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azure-pipelines.yml
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# Starter pipeline
# Start with a minimal pipeline that you can customize to build and deploy your code.
# Add steps that build, run tests, deploy, and more:
# https://aka.ms/yaml
trigger:
- master
jobs:
- job: Linux
timeoutInMinutes: 120
pool:
vmImage: 'ubuntu-latest'
steps:
- script: echo "##vso[task.prependpath]$CONDA/bin"
displayName: Add conda to PATH
- script: |
echo HELLO FROM Linux
pwd
ls
echo [process] create env
conda create -n probeit -c conda-forge -c anaconda -c bioconda pandas entrez-direct primer3-py bedtools mmseqs2 seqkit genmap primer3 biopython -y -v
echo [process] activate env
eval "$(conda shell.bash hook)"
conda activate probeit
conda info —envs
echo [process] setup
bash install.sh
probeit -h
echo [process] run probeit posnegset
probeit posnegset -p sample/positive.fa -n sample/negative.fa -o posnegset1
echo [process] run probeit snp
probeit snp -r sample/ref.fa -a sample/ref.gff -s sample/str.fa -p "10,11,19,20,21,22" -m "aa:orf1ab:L4715F,aa:S:Q52R,aa:S:E484K,aa:S:Q677H,aa:S:F888L,aa:E:L21F,aa:M:I82T" -o snp1
probeit snp -r sample/ref.fa -a sample/ref.gff -s sample/str.fa -p "10,11,19,20,21,22" -m "nt:A21716G,nt:G23011A,nt:G23592C,nt:T24223C,nt:C26304T,nt:T26766C,nt:A21716G" -o snp3
echo [process] compare outputs
echo posnegset 1
diff posnegset1/probe1.fa sample/posnegset1.fa -s
echo posnegset 2
diff posnegset1/probe2.fa sample/posnegset2.fa -s
echo snp aa 1
diff snp1/probe1.fa sample/snp_aa1.fa -s
echo snp aa 2
diff snp1/probe2.fa sample/snp_aa2.fa -s
echo snp nt 1
diff snp3/probe1.fa sample/snp_nt1.fa -s
echo snp nt 2
diff snp3/probe2.fa sample/snp_nt2.fa -s
exit 0
- job: macOS
timeoutInMinutes: 120
pool:
vmImage: 'macOS-latest'
steps:
- script: echo "##vso[task.prependpath]$CONDA/bin"
displayName: Add conda to PATH
- script: sudo chown -R $USER $CONDA
displayName: Take ownership of conda installation
- script: |
echo HELLO FROM MacOS
pwd
ls
echo [process] create env
conda create -n probeit -c conda-forge -c anaconda -c bioconda pandas entrez-direct primer3-py bedtools mmseqs2 seqkit genmap primer3 biopython -y -v
echo [process] activate env
eval "$(conda shell.bash hook)"
conda activate probeit
conda info —envs
echo [process] setup
bash install.sh
probeit -h
echo [process] run probeit posnegset
probeit posnegset -p sample/positive.fa -n sample/negative.fa -o posnegset2
echo [process] run probeit snp
probeit snp -r sample/ref.fa -a sample/ref.gff -s sample/str.fa -p "10,11,19,20,21,22" -m "aa:orf1ab:L4715F,aa:S:Q52R,aa:S:E484K,aa:S:Q677H,aa:S:F888L,aa:E:L21F,aa:M:I82T" -o snp2
probeit snp -r sample/ref.fa -a sample/ref.gff -s sample/str.fa -p "10,11,19,20,21,22" -m "nt:A21716G,nt:G23011A,nt:G23592C,nt:T24223C,nt:C26304T,nt:T26766C,nt:A21716G" -o snp4
echo [process] compare outputs
echo posneget 1
diff posnegset2/probe1.fa sample/posnegset1.fa -s
echo posnegset 2
diff posnegset2/probe2.fa sample/posnegset2.fa -s
echo snp aa 1
diff snp2/probe1.fa sample/snp_aa1.fa -s
echo snp aa 2
diff snp2/probe2.fa sample/snp_aa2.fa -s
echo snp nt 1
diff snp4/probe1.fa sample/snp_nt1.fa -s
echo snp nt 2
diff snp4/probe2.fa sample/snp_nt2.fa -s
exit 0