update installation method for search with kraken2 #116
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| # This is a subsampling unit test to get early results | |
| on: | |
| push: | |
| branches: [master, dev, esearch-input] | |
| name: Listeria-with-Kraken1 | |
| env: | |
| TSV: "Kalamari/src/Listeria.tsv" | |
| OUTDIR: "Listeria.out" | |
| jobs: | |
| build: | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| matrix: | |
| os: ['ubuntu-20.04' ] | |
| 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@v4 | |
| with: | |
| path: Kalamari | |
| - name: env check | |
| run: | | |
| echo $PATH | tr ':' '\n' | sort | |
| - name: apt-get install | |
| run: sudo apt-get install ca-certificates tree | |
| - name: install jellyfish | |
| run: | | |
| wget https://github.com/gmarcais/Jellyfish/releases/download/v1.1.12/jellyfish-linux -O jellyfish1 | |
| chmod -v +x jellyfish1 | |
| ln -sv jellyfish1 jellyfish | |
| echo $(realpath .) >> $GITHUB_PATH | |
| tree $(realpath .) | |
| - name: install-edirect | |
| run: | | |
| sh -c "$(curl -fsSL https://ftp.ncbi.nlm.nih.gov/entrez/entrezdirect/install-edirect.sh)" | |
| echo $HOME/edirect >> $GITHUB_PATH | |
| echo $GITHUB_WORKSPACE/Kalamari/bin >> $GITHUB_PATH | |
| tree $HOME/edirect | |
| - name: check-env | |
| run: echo "$PATH" | |
| - name: select for only Listeria | |
| run: | | |
| head -n 1 Kalamari/src/chromosomes.tsv > ${{ env.TSV }} | |
| grep -m 2 Listeria Kalamari/src/chromosomes.tsv >> ${{ env.TSV }} | |
| echo "These are the Listeria genomes for downstream tests" | |
| column -ts $'\t' ${{ env.TSV }} | |
| hexdump -c ${{ env.TSV }} | |
| - name: download | |
| run: | | |
| perl Kalamari/bin/downloadKalamari.pl --outdir ${{ env.OUTDIR }} ${{ env.TSV }} | |
| find ${{ env.OUTDIR }} -name '*.fasta.gz' | xargs gunzip -v | |
| - name: check-results | |
| run: tree ${{ env.OUTDIR }} | |
| - name: install kraken | |
| run: | | |
| wget https://github.com/DerrickWood/kraken/archive/refs/tags/v1.1.1.tar.gz -O kraken-v1.1.1.tar.gz | |
| tar zxvf kraken-v1.1.1.tar.gz | |
| cd kraken-1.1.1 && bash install_kraken.sh kraken-src && cd - | |
| chmod -v +x kraken-1.1.1/kraken-src/* | |
| echo $(realpath kraken-1.1.1/kraken-src) >> $GITHUB_PATH | |
| tree $(realpath) kraken-1.1.1 | |
| - name: build taxonomy | |
| run: | | |
| export PATH=$PATH:Kalamari/bin | |
| buildTaxonomy.sh | |
| ls -lh Kalamari/share | |
| - name: Kraken1 database | |
| run: | | |
| echo $PATH | |
| which kraken-build | |
| mkdir -pv kraken | |
| cp -rv Kalamari/share/kalamari-*/taxonomy kraken/taxonomy | |
| find ${{ env.OUTDIR }} -name '*.fasta' -exec kraken-build --db kraken --add-to-library {} \; | |
| tree kraken | |
| # Some super debugging here with -x | |
| #sed -i.bak 's/set -e/set -e; set -x/' $(which build_kraken_db.sh) | |
| #grep -v '^#' -m 20 -C 2 $a_bin/build_kraken_db.sh | |
| echo ".....Building the database....." | |
| kraken-build --minimizer-len 9 --rebuild --db kraken --threads 2 --work-on-disk | |
| - name: Kraken1 query | |
| run: | | |
| QUERY=$(find ${{ env.OUTDIR }} -name '*.fasta' | head -n 1) | |
| echo "Query is $QUERY" | |
| kraken --db kraken -output kraken.raw --fasta-input $QUERY | |
| - name: Kraken1 view results | |
| run: | | |
| tree kraken | |
| ls -lhSR kraken | |
| echo | |
| head kraken.raw | |