Verified Commit 6156f635 authored by Aurélien Ginolhac's avatar Aurélien Ginolhac 🚴
Browse files

add bowtie2 for fastq_screen

parent eadc98c5
......@@ -156,6 +156,15 @@ RUN cd /opt && \
install2.r --error caTools optparse reshape2 && \
Rscript -e 'install.packages("1.15.2.tar.gz")' && ln -s /opt/phantompeakqualtools-1.2.2/run_spp.R /usr/local/bin/
# Bowtie2
ARG BT2_VERSION="2.4.4"
RUN cd /opt && \
wget --no-check-certificate https://github.com/BenLangmead/bowtie2/releases/download/v${BT2_VERSION}/bowtie2-${BT2_VERSION}-linux-x86_64.zip && \
unzip bowtie2-${BT2_VERSION}-linux-x86_64.zip && rm bowtie2-${BT2_VERSION}-linux-x86_64.zip && \
mv bowtie2-${BT2_VERSION}-linux-x86_64/bowtie2* /usr/local/bin/ && rm -rf bowtie2-${BT2_VERSION}-linux-x86_64
# clean up
RUN apt-get clean && \
rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* && \
......
......@@ -8,6 +8,9 @@ This workflow is a Snakemake port of the [nextflow chipseq pipeline](https://nf-
The usage of this workflow is described in the [Snakemake Workflow Catalog](https://snakemake.github.io/snakemake-workflow-catalog/?usage=snakemake-workflows/chipseq).
```
snakemake --use-singularity --singularity-args "-B /scratch/users/aginolhac:/scratch/users/aginolhac" -j 6
```
# Credits
......
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