add spreadsheet as a strategy variable #121
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| on: | ||
| push: | ||
| branches: [master] | ||
| name: Pull-down-all-accessions | ||
| jobs: | ||
| build: | ||
| runs-on: ${{ matrix.os }} | ||
| strategy: | ||
| matrix: | ||
| os: ['ubuntu-20.04' ] | ||
| perl: [ '5.32' ] | ||
| in_tsv: ['Kalamari/src/chromosomes.tsv', 'Kalamari/src/plasmids.tsv'] | ||
| 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 --numcpus 2 --outdir kalamari.out ${{ in_tsv }} | ||
|
Check failure on line 43 in .github/workflows/unit-testing.yml
|
||
| - 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 | ||
