remove random single quotes #159
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| on: | |
| push: | |
| branches: [master, dev, validate-taxonomy] | |
| name: Pull-down-all-accessions | |
| jobs: | |
| build: | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| matrix: | |
| os: ['ubuntu-20.04' ] | |
| perl: [ '5.32' ] | |
| runner_id: [0, 1] | |
| name: chunk ${{ matrix.runner_id }} 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: | | |
| runner_id=${{ matrix.runner_id }} | |
| echo "Runner_id is $runner_id" | |
| # Make a chunk input spreadsheet by just adding | |
| # each sample to chromosomes.tsv | |
| head -n 1 Kalamari/src/chromosomes.tsv > header.tsv | |
| tail -n +2 Kalamari/src/plasmids.tsv > in.tsv | |
| tail -n +2 Kalamari/src/chromosomes.tsv >> in.tsv | |
| total_lines=$(wc -l < in.tsv) | |
| start_line=$(( $runner_id * $total_lines / 2 + 1 )) | |
| end_line=$(( ($runner_id + 1) * $total_lines / 2 -1 )) | |
| echo "($runner_id) start_line: $start_line" | |
| echo "($runner_id) end_line: $end_line" | |
| cat header.tsv > chunk_${runner_id}.tsv | |
| sed -n "${start_line},${end_line}p" in.tsv >> chunk_${runner_id}.tsv | |
| perl Kalamari/bin/downloadKalamari.pl --numcpus 1 --outdir kalamari.out --buffersize 100 chunk_${runner_id}.tsv | |
| - name: check-results | |
| run: tree kalamari.out | |
| - name: check-file-sizes | |
| run: | | |
| find kalamari.out -name '*.fasta.gz' > fasta.sizes | |
| #cat fasta.sizes | xargs -n 100 ls -lhS | |