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Merge pull request #971 from maxplanck-ie/develop
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‎.ci_stuff/ChIP.sample_broad_config.yaml

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chip_dict:
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sample1:
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control: sample7
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broad: True
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sample2:
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control: sample7
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broad: True
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sample3:
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control: sample8
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broad: True
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sample4:
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control: sample8
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broad: True
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sample5:
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control: sample9
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broad: True
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sample6:
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control: sample9
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broad: True

‎.ci_stuff/ChIP.sample_config.yaml

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chip_dict:
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sample1:
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control: sample3
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control: sample7
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broad: False
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sample2:
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control: sample3
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control: sample7
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broad: False
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sample3:
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control: sample8
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broad: False
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sample4:
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control: sample6
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control: sample8
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broad: False
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sample5:
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control: sample6
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control: sample9
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broad: False
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sample6:
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control: sample9
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broad: False

‎.ci_stuff/ChIP.sample_noControl_config.yaml

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chip_dict:
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sample1:
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control:
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broad: False
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sample2:
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control:
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broad: False
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sample3:
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control:
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broad: False
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sample4:
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control:
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broad: False
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sample5:
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control:
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broad: False
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sample6:
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control:
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broad: False

‎.ci_stuff/ChIP.sample_short_config.yaml

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chip_dict:
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sample1:
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control: sample3
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broad: False
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sample2:
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control: sample3
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broad: False
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sample4:
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control: sample6
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broad: False
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sample5:
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control: sample6
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broad: False

‎.ci_stuff/organism.yaml

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genome_size: 2652783500
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genome_fasta: "/tmp/genome.fa"
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genome_index: "/tmp/genome.fa.fai"
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genome_2bit: ".ci_stuff/genome_fasta/genome.2bit"
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genome_2bit: "/tmp/genome.2bit"
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bowtie2_index: ".ci_stuff/BowtieIndex/genome"
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hisat2_index: ".ci_stuff/HISAT2Index/genome"
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bwa_index: ".ci_stuff/BWAindex/genome.fa"
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bwameth2_index: "/tmp/genome.fa"
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known_splicesites: ".ci_stuff/gencode/m9/HISAT2/splice_sites.txt"
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star_index: ".ci_stuff/STARIndex/"
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salmon_index: "/tmp/SalmonIndex/"
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salmon_velocity_index: "/tmp/SalmonIndex_RNAVelocity/"
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t2g_velocity: "/tmp/annotation/cDNA_introns.joint.t2g"
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genes_bed: "/tmp/genes.bed"
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genes_gtf: "/tmp/genes.gtf"
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genes_t2g: "/tmp/genes.t2g"
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extended_coding_regions_gtf: ".ci_stuff/gencode/m9/genes.slop.gtf"
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blacklist_bed: ".ci_stuff/DKFZ/GRCm38_General_readAttractingRegions.UseThisOne.bed"
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ignoreForNormalization: "MT X Y JH584299.1 GL456233.1 JH584301.1 GL456211.1 GL456350.1 JH584293.1 GL456221.1 JH584297.1 JH584296.1 GL456354.1 JH584294.1 JH584298.1 JH584300.1 GL456219.1 GL456210.1 JH584303.1 JH584302.1 GL456212.1 JH584304.1 GL456379.1 GL456216.1 GL456393.1 GL456366.1 GL456367.1 GL456239.1 GL456213.1 GL456383.1 GL456385.1 GL456360.1 GL456378.1 GL456389.1 GL456372.1 GL456370.1 GL456381.1 GL456387.1 GL456390.1 GL456394.1 GL456392.1 GL456382.1 GL456359.1 GL456396.1 GL456368.1 JH584292.1 JH584295.1"

‎.ci_stuff/spikein_organism.yaml

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bwameth_index: "/tmp/genome.fa"
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known_splicesites: ".ci_stuff/gencode/m9/HISAT2/splice_sites.txt"
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star_index: ".ci_stuff/STARIndex/"
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salmon_index: "/tmp/SalmonIndex/"
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salmon_velocity_index: "/tmp/SalmonIndex_RNAVelocity/"
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t2g_velocity: "/tmp/annotation/cDNA_introns.joint.t2g"
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genes_bed: "/tmp/genes.bed"
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genes_gtf: "/tmp/genes.gtf"
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genes_t2g: "/tmp/genes.t2g"
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spikein_genes_gtf: "/tmp/spikein_genes.gtf"
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extended_coding_regions_gtf: ".ci_stuff/gencode/m9/genes.slop.gtf"
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blacklist_bed: ".ci_stuff/DKFZ/GRCm38_General_readAttractingRegions.UseThisOne.bed"

‎.ci_stuff/test_dag.sh

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‎.github/snakePipesEnvCI.yml

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name: snakePipes_CI
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channels:
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- conda-forge
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- bioconda
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dependencies:
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- python=3.9
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- snakemake=6.2.1
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- fuzzywuzzy
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- snakemake=7.18.2
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- thefuzz[speedup]
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- mock
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- sphinx=4.2.0
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- sphinx-argparse
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- sphinx_rtd_theme=1.0.0
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- flake8
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- coreutils
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- mamba
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- graphviz

‎.github/workflows/linux.yml

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- uses: mamba-org/setup-micromamba@main
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with:
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environment-file: .github/snakePipesEnvCI.yml
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condarc: |
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channels:
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- conda-forge
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- bioconda
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- defaults
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channel_priority: 'strict'
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cache-downloads: true
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- name: Install snakePipes
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run: |
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micromamba run -n snakePipes_CI python -m pip install . --no-deps --ignore-installed -vvv
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- name: docs
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micromamba activate snakePipes_CI
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snakePipes config --tempDir /tmp
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cd docs
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make html
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flake:
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- uses: mamba-org/setup-micromamba@main
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with:
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environment-file: .github/snakePipesEnvCI.yml
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condarc: |
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channels:
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- conda-forge
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- bioconda
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- defaults
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channel_priority: 'strict'
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cache-downloads: true
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- name: Install snakePipes
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run: |
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micromamba run -n snakePipes_CI python -m pip install . --no-deps --ignore-installed -vvv
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- name: flake
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micromamba activate snakePipes_CI
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flake8 --ignore=E501,E722,E402 --exclude docs/conf.py .
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snakePipes config --tempDir /tmp
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flake8 --ignore=E501,E722,E402 --exclude tests,docs/conf.py,build/lib/snakePipes/shared/tools/three_prime_seq,snakePipes/shared/tools/three_prime_seq .
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CI:
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runs-on: ubuntu-latest
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steps:
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- uses: mamba-org/setup-micromamba@main
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with:
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environment-file: .github/snakePipesEnvCI.yml
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condarc: |
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channels:
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- conda-forge
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- bioconda
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- defaults
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channel_priority: 'strict'
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cache-downloads: true
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channel-priority: 'flexible'
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- name: Install snakePipes
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micromamba run -n snakePipes_CI python -m pip install . --no-deps --ignore-installed -vvv
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- name: CI
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micromamba activate snakePipes_CI
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snakePipes config --tempDir /tmp
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./.ci_stuff/test_dag.sh
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- name: pytest
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run: |
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micromamba activate snakePipes_CI
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snakePipes config --tempDir /tmp
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pytest --verbosity=2
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createEnvs:
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needs: CI
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strategy:
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- uses: mamba-org/setup-micromamba@main
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with:
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environment-file: .github/snakePipesEnvCI.yml
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condarc: |
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channels:
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- conda-forge
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- bioconda
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- defaults
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channel_priority: 'strict'
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cache-downloads: true
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- name: install snakePipes
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micromamba run -n snakePipes_CI python -m pip install . --no-deps --ignore-installed -vvv
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- name: createEnvs
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micromamba activate snakePipes_CI
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conda config --set channel_priority strict
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snakePipes createEnvs --force --only ${{matrix.envs}}
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snakePipes config --tempDir /tmp
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snakePipes createEnvs --autodetectCondaEnvDir --force --only ${{matrix.envs}}

‎.github/workflows/osx.yml

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with:
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condarc: |
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channels:
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- conda-forge
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- bioconda
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- defaults
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channel_priority: 'strict'
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cache-downloads: true
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- name: install snakePipes_OSX
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micromamba run -n snakePipes_CI python -m pip install . --no-deps --ignore-installed -vvv
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- name: createEnvsOSX
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micromamba activate snakePipes_CI
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conda config --set channel_priority strict
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snakePipes createEnvs --force --only ${{matrix.envs}}
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snakePipes createEnvs --force --autodetectCondaEnvDir --only ${{matrix.envs}}
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‎.gitignore

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*.pyc
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dist
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build
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*.swp
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# sphinx build folder
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_build
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# pip stuff
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snakePipes.egg-info
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# misc
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.vscode/

‎.readthedocs.yaml

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#conda:
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# file: docs/environment.yaml
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version: 2
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build:
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os: ubuntu-22.04
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tools:
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python: "3.7"
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sphinx:
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configuration: docs/conf.py
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python:
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version: 3.7
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pip_install: true
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install:
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- requirements: docs/requirements.txt
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- method: pip
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path: .
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- requirements: docs/requirements.txt

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