add bowtie2 for fastq_screen

Dockerfile

@@ -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/* && \

README.md

@@ -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