first commit, missing macs2

.gitignore

+.Rproj.user
+.Rhistory
+.RData
+.Ruserdata

Dockerfile

+FROM eddelbuettel/r2u:jammy
+
+LABEL org.opencontainers.image.authors="Aurelien Ginolhac <aurelien.ginolhac@uni.lu>"
+
+# build with docker build -f Dockerfile -t ginolhac/snake-cut-and-tag:0.1 .
+# docker push ginolhac/snake-cut-and-tag:0.1
+
+LABEL version="0.1"
+LABEL description="Docker image to build the snakemake cut&tag singularity"
+
+ARG DEBIAN_FRONTEND=noninteractive
+
+RUN apt-get update && apt-get install -y software-properties-common && add-apt-repository -y ppa:openjdk-r/ppa && \
+    apt-get update && apt-get install -y \
+        bwa \
+        build-essential \
+        cmake \
+        curl \
+        libboost-all-dev \
+        libbz2-dev \
+        libcurl4-openssl-dev \
+        liblzma-dev \
+        libncurses5-dev \
+        libssl-dev \
+        libxml2-dev \
+        libgd-perl libgd-graph-perl \
+        openjdk-8-jdk \
+        python3 \
+        python3-pip \
+        unzip \
+        vim-common \
+        wget \
+        zlib1g-dev \
+    && rm -rf /var/lib/apt/lists/*
+
+# default to python3
+# better to use https://stackoverflow.com/a/50331137/1395352
+RUN ln -sf /usr/bin/python-config /usr/bin/python3.8-config && ln -sf /usr/bin/python3 /usr/bin/python
+
+# htslib
+ARG HTS_VERSION="1.16"
+RUN cd /opt && \
+    wget --no-check-certificate https://github.com/samtools/htslib/releases/download/${HTS_VERSION}/htslib-${HTS_VERSION}.tar.bz2 && \
+    tar -xf htslib-${HTS_VERSION}.tar.bz2 && rm htslib-${HTS_VERSION}.tar.bz2 && cd htslib-${HTS_VERSION} && \
+    ./configure --enable-libcurl --enable-s3 --enable-plugins --enable-gcs && \
+    make && make install && make clean
+
+
+# samtools
+ARG SAM_VERSION="1.16"
+RUN cd /opt && \
+    wget --no-check-certificate https://github.com/samtools/samtools/releases/download/${SAM_VERSION}/samtools-${SAM_VERSION}.tar.bz2 && \
+    tar -xf samtools-${SAM_VERSION}.tar.bz2 && rm samtools-${SAM_VERSION}.tar.bz2 && cd samtools-${SAM_VERSION} && \
+    ./configure --with-htslib=/opt/htslib-${HTS_VERSION} && make && make install && make clean
+
+
+# bedtools
+ARG BT_VERSION="2.30.0"
+RUN cd /opt && \
+    wget --no-check-certificate https://github.com/arq5x/bedtools2/releases/download/v${BT_VERSION}/bedtools-${BT_VERSION}.tar.gz && \
+    tar -xf bedtools-${BT_VERSION}.tar.gz && rm bedtools-${BT_VERSION}.tar.gz && \
+    cd bedtools2 && make && make install && make clean
+
+# AdapterRemoval
+ARG AR_VERSION="2.3.3"
+RUN cd /opt && \
+    wget --no-check-certificate https://github.com/MikkelSchubert/adapterremoval/archive/v${AR_VERSION}.tar.gz && \
+    tar -xf v${AR_VERSION}.tar.gz && rm v${AR_VERSION}.tar.gz && \
+    cd adapterremoval-${AR_VERSION} && make && make install && make clean
+
+
+# Bowtie2
+ARG BT2_VERSION="2.5.0"
+RUN cd /opt && \
+    wget --no-check-certificate https://github.com/BenLangmead/bowtie2/releases/download/v${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-${BT2_VERSION}-linux-x86_64
+
+# FastScreen
+ENV PERL_MM_USE_DEFAULT=1
+ARG FQ_SCREEN_VERSION="0.15.2"
+RUN cd /opt && \
+    wget --no-check-certificate https://github.com/StevenWingett/FastQ-Screen/archive/refs/tags/v${FQ_SCREEN_VERSION}.tar.gz && \
+    tar -xf v${FQ_SCREEN_VERSION}.tar.gz && rm v${FQ_SCREEN_VERSION}.tar.gz
+ENV PATH /opt/FastQ-Screen-${FQ_SCREEN_VERSION}:$PATH
+
+# FastQC
+RUN cd /opt && \
+    wget --no-check-certificate https://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v0.11.9.zip && \
+    unzip fastqc_v0.11.9.zip && rm fastqc_v0.11.9.zip && chmod +x FastQC/fastqc
+ENV PATH /opt/FastQC:$PATH
+
+RUN mkdir /opt/ucsc && \
+    wget --no-check-certificate -P /opt/ucsc/ http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/bigWigToBedGraph && \
+    wget --no-check-certificate -P /opt/ucsc/ http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/bedGraphToBigWig && \
+    chmod 755 /opt/ucsc/*
+ENV PATH /opt/ucsc:$PATH
+
+# gopeaks
+ARG GOPEAKS_VERSION="1.0.0"
+RUN cd /opt && \
+    wget --no-check-certificate https://github.com/maxsonBraunLab/gopeaks/releases/download/v${GOPEAKS_VERSION}/gopeaks-linux-amd64 && \
+    mv gopeaks-linux-amd64 /usr/local/bin/gopeaks && chmod +x /usr/local/bin/gopeaks
+
+# Preseq
+ARG PRESEQ_VERSION="3.2.0"
+RUN cd /opt && \
+    wget --no-check-certificate https://github.com/smithlabcode/preseq/releases/download/v${PRESEQ_VERSION}/preseq-${PRESEQ_VERSION}.tar.gz && \
+    tar -xf preseq-${PRESEQ_VERSION}.tar.gz && rm preseq-${PRESEQ_VERSION}.tar.gz && \
+    cd preseq-${PRESEQ_VERSION} && ./configure --prefix=/usr/local/ && make && make install && make clean
+
+# HOMER
+RUN mkdir /opt/HOMER && cd /opt/HOMER && \
+    wget --no-check-certificate http://homer.ucsd.edu/homer/configureHomer.pl && \
+    perl configureHomer.pl -install
+ENV PATH /opt/HOMER/bin:$PATH
+
+
+# python modules
+RUN python3 -m pip install snakemake multiqc pandas pyBigWig deeptools
+
+RUN install.r ggplot2 hexbin ggrepel cowplot stringr \
+  deseq2 apeglm
+
+    # clean up
+#RUN apt-get clean && \
+#    rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* && \
+#    apt-get autoclean && \
+#    apt-get autoremove -y && rm -rf /var/lib/{dpkg,cache,log}/ # keep /var/lib/apt
+
+

README.md

+
+
+## Analysis Workflow
+
+A snakemake pipeline is available: https://github.com/maxsonBraunLab/cutTag-pipeline
+
+
+It used a specific peak caller for Cut&Tag: [gopeaks](https://github.com/maxsonBraunLab/gopeaks) and published in [Genome Biol](https://doi.org/10.1186/s13059-022-02707-w)
\ No newline at end of file