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updated tests to reflect build-taxonomy #40

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merged 7 commits into from
May 7, 2024
Merged

updated tests to reflect build-taxonomy #40

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b66692d
fix path to taxonomy files
lskatz May 7, 2024
a6fde6e
download and build taxonomy
lskatz May 7, 2024
d86b911
merge Listeria into Yersinia matrix
lskatz May 7, 2024
9b0901e
m
lskatz May 7, 2024
eefda4e
updated output directory as matrix.GENUS
lskatz May 7, 2024
2bb562c
kraken1 tests patches
lskatz May 7, 2024
2fd6875
m
lskatz May 7, 2024
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kraken1 tests patches
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@lskatz
lskatz committed May 7, 2024
commit 2bb562ce1cbd9d713f5c8f0717dbef7ef28b11aa
17 changes: 10 additions & 7 deletions .github/workflows/unit-testing.Listeria.Kraken1.yml
View file
Original file line number Diff line number Diff line change
@@ -23,7 +23,7 @@ jobs:
perl-version: ${{ matrix.perl }}
multi-thread: "true"
- name: checkout my repo
uses: actions/checkout@v2
uses: actions/checkout@v4
with:
path: Kalamari

@@ -48,7 +48,9 @@ jobs:
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"
echo $GITHUB_WORKSPACE/edirect >> $GITHUB_PATH
echo $GITHUB_WORKSPACE/Kalamari/bin >> $GITHUB_PATH
#export PATH=${PATH}:$HOME/edirect >& /dev/null || setenv PATH "${PATH}:$HOME/edirect"
yes Y | ./edirect/setup.sh
tree edirect
- name: check-env
@@ -64,10 +66,6 @@ jobs:
run: perl Kalamari/bin/downloadKalamari.pl --outdir ${{ env.OUTDIR }} ${{ env.TSV }}
- name: check-results
run: tree ${{ env.OUTDIR }}
#- name: download-more
# run: perl Kalamari/bin/downloadKalamari.pl --outdir ${{ env.OUTDIR }} ${{ env.TSV }} --and protein --and nucleotide
#- 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
@@ -76,12 +74,17 @@ jobs:
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/src/taxonomy kraken/taxonomy
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
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