config /data/config.json | |
| apollo assembly get | apollo assembly delete --verbose --assembly - | |
| apollo file get | apollo file delete | |
| apollo assembly \ | |
| add-from-fasta \ | |
| /data/schistosoma_haematobium.TD2_PRJEB44434.WBPS19.genomic.fa.gz \ | |
| --fai /data/schistosoma_haematobium.TD2_PRJEB44434.WBPS19.genomic.fa.gz.fai \ | |
| --gzi /data/schistosoma_haematobium.TD2_PRJEB44434.WBPS19.genomic.fa.gz.gzi \ | |
| --assembly 'Schistosoma haematobium' | |
| apollo assembly \ | |
| add-from-fasta \ | |
| /data/schistosoma_mansoni.PRJEA36577.WBPS19.genomic.fa.gz \ | |
| --fai /data/schistosoma_mansoni.PRJEA36577.WBPS19.genomic.fa.gz.fai \ | |
| --gzi /data/schistosoma_mansoni.PRJEA36577.WBPS19.genomic.fa.gz.gzi \ | |
| --assembly 'Schistosoma mansoni' | |
| apollo feature \ | |
| import \ | |
| /data/schistosoma_haematobium.TD2_PRJEB44434.WBPS19.annotations.genes.gff3 \ | |
| --assembly 'Schistosoma haematobium' | |
| apollo feature \ | |
| import \ | |
| /data/schistosoma_mansoni.PRJEA36577.WBPS19.annotations.genes.gff3 \ | |
| --assembly 'Schistosoma mansoni' |