bash downloadKalamari.sh #118
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| on: | |
| push: | |
| branches: [master] | |
| name: Pull-down-all-accessions | |
| jobs: | |
| build: | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| matrix: | |
| os: ['ubuntu-18.04' ] | |
| perl: [ '5.32' ] | |
| name: Perl ${{ matrix.perl }} on ${{ matrix.os }} | |
| steps: | |
| - name: Set up perl | |
| uses: shogo82148/actions-setup-perl@v1 | |
| with: | |
| perl-version: ${{ matrix.perl }} | |
| multi-thread: "true" | |
| - name: checkout my repo | |
| uses: actions/checkout@v2 | |
| with: | |
| path: Kalamari | |
| - name: apt-get install | |
| run: sudo apt-get install ca-certificates tree | |
| - name: install-edirect | |
| run: | | |
| sudo apt-get install ncbi-entrez-direct | |
| echo "installed edirect the apt way" | |
| exit | |
| cd $HOME | |
| perl -MNet::FTP -e '$ftp = new Net::FTP("ftp.ncbi.nlm.nih.gov", Passive => 1); $ftp->login; $ftp->binary; $ftp->get("/entrez/entrezdirect/edirect.tar.gz");' | |
| gunzip -cv edirect.tar.gz | tar xf - | |
| rm -v edirect.tar.gz | |
| export PATH=${PATH}:$HOME/edirect >& /dev/null || setenv PATH "${PATH}:$HOME/edirect" | |
| yes Y | ./edirect/setup.sh | |
| tree edirect | |
| - name: check-env | |
| run: echo "$PATH" | |
| - name: download | |
| run: perl Kalamari/bin/downloadKalamari.pl --outdir kalamari.out Kalamari/src/chromosomes.tsv | |
| - name: check-results | |
| run: tree kalamari.out | |
| - name: check-file-sizes | |
| run: | | |
| find kalamari.out -name '*.fasta' > fasta.sizes | |
| echo "by size" | |
| cat fasta.sizes | xargs ls -lhS | |
| echo "by name" | |
| cat fasta.sizes | xargs ls -lh | |