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Bioconda #10

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merged 14 commits into from
May 30, 2018
Merged

Bioconda #10

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6ddcf60
WIP: Bioconda environment file.
ewels Apr 24, 2018
f06974b
Updated Environment YAML - that should do the trick ;-)
May 16, 2018
c8bff17
Added r-spp to environment.yaml file
May 17, 2018
3cc6e25
Cleaned package names in docker file
May 17, 2018
8b8de8a
DeepTools requires pysam >=0.14.1 which requires samtools 1.7
May 17, 2018
30a4527
INstalls just fine :-)
May 17, 2018
4bbf815
Doublechecked tool names and corrected some
May 17, 2018
a8dc927
phantompeakqualtools fixed, installing ngsplot genomes, fixing deepTools
tiagochst May 27, 2018
4468e1a
phantompeakqualtools fixed, installing ngsplot genomes, fixing deepTools
tiagochst May 27, 2018
181c3a3
fix identing
tiagochst May 27, 2018
dfee534
fixing arguemnt for bamCoverage
tiagochst May 28, 2018
8163158
Merge branch 'bioconda' into bioconda
tiagochst May 28, 2018
e7e61b8
Adding doparallel to docker for improvement in bin/post_peak_calling_…
tiagochst May 29, 2018
4a5a08f
Revert docker file
tiagochst May 30, 2018
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4 changes: 2 additions & 2 deletions Dockerfile
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Original file line number Diff line number Diff line change
@@ -1,8 +1,8 @@
FROM nfcore/base
MAINTAINER Phil Ewels <phil.ewels@scilifelab.se>
LABEL authors="phil.ewels@scilifelab.se" \
description="Docker image containing all requirements for the nfcore/ChIPseq pipeline"
description="Docker image containing all requirements for the nfcore/ChIPseq pipeline"

COPY environment.yml /
RUN conda env create -f /environment.yml && conda clean -a
ENV PATH /opt/conda/envs/nfcore-chipseq-1.4dev/bin:$PATH
ENV PATH /opt/conda/envs/nfcore-chipseq-1.4dev/bin:$PATH
5 changes: 4 additions & 1 deletion environment.yml
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Expand Up @@ -10,6 +10,7 @@ dependencies:
- fastqc=0.11.7
- trim-galore=0.4.5
- bwa=0.7.17
- conda-forge::gawk=4.2.1
- conda-forge::r-markdown=0.8
- bioconda::r-spp=1.15.2
- bedtools=2.27.1
Expand All @@ -28,6 +29,7 @@ dependencies:
- conda-forge::r-ggplot2=2.2.1
- conda-forge::r-knitr=1.20
- conda-forge::r-rmysql=0.10.13
- conda-forge::r-doparallel=1.0.11
- bioconda::bioconductor-bsgenome=1.46.0
- bioconda::bioconductor-rsamtools=1.30.0
- bioconda::bioconductor-shortread=1.36.0
Expand All @@ -41,4 +43,5 @@ dependencies:
- bioconda::bioconductor-org.hs.eg.db=3.5.0
- bioconda::bioconductor-bsgenome.mmusculus.ucsc.mm10=1.4.0
- bioconda::bioconductor-org.mm.eg.db=3.5.0
- bioconda::r-spp=1.15.2
- deeptools=3.0.2
- bioconda::r-spp=1.15.2
4 changes: 2 additions & 2 deletions main.nf
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Expand Up @@ -597,7 +597,7 @@ process deepTools {
bamCoverage \\
-b $bam \\
--extendReads ${params.extendReadsLen} \\
--normalizeUsingRPKM \\
--normalizeUsing RPKM \\
-o ${bam}.bw
"""
} else {
Expand All @@ -619,7 +619,7 @@ process deepTools {
bamCoverage \\
-b \$bamfile \\
--extendReads ${params.extendReadsLen} \\
--normalizeUsingRPKM \\
--normalizeUsing RPKM \\
-o \${bamfile}.bw
done

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