Merge branch 'master' of gitbio.ens-lyon.fr:LBMC/nextflow

.gitignore

@@ -3,3 +3,4 @@ nextflow
 .nextflow/
 work/
 results
+workspace.code-workspace

src/.docker_modules/alntools/dd96682/Dockerfile

+FROM python:3.9-buster as build
+MAINTAINER Laurent Modolo
+
+ENV ALNTOOLS_VERSION=dd96682
+ENV PACKAGES git \
+    ca-certificates \
+    procps
+
+RUN apt-get update \
+    && apt-get install -y --no-install-recommends ${PACKAGES}\
+    && apt-get clean \
+    && git clone https://github.com/churchill-lab/alntools.git \
+    && cd alntools \
+    && git checkout ${ALNTOOLS_VERSION} \
+    && python setup.py install \
+    && cd .. \
+    && rm -R alntools \
+    && apt-get autoremove --purge -y git ca-certificates
+
+CMD ["bash"] 
\ No newline at end of file

src/.docker_modules/alntools/dd96682/docker_init.sh

+#!/bin/sh
+docker pull lbmc/alntools:dd96682
+docker build src/.docker_modules/alntools/dd96682 -t 'lbmc/alntools:dd96682'
+docker push lbmc/alntools:dd96682

src/.docker_modules/bwa/0.7.17/Dockerfile

-FROM lbmc/sambamba:0.6.9
+FROM lbmc/samtools:1.11
 MAINTAINER Laurent Modolo
 
 ENV BWA_VERSION=0.7.17
 ENV SAMBLASTER_VERSION=0.1.24
 
-ENV PACKAGES curl=7.58* \
-    ca-certificates=20180409 \
-    build-essential=12.4* \
-    zlib1g-dev=1:1.2.11*
+ENV PACKAGES curl \
+  g++
 
-RUN apt-get update && \
-    apt-get install -y --no-install-recommends ${PACKAGES} && \
-    apt-get clean
+RUN apk update && \
+    apk add ${PACKAGES}
 
 RUN curl -k -L https://github.com/lh3/bwa/releases/download/v${BWA_VERSION}/bwa-${BWA_VERSION}.tar.bz2 -o bwa-v${BWA_VERSION}.tar.bz2 && \
 tar xjf bwa-v${BWA_VERSION}.tar.bz2 && \
@@ -21,10 +18,3 @@ cp bwa /usr/bin && \
 cd .. && \
 rm -R bwa-${BWA_VERSION}/
 
-RUN curl -k -L https://github.com/GregoryFaust/samblaster/releases/download/v.${SAMBLASTER_VERSION}/samblaster-v.${SAMBLASTER_VERSION}.tar.gz -o samblaster-v.${SAMBLASTER_VERSION}.tar.gz && \
-tar xvf samblaster-v.${SAMBLASTER_VERSION}.tar.gz && \
-cd samblaster-v.${SAMBLASTER_VERSION}/ && \
-make && \
-cp samblaster /usr/bin && \
-cd .. && \
-rm -R samblaster-v.${SAMBLASTER_VERSION}/

src/.docker_modules/deeptools/3.5.0/Dockerfile

+FROM python:3.9-slim
+MAINTAINER Lauret Modolo
+
+ENV DEEPTOOLS_VERSION=3.5.0
+RUN apt-get update -qq \
+    && apt-get install --no-install-recommends --yes \
+        build-essential \
+        zlib1g-dev \
+        libbz2-dev \
+        liblzma-dev \
+        libcurl4-gnutls-dev \
+        libssl-dev \
+        libncurses5-dev
+RUN pip3 install deeptools==${DEEPTOOLS_VERSION}

src/.docker_modules/deeptools/3.5.0/docker_init.sh

+#!/bin/sh
+docker pull lbmc/deeptools:3.5.0
+docker build src/.docker_modules/deeptools/3.5.0 -t 'lbmc/deeptools:3.5.0'
+docker push lbmc/deeptools:3.5.0

src/.docker_modules/emase-zero/0.3.1/Dockerfile

+FROM debian:buster as build
+MAINTAINER Laurent Modolo
+
+ENV EMASEZERO_VERSION=0.3.1
+ENV PACKAGES build-essential \
+    ca-certificates \
+    zlib1g-dev \
+    git
+
+RUN apt-get update && \
+    apt-get install -y --no-install-recommends ${PACKAGES} && \
+    apt-get clean
+
+RUN git clone https://github.com/churchill-lab/emase-zero.git \
+    && cd emase-zero/src/ \
+    && make \
+    && mv emase-zero /usr/local/bin/ \
+    && ldd /usr/local/bin/emase-zero
+# linux-vdso.so.1 (0x00007ffe8e35f000)
+# libz.so.1 => /lib/x86_64-linux-gnu/libz.so.1 (0x00007fbd358b5000)
+# libstdc++.so.6 => /usr/lib/x86_64-linux-gnu/libstdc++.so.6 (0x00007fbd35731000)
+# libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007fbd355ae000)
+# libgcc_s.so.1 => /lib/x86_64-linux-gnu/libgcc_s.so.1 (0x00007fbd35594000)
+# libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007fbd353d3000)
+# /lib64/ld-linux-x86-64.so.2 (0x00007fbd35af7000)
+
+FROM debian:buster-slim
+
+COPY --from=build /usr/local/bin/emase-zero /usr/local/bin/
+COPY --from=build /lib/x86_64-linux-gnu/libz.so.1 /lib/x86_64-linux-gnu/
+COPY --from=build /lib/x86_64-linux-gnu/libm.so.6 /lib/x86_64-linux-gnu/
+COPY --from=build /lib/x86_64-linux-gnu/libgcc_s.so.1 /lib/x86_64-linux-gnu/
+
+RUN apt-get update && \
+    apt-get install -y procps bash

src/.docker_modules/emase-zero/0.3.1/docker_init.sh

+#!/bin/sh
+docker pull lbmc/emase-zero:0.3.1
+docker build src/.docker_modules/emase-zero/0.3.1 -t 'lbmc/emase-zero:0.3.1'
+docker push lbmc/emase-zero:0.3.1

src/.docker_modules/fastp/0.20.1/Dockerfile

+FROM quay.io/biocontainers/fastp:0.20.1--h8b12597_0
+MAINTAINER Laurent Modolo

src/.docker_modules/fastp/0.20.1/docker_init.sh

+#!/bin/sh
+docker pull lbmc/fastp:0.20.1
+docker build src/.docker_modules/fastp/0.20.1 -t 'lbmc/fastp:0.20.1'
+docker push lbmc/fastp:0.20.1

src/.docker_modules/g2gtools/0.2.8/Dockerfile

-FROM python:3.8-alpine
+FROM python:3.9-slim
 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 \
+RUN apt update \
+ && apt install -y wget build-essential zlib1g-dev libbz2-dev liblzma-dev procps \
  && 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 \
+ && pip install pysam \
  && make install 
+
+
+CMD ["bash"]

src/.docker_modules/macs3/3.0.0a6/Dockerfile

+FROM python:3.9-slim
+MAINTAINER Laurent Modolo
+
+ENV MACS3_VERSION=3.0.0a6
+RUN apt-get update -qq \
+    && apt-get install --no-install-recommends --yes \
+        build-essential \
+        zlib1g-dev \
+        libbz2-dev \
+        liblzma-dev \
+        libcurl4-gnutls-dev \
+        libssl-dev \
+        libncurses5-dev \
+        procps
+RUN pip install macs3==${MACS3_VERSION}

src/.docker_modules/macs3/3.0.0a6/docker_init.sh

+#!/bin/sh
+docker pull lbmc/macs3:3.0.0a6
+docker build src/.docker_modules/macs3/3.0.0a6 -t 'lbmc/macs3:3.0.0a6'
+docker push lbmc/macs3:3.0.0a6

src/.docker_modules/minimap2/2.17/Dockerfile

+FROM quay.io/biocontainers/samtools:0.1.18--hfb9b9cc_10 AS samtools 
+# /usr/local/bin/samtools
+# / # ldd /usr/local/bin/samtools
+#         /lib64/ld-linux-x86-64.so.2 (0x7efddcdcc000)
+#         libncurses.so.6 => /usr/local/bin/../lib/libncurses.so.6 (0x7efddcfad000)
+#         libtinfo.so.6 => /usr/local/bin/../lib/libtinfo.so.6 (0x7efddcf6f000)
+#         libm.so.6 => /lib64/ld-linux-x86-64.so.2 (0x7efddcdcc000)
+#         libz.so.1 => /usr/local/bin/../lib/libz.so.1 (0x7efddcf55000)
+#         libc.so.6 => /lib64/ld-linux-x86-64.so.2 (0x7efddcdcc000)
+
+FROM quay.io/biocontainers/minimap2:2.17--hed695b0_3
+MAINTAINER Laurent Modolo
+ENV MINIMAP2_VERSION=2.17
+
+COPY --from=samtools /usr/local/bin/samtools /usr/local/bin/
+COPY --from=samtools /usr/local//lib/libncurses.so.6 /usr/local/lib/
+COPY --from=samtools /usr/local//lib/libtinfo.so.6 /usr/local/lib/
+
+# /usr/local/bin/minimap2
+# / # ldd /usr/local/bin/minimap2
+#         /lib64/ld-linux-x86-64.so.2 (0x7fe14f5a8000)
+#         libm.so.6 => /lib64/ld-linux-x86-64.so.2 (0x7fe14f5a8000)
+#         libz.so.1 => /usr/local/bin/../lib/libz.so.1 (0x7fe14f7c4000)
+#         libpthread.so.0 => /lib64/ld-linux-x86-64.so.2 (0x7fe14f5a8000)
+#         libc.so.6 => /lib64/ld-linux-x86-64.so.2 (0x7fe14f5a8000)
\ No newline at end of file

src/.docker_modules/minimap2/2.17/docker_init.sh

+#!/bin/sh
+docker pull lbmc/minimap2:2.17
+docker build src/.docker_modules/minimap2/2.17 -t 'lbmc/minimap2:2.17'
+docker push lbmc/minimap2:2.17

src/.docker_modules/multiqc/1.9/Dockerfile

+FROM debian:stretch
+MAINTAINER Laurent Modolo
+
+ENV MULTIQC_VERSION=1.9
+ENV PACKAGES build-essential \
+             python3-pip \
+             python3-setuptools \
+             python3-dev \
+             python3-wheel \
+             procps \
+             locales
+
+RUN apt-get update && \
+    apt-get install -y --no-install-recommends ${PACKAGES} && \
+    apt-get clean
+
+RUN locale-gen en_US.UTF-8
+ENV LC_ALL=en_US.utf-8
+ENV LANG=en_US.utf-8
+ENV LC_ALL=C.UTF-8
+ENV LANG=C.UTF-8
+
+
+RUN pip3 install multiqc==${MULTIQC_VERSION}
+

src/.docker_modules/multiqc/1.9/docker_init.sh

+#!/bin/sh
+docker pull lbmc/multiqc:1.9
+docker build src/.docker_modules/multiqc/1.9 -t 'lbmc/multiqc:1.9'
+docker push lbmc/multiqc:1.9

src/.docker_modules/pandoc/2.11/Dockerfile

+FROM alpine:3.13
+MAINTAINER Laurent Modolo
+
+ENV PANDOC_VERSION=2.11
+
+RUN echo "https://dl-cdn.alpinelinux.org/alpine/edge/testing" >> /etc/apk/repositories \
+  && apk update \
+  && apk add pandoc~=${PANDOC_VERSION} make

src/.docker_modules/pandoc/2.11/docker_init.sh

+#!/bin/sh
+docker pull lbmc/pandoc:2.11
+docker build src/.docker_modules/pandoc/2.11 -t 'lbmc/pandoc:2.11'
+docker push lbmc/pandoc:2.11

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

@@ -23,7 +23,9 @@ ENV R_DEPS g++ \
   libexecinfo-dev \
   file \
   ttf-linux-libertine \
-  git
+  git \
+  openssl \
+  bash
 
 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 \