Merge branch 'master' of https://gitbio.ens-lyon.fr/LBMC/RMI2/rmi2_pipelines

results/.gitignore

-*

src/.docker_modules/bedops/2.4.39/Dockerfile

+FROM quay.io/biocontainers/bedops:2.4.39--hc9558a2_0
+MAINTAINER Laurent Modolo

src/.docker_modules/bedops/2.4.39/docker_init.sh

+#!/bin/sh
+docker pull lbmc/bedops:2.4.39
+docker build src/.docker_modules/bedops/2.4.39 -t 'lbmc/bedops:2.4.39'
+docker push lbmc/bedops:2.4.39

src/.docker_modules/crossmap/0.4.1/Dockerfile

+FROM quay.io/biocontainers/crossmap:0.4.1--pyh5ca1d4c_0
+MAINTAINER Laurent Modolo

src/.docker_modules/crossmap/0.4.1/docker_init.sh

+#!/bin/sh
+docker pull lbmc/crossmap:0.4.1
+docker build src/.docker_modules/crossmap/0.4.1/ -t 'lbmc/crossmap:0.4.1'
+docker push lbmc/crossmap:0.4.1

src/.docker_modules/g2gtools/0.2.7/Dockerfile

+FROM jcrist/alpine-conda:4.6.8
+
+RUN /opt/conda/bin/conda config --add channels r \
+    && /opt/conda/bin/conda config --add channels bioconda \
+    && /opt/conda/bin/conda install --yes \
+        -c kbchoi g2gtools pycparser setuptools\
+        nomkl \
+    && /opt/conda/bin/conda clean -afy \
+    && find /opt/conda/ -follow -type f -name '*.a' -delete \
+    && find /opt/conda/ -follow -type f -name '*.pyc' -delete \
+    && find /opt/conda/ -follow -type f -name '*.js.map' -delete
+

src/.docker_modules/g2gtools/0.2.7/docker_init.sh

+#!/bin/sh
+docker pull lbmc/g2gtools:0.2.7
+docker build src/.docker_modules/g2gtools/0.2.7 -t 'lbmc/g2gtools:0.2.7'
+docker push lbmc/g2gtools:0.2.7

src/.docker_modules/g2gtools/0.2.8/Dockerfile

+FROM python:3.8-alpine
+MAINTAINER Laurent Modolo
+
+ENV G2GTOOLS_VERSION=0.2.8
+
+RUN apk add --update --no-cache bash musl-dev linux-headers g++ cmake make build-base bzip2-dev zlib-dev xz-dev autoconf \
+ && wget https://github.com/churchill-lab/g2gtools/archive/v${G2GTOOLS_VERSION}.tar.gz \
+ && tar -xvf v${G2GTOOLS_VERSION}.tar.gz \
+ && cd g2gtools-${G2GTOOLS_VERSION} \
+ && pip install numpy \
+ && make install 

src/.docker_modules/g2gtools/0.2.8/docker_init.sh

+#!/bin/sh
+docker pull lbmc/g2gtools:0.2.8
+docker build src/.docker_modules/g2gtools/0.2.8 -t 'lbmc/g2gtools:0.2.8'
+docker push lbmc/g2gtools:0.2.8

src/.docker_modules/gffread/0.11.8/Dockerfile

+FROM alpine:3.12
+MAINTAINER Laurent Modolo
+
+ENV GFFREAD_VERSION=0.11.8
+ENV PACKAGES make \
+             g++ \
+             bash \
+             perl
+
+RUN apk update && \
+    apk add ${PACKAGES} && \
+wget http://ccb.jhu.edu/software/stringtie/dl/gffread-${GFFREAD_VERSION}.tar.gz && \
+tar -xvf gffread-${GFFREAD_VERSION}.tar.gz && \
+cd gffread-${GFFREAD_VERSION}/ && \
+make && \
+cp gffread /usr/bin/

src/.docker_modules/gffread/0.11.8/docker_init.sh

+#!/bin/sh
+docker pull lbmc/gffread:0.11.8
+docker build src/.docker_modules/gffread/0.11.8 -t 'lbmc/gffread:0.11.8'
+docker push lbmc/gffread:0.11.8

src/.docker_modules/kallistobustools/0.39.3/Dockerfile

+FROM python:3.8-alpine
+MAINTAINER Laurent Modolo
+
+ENV B_VERSION=0.39.3
+ENV K_VERSION=0.46.1
+
+RUN apk add  --update --no-cache bash musl-dev linux-headers g++ cmake make build-base hdf5 hdf5-dev zlib-dev autoconf && \
+wget https://github.com/BUStools/bustools/archive/v${B_VERSION}.tar.gz && \
+tar xvf v${B_VERSION}.tar.gz && \
+cd bustools-${B_VERSION} && \
+mkdir build && \
+cd build && \
+cmake .. && \
+sed -i -e 's/"Common\.hpp"/"Common\.hpp"\n#include <cmath>/g' ../src/bustools_whitelist.h && \
+sed -i 's/pow/std::pow/g' ../src/bustools_whitelist.cpp && \
+make && \
+make install && \
+wget https://github.com/pachterlab/kallisto/archive/v${K_VERSION}.tar.gz && \
+tar xvf v${K_VERSION}.tar.gz && \
+cd kallisto-${K_VERSION} && \
+mkdir build && \
+cd build && \
+cmake .. && \
+make && \
+make install && \
+wget https://github.com/BUStools/getting_started/releases/download/getting_started/t2g.py && \
+chmod +x t2g.py && \
+mv t2g.py /usr/local/bin/ && \
+rm -R kallisto* bustools* v${K_VERSION}.tar.gz v${B_VERSION}.tar.gz
+
+CMD ["sh"]

src/.docker_modules/kallistobustools/0.39.3/docker_init.sh

+#!/bin/sh
+docker pull lbmc/kallistobustools:0.39.3
+docker build src/.docker_modules/kallistobustools/0.39.3 -t 'lbmc/kallistobustools:0.39.3'
+docker push lbmc/kallistobustools:0.39.3

src/.docker_modules/r/3.5.3/docker_init.sh → src/.docker_modules/r-base/3.5.3/docker_init.sh

 #!/bin/sh
 docker pull lbmc/r:3.5.3
-docker build src/.docker_modules/r/3.5.3 -t 'lbmc/r:3.5.3'
+docker build src/.docker_modules/r-base/3.5.3 -t 'lbmc/r:3.5.3'
 docker push lbmc/r:3.5.3

src/.docker_modules/r/3.6.2/docker_init.sh → src/.docker_modules/r-base/3.6.2/docker_init.sh

 #!/bin/sh
 docker pull lbmc/r-base:3.6.2
-docker build src/.docker_modules/r/3.6.2 -t 'lbmc/r-base:3.6.2'
+docker build src/.docker_modules/r-base/3.6.2 -t 'lbmc/r-base:3.6.2'
 docker push lbmc/r-base:3.6.2

src/.docker_modules/r/4.0.0/docker_init.sh → src/.docker_modules/r-base/4.0.0/docker_init.sh

 #!/bin/sh
 docker pull lbmc/r-base:4.0.0
-docker build src/.docker_modules/r/4.0.0 -t 'lbmc/r-base:4.0.0'
+docker build src/.docker_modules/r-base/4.0.0 -t 'lbmc/r-base:4.0.0'
 docker push lbmc/r-base:4.0.0

src/.docker_modules/r-base/4.0.2/Dockerfile

+FROM alpine:3.12.0
+MAINTAINER Lauret Modolo
+
+ENV R_PKGS R=~4.0.2 \
+  R-mathlib=~4.0.2 \
+  R-dev=~4.0.2 \
+  R-doc=~4.0.2
+
+ENV R_DEPS g++ \
+  libxml2-dev \
+  make \
+  cmake \
+  linux-headers \
+  cairo-dev \
+  libxmu-dev \
+  pango-dev \
+  perl \
+  tiff-dev \
+  icu-dev \
+  libjpeg-turbo \
+  pcre-dev \
+  readline-dev \
+  libexecinfo-dev \
+  file \
+  ttf-linux-libertine \
+  git
+
+RUN echo "http://ftp.acc.umu.se/mirror/alpinelinux.org/v3.11/main" > /etc/apk/repositories \
+&& echo "http://ftp.acc.umu.se/mirror/alpinelinux.org/v3.11/community" >> /etc/apk/repositories \
+&& sed -i -e 's/v[[:digit:]]\..*\//edge\//g' /etc/apk/repositories \
+&& apk add --update --no-cache ${R_PKGS} ${R_DEPS}
+
+CMD ["R", "--no-save"]