Merge pull request #615 from maxplanck-ie/develop

Develop

.azure-pipelines/macosx_setup.yml

@@ -0,0 +1,15 @@
+steps:
+#- task: CondaEnvironment@1
+#  inputs:
+#    createCustomEnvironment: true
+#    environmentName: foo
+#    packageSpecs: snakemake fuzzywuzzy mock sphinx sphinx-argparse sphinx_rtd_theme flake8 "python=3.7" pip
+#    installOptions: -c conda-forge -c bioconda --quiet
+#    createOptions: -c conda-forge -c bioconda --quiet --yes
+- bash: |
+    conda create -n foo -q --yes --quiet -c conda-forge -c bioconda snakemake fuzzywuzzy mock sphinx sphinx-argparse sphinx_rtd_theme flake8 coreutils python=3.7
+  displayName: Installing dependencies
+- bash: |
+    source activate foo
+    python -m pip install . --no-deps --ignore-installed -vvv
+  displayName: Installing snakePipes

.azure-pipelines/setup.yml

@@ -7,7 +7,7 @@ steps:
 #    installOptions: -c conda-forge -c bioconda --quiet
 #    createOptions: -c conda-forge -c bioconda --quiet --yes
 - bash: |
-    conda create -n foo -q --yes --quiet -c conda-forge -c bioconda snakemake fuzzywuzzy mock sphinx sphinx-argparse sphinx_rtd_theme flake8 coreutils
+    conda create -n foo -q --yes --quiet -c conda-forge -c bioconda snakemake fuzzywuzzy mock sphinx sphinx-argparse sphinx_rtd_theme flake8 coreutils python=3.7
   displayName: Installing dependencies
 - bash: |
     source activate foo

.ci_stuff/organism.yaml

@@ -8,8 +8,9 @@ bwa_index: ".ci_stuff/BWAindex/genome.fa"
 bwameth_index: "/tmp/genome.fa"
 known_splicesites: ".ci_stuff/gencode/m9/HISAT2/splice_sites.txt"
 star_index: ".ci_stuff/STARIndex/"
-genes_bed: ".ci_stuff/gencode/m9/genes.bed"
+genes_bed: "/tmp/genes.bed"
 genes_gtf: "/tmp/genes.gtf"
 extended_coding_regions_gtf: ".ci_stuff/gencode/m9/genes.slop.gtf"
 blacklist_bed: ".ci_stuff/DKFZ/GRCm38_General_readAttractingRegions.UseThisOne.bed"
 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"
+rmsk_file: "/tmp/rmsk.txt"

BAM_input/ChIP-seq.cluster_config.yaml

@@ -0,0 +1,52 @@
+CSAW:
+  memory: 10G
+FASTQdownsample:
+  memory: 3G
+Genrich_peaks:
+  memory: 20G
+MACS2:
+  memory: 8G
+__default__:
+  memory: 1G
+bamCoverage:
+  memory: 5G
+bamCoverage_RPKM:
+  memory: 5G
+bamCoverage_coverage:
+  memory: 5G
+bamCoverage_raw:
+  memory: 5G
+bamCoverage_unique_mappings:
+  memory: 5G
+create_snpgenome:
+  memory: 30G
+filter_reads_umi:
+  memory: 10G
+histoneHMM:
+  memory: 4G
+plotCorrelation_pearson:
+  memory: 3G
+plotCorrelation_pearson_allelic:
+  memory: 5G
+plotCorrelation_spearman:
+  memory: 3G
+plotCorrelation_spearman_allelic:
+  memory: 2G
+plotCoverage:
+  memory: 1G
+plotEnrichment:
+  memory: 1G
+plotFingerprint:
+  memory: 1G
+plotPCA:
+  memory: 4G
+plotPCA_allelic:
+  memory: 4G
+plot_heatmap_CSAW_up:
+  memory: 10G
+snakePipes_cluster_logDir: cluster_logs
+snakemake_cluster_cmd: module load slurm; SlurmEasy --mem-per-cpu {cluster.memory}
+  --threads {threads} --log cluster_logs --name {rule}.snakemake
+snakemake_latency_wait: 300
+snp_split:
+  memory: 10G

BAM_input/ChIP-seq.config.yaml

@@ -0,0 +1,42 @@
+absBestLFC: 1
+bamExt: .filtered.bam
+baseDir: /data/manke/sikora/miniconda3/envs/snakemake/lib/python3.6/site-packages/snakePipes
+bigWigType: both
+bwBinSize: 25
+clusterConfig: shared/cluster.yaml
+clusterConfigFile: null
+configFile: null
+createDAG: false
+emailAddress: null
+emailSender: null
+fdr: 0.05
+filterGTF: null
+fragmentLength: 200
+fromBAM: /data/manke/sikora/snakepipes/BAM_input/filtered_bam
+genome: /data/manke/sikora/snakepipes/.ci_stuff/organism.yaml
+keepTemp: false
+local: false
+maxJobs: 5
+mfold: 0 50
+onlySSL: false
+organismsDir: shared/organisms
+outdir: /data/manke/sikora/snakepipes/BAM_input
+pairedEnd: true
+peakCaller: MACS2
+pipeline: chip-seq
+plotFormat: png
+predictChIPDict: null
+qval: 0.001
+sampleSheet: /data/manke/sikora/snakepipes/.ci_stuff/test_sampleSheet.tsv
+samples_config: /data/manke/sikora/snakepipes/.ci_stuff/ChIP.sample_config.yaml
+smtpPassword: null
+smtpPort: 0
+smtpServer: null
+smtpUsername: null
+snakemakeOptions: ' --use-conda --conda-prefix /package/anaconda3/envs/   --dryrun
+  --conda-prefix /tmp'
+tempDir: /data/extended/
+toolsVersion: true
+verbose: false
+windowSize: 150
+workingdir: /data/manke/sikora/snakepipes/BAM_input

BAM_input/ChIP-seq_organism.yaml

@@ -0,0 +1,16 @@
+genome_size: 2652783500
+genome_fasta: "/tmp/genome.fa"
+genome_index: "/tmp/genome.fa.fai"
+genome_2bit: ".ci_stuff/genome_fasta/genome.2bit"
+bowtie2_index: ".ci_stuff/BowtieIndex/genome"
+hisat2_index: ".ci_stuff/HISAT2Index/genome"
+bwa_index: ".ci_stuff/BWAindex/genome.fa"
+bwameth_index: "/tmp/genome.fa"
+known_splicesites: ".ci_stuff/gencode/m9/HISAT2/splice_sites.txt"
+star_index: ".ci_stuff/STARIndex/"
+genes_bed: "/tmp/genes.bed"
+genes_gtf: "/tmp/genes.gtf"
+extended_coding_regions_gtf: ".ci_stuff/gencode/m9/genes.slop.gtf"
+blacklist_bed: ".ci_stuff/DKFZ/GRCm38_General_readAttractingRegions.UseThisOne.bed"
+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"
+rmsk_file: "/tmp/rmsk.txt"