fixing master to release v2.3.0

Merge commit '7f3d02480f07d5491145dd40dac129571e75d2b8' of github.com:NCIP/ctat-mutations

.gitmodules

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+[submodule "ctat-mutations.wiki"]
+ path = ctat-mutations.wiki
+ url = https://github.com/NCIP/ctat-mutations.wiki.git

Docker/.dockerignore

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+*.simg

Docker/Dockerfile

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+FROM ubuntu:18.04
+
+
+MAINTAINER [email protected]
+
+
+RUN apt-get update && apt-get install -y gcc g++ perl python3 automake make \
+ wget curl libdb-dev \
+ bzip2 zlibc zlib1g zlib1g-dev default-jre \
+ python3-setuptools python3-dev build-essential python3-distutils \
+ unzip libbz2-dev liblzma-dev && \
+ apt-get clean
+
+
+# make python3 be the default python
+RUN ln -sf /usr/bin/python3 /usr/bin/python
+
+RUN curl https://bootstrap.pypa.io/get-pip.py -o get-pip.py && \
+ python get-pip.py
+
+
+
+RUN pip install igv-reports requests 
+
+
+
+ENV SRC /usr/local/src
+ENV BIN /usr/local/bin
+
+
+## pull down gatk
+WORKDIR $SRC
+
+
+ENV GATK_VERSION=4.1.4.0
+RUN wget https://github.com/broadinstitute/gatk/releases/download/${GATK_VERSION}/gatk-${GATK_VERSION}.zip && \
+ unzip gatk-${GATK_VERSION}.zip
+
+ENV GATK_HOME $SRC/gatk-${GATK_VERSION}
+
+
+## Picard
+WORKDIR $SRC
+
+RUN wget https://github.com/broadinstitute/picard/releases/download/2.20.3/picard.jar
+
+ENV PICARD_HOME $SRC
+
+
+## Samtools
+ENV SAMTOOLS_VERSION=1.7
+
+RUN SAMTOOLS_URL="https://github.com/samtools/samtools/releases/download/${SAMTOOLS_VERSION}/samtools-${SAMTOOLS_VERSION}.tar.bz2" && \
+ cd $SRC && \
+ wget $SAMTOOLS_URL && \
+ tar xvf samtools-${SAMTOOLS_VERSION}.tar.bz2 && \
+ cd samtools-${SAMTOOLS_VERSION}/htslib-${SAMTOOLS_VERSION} && ./configure && make && make install && \
+ cd ../ && ./configure --without-curses && make && make install
+
+
+
+## BCFtools
+WORKDIR $SRC
+RUN wget https://github.com/samtools/bcftools/releases/download/1.9/bcftools-1.9.tar.bz2 && \
+ tar xvf bcftools-1.9.tar.bz2 && \
+ cd bcftools-1.9 && ./configure && make && make install
+
+
+
+## STAR Aligner
+WORKDIR $SRC
+
+ENV STAR_VERSION=2.7.2b
+RUN STAR_URL="https://github.com/alexdobin/STAR/archive/${STAR_VERSION}.tar.gz" &&\
+ wget -P $SRC $STAR_URL &&\
+ tar -xvf $SRC/${STAR_VERSION}.tar.gz -C $SRC && \
+ mv $SRC/STAR-${STAR_VERSION}/bin/Linux_x86_64_static/STAR /usr/local/bin
+
+
+## Bedtools
+RUN wget https://github.com/arq5x/bedtools2/releases/download/v2.28.0/bedtools-2.28.0.tar.gz && \
+ tar -zxvf bedtools-2.28.0.tar.gz && \
+ cd bedtools2 && \
+ make && \
+ cp bin/* $BIN/
+
+
+
+## NCIP CTAT mutations
+
+WORKDIR $SRC
+
+RUN apt-get install -y git && apt-get clean
+
+ENV CTAT_MUTATIONS_COMMIT 958801d46bc0951aca55c4de1a0469a839b0527f
+
+RUN git clone https://github.com/NCIP/ctat-mutations.git && \
+ cd ctat-mutations && \
+ git checkout ${CTAT_MUTATIONS_COMMIT}
+
+
+
+

Docker/VERSION.txt

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+2.3.0

Docker/build_docker.sh

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+#!/bin/bash
+
+set -e
+
+VERSION=`cat VERSION.txt`
+
+docker build -t trinityctat/ctat_mutations:$VERSION .
+docker build -t trinityctat/ctat_mutations:latest .
+
+

Docker/install_R_packages.R

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+options(warn = 2) # treat warnings as errors, otherwise script can fail silently if a package fails to install
+
+InstallPackageFromArchive = function(packageName, packageURL) {
+ # make sure to use http not https as this will give an "unsupported URL scheme" error
+ if (!(packageName %in% rownames(installed.packages()))) {
+ install.packages(packageURL, repos = NULL, type = "source", clean = TRUE)
+ }
+}
+
+dependencies = c("gplots",
+ "digest", "gtable", "MASS", "plyr", "reshape2", "scales", "tibble", "lazyeval") # for ggplot2
+repos <- c("http://cran.cnr.Berkeley.edu", "http://cran.mtu.edu")
+install.packages(dependencies, repos = repos, clean = TRUE)
+
+InstallPackageFromArchive("getopt", "http://cran.r-project.org/src/contrib/Archive/getopt/getopt_1.20.0.tar.gz")
+InstallPackageFromArchive("optparse", "http://cran.r-project.org/src/contrib/Archive/optparse/optparse_1.3.2.tar.gz")
+InstallPackageFromArchive("data.table", "http://cran.r-project.org/src/contrib/Archive/data.table/data.table_1.10.4-2.tar.gz")
+InstallPackageFromArchive("gsalib", "http://cran.r-project.org/src/contrib/gsalib_2.1.tar.gz")
+InstallPackageFromArchive("ggplot2", "http://cran.r-project.org/src/contrib/Archive/ggplot2/ggplot2_2.2.1.tar.gz")
+
+ # HMM is only required for testing and not in production:
+InstallPackageFromArchive("HMM", "http://cran.r-project.org/src/contrib/HMM_1.0.tar.gz")
+
+q(save = "no")

Docker/make_simg.sh

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+#!/bin/bash
+
+set -ex
+
+VERSION=`cat VERSION.txt`
+
+singularity build ctat_mutations.v${VERSION}.simg docker://trinityctat/ctat_mutations:$VERSION
+
+singularity exec -e ctat_mutations.v${VERSION}.simg env
+

Docker/push_docker.sh

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+#!/bin/bash
+
+set -e
+
+VERSION=`cat VERSION.txt`
+
+docker push trinityctat/ctat_mutations:$VERSION 
+docker push trinityctat/ctat_mutations:latest 
+
+