merged file

Author: nalcala

.circleci/config.yml

@@ -0,0 +1,22 @@
+version: 2
+
+jobs:
+        build:
+                machine: true
+                steps:
+                        - checkout
+                        - run: cd ~ ; wget -qO- get.nextflow.io | bash ; chmod 755 nextflow ; sudo ln -s ~/nextflow /usr/local/bin/ ; sudo apt-get install graphviz
+                        - run: cd ~ && git clone https://github.com/iarcbioinfo/data_test.git
+                        - run: echo " docker.runOptions = '-u $(id -u):$(id -g)' " > ~/.nextflow/config
+                        - run: cd ~/project/ ; docker build -t iarcbioinfo/rnaseq-nf .
+                        - run: cd ; nextflow run ~/project/RNAseq.nf --help
+                        - run: cd ; nextflow run ~/project/RNAseq.nf -with-docker iarcbioinfo/rnaseq-nf --input_folder ~/data_test/BAM/ --output_folder BAM_realigned --ref_folder  ~/data_test/REF --gtf ~/data_test/REF/TP53_small.gtf --bed ~/data_test/BED/TP53_small.bed --cpu 2 --mem 4 -with-dag dag_STAR.png
+                        - run: cd ; nextflow run ~/project/RNAseq.nf -with-docker iarcbioinfo/rnaseq-nf --input_folder ~/data_test/BAM/ --output_folder BAM_realigned --ref_folder  ~/data_test/REF --gtf ~/data_test/REF/TP53_small.gtf --bed ~/data_test/BED/TP53_small.bed --cpu 2 --mem 4 -with-dag dag_STAR.html
+                        - run: cd ; nextflow run ~/project/RNAseq.nf -with-docker iarcbioinfo/rnaseq-nf --input_folder ~/data_test/BAM/ --output_folder BAM_realigned_sjtrim --ref_folder  ~/data_test/REF --gtf ~/data_test/REF/TP53_small.gtf --bed ~/data_test/BED/TP53_small.bed --cpu 2 --mem 4 --sjtrim --ref ~/data_test/REF/17_7572000-7591000.fasta -with-dag dag_STAR_sjtrim.png
+                        - run: cd ; nextflow run ~/project/RNAseq.nf -with-docker iarcbioinfo/rnaseq-nf --input_folder ~/data_test/BAM/ --output_folder BAM_realigned_sjtrim --ref_folder  ~/data_test/REF --gtf ~/data_test/REF/TP53_small.gtf --bed ~/data_test/BED/TP53_small.bed --cpu 2 --mem 4 --sjtrim --ref ~/data_test/REF/17_7572000-7591000.fasta -with-dag dag_STAR_sjtrim.html
+                        - run: cd ; nextflow run ~/project/RNAseq.nf -with-docker iarcbioinfo/rnaseq-nf --input_folder ~/data_test/BAM/ --output_folder BAM_realigned_sjtrim --ref_folder  ~/data_test/REF --gtf ~/data_test/REF/TP53_small.gtf --bed ~/data_test/BED/TP53_small.bed --cpu 2 --mem 4 --sjtrim --recalibration --snp_vcf ~/data_test/REF/dbsnp_138.17_7572000-7591000.vcf.gz --indel_vcf ~/data_test/REF/1000G_phase1.indels.17_7572000-7591000.sites.vcf.gz --ref ~/data_test/REF/17_7572000-7591000.fasta -with-dag dag_STAR_sjtrim_bqsr.png
+                        - run: cd ; nextflow run ~/project/RNAseq.nf -with-docker iarcbioinfo/rnaseq-nf --input_folder ~/data_test/BAM/ --output_folder BAM_realigned_sjtrim --ref_folder  ~/data_test/REF --gtf ~/data_test/REF/TP53_small.gtf --bed ~/data_test/BED/TP53_small.bed --cpu 2 --mem 4 --sjtrim --recalibration --snp_vcf ~/data_test/REF/dbsnp_138.17_7572000-7591000.vcf.gz --indel_vcf ~/data_test/REF/1000G_phase1.indels.17_7572000-7591000.sites.vcf.gz --ref ~/data_test/REF/17_7572000-7591000.fasta -with-dag dag_STAR_sjtrim_bqsr.html
+                        - run: cd ; cp ~/dag* ~/project/.
+                        - deploy:
+                                branch: [master, dev]
+                                command: chmod +x deploy.sh && ./deploy.sh

Dockerfile

@@ -1,125 +1,34 @@
-# Set the base image to Debian
-FROM debian:9.0
+################## BASE IMAGE #####################
+FROM nfcore/base
 
-# File Author / Maintainer
-MAINTAINER **nalcala** <**alcalan@fellows.iarc.fr**>
-
-RUN mkdir -p /var/cache/apt/archives/partial && \
-	touch /var/cache/apt/archives/lock && \
-	chmod 640 /var/cache/apt/archives/lock && \
-	apt-get update -y &&\
-	apt-get install -y gnupg2
-	
-RUN	apt-key adv --keyserver keyserver.ubuntu.com --recv-keys F76221572C52609D && \
-	apt-get clean && \
-	apt-get update -y && \
-
-
-  # Install dependences
-  DEBIAN_FRONTEND=noninteractive apt-get install --no-install-recommends -y \
-  make \
-  g++ \
-  perl \
-  default-jre \
-  zlib1g-dev \
-  libncurses5-dev \
-  libncurses5 \
-  git \
-  wget \
-  ca-certificates \
-  python-dev \
-  python-pip \
-  bzip2 \
-  libbz2-dev \
-  liblzma-dev \
-  libcurl4-openssl-dev \
-  libfreetype6-dev \
-  libpng-dev \
-  unzip \
-  r-base \
-  r-cran-ggplot2 \
-  r-cran-gplots \
-  r-cran-reshape && \
-  cp /usr/include/freetype2/*.h /usr/include/. && \
-
-  Rscript -e 'install.packages("gsalib",repos="http://cran.us.r-project.org")' && \
-  
-  # Install samtools specific version manually
-  wget https://github.com/samtools/samtools/releases/download/1.3.1/samtools-1.3.1.tar.bz2 && \
-  tar -jxf samtools-1.3.1.tar.bz2 && \
-  cd samtools-1.3.1 && \
-  make && \
-  make install && \
-  cd .. && \
-  rm -rf samtools-1.3.1 samtools-1.3.1.tar.bz2 && \
-
-  # Install FastQC
-  wget http://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v0.11.5.zip && \
-  unzip fastqc_v0.11.5.zip && \
-  chmod 755 FastQC/fastqc && \
-  cp -r FastQC /usr/local/bin/. && \
-  ln -s /usr/local/bin/FastQC/fastqc /usr/local/bin/ && \
-  rm -rf fastqc_v0.11.5.zip FastQC && \
-
-  # Install cutadapt
-  pip install cutadapt && \
 
-  # Install trim_galore
-  wget https://github.com/FelixKrueger/TrimGalore/archive/0.4.3.tar.gz && \
-  tar xvzf 0.4.3.tar.gz && \
-  mv TrimGalore-0.4.3/trim_galore /usr/bin && \
-  rm -rf TrimGalore-0.4.3 0.4.3.tar.gz && \
+################## METADATA #######################
 
-  # Install hisat2
+LABEL base_image="nfcore/base"
+LABEL version="1.0"
+LABEL software="rnaseq-nf"
+LABEL software.version="2.1"
+LABEL about.summary="Container image containing all requirements for rnaseq-nf"
+LABEL about.home="http://github.com/IARCbioinfo/RNAseq-nf"
+LABEL about.documentation="http://github.com/IARCbioinfo/RNAseq-nf/README.md"
+LABEL about.license_file="http://github.com/IARCbioinfo/RNAseq-nf/LICENSE.txt"
+LABEL about.license="GNU-3.0"
 
-  # Install htseq
-  pip install numpy && \
-  pip install setuptools && \
-  pip install HTSeq && \
-
-  # Install multiqc
-  pip install --upgrade --force-reinstall git+https://github.com/nalcala/MultiQC.git && \
-
-  # Install STAR specific version manually
-  wget https://github.com/alexdobin/STAR/archive/2.5.3a.tar.gz && \
-  tar -xzf 2.5.3a.tar.gz && \
-  cp STAR-2.5.3a/bin/Linux_x86_64_static/STAR /usr/local/bin/. && \
-  rm -rf 2.5.3a.tar.gz STAR-2.5.3a && \
-
-  # Install hisat2
-  wget ftp://ftp.ccb.jhu.edu/pub/infphilo/hisat2/downloads/hisat2-2.1.0-Linux_x86_64.zip && \
-  unzip hisat2-2.1.0-Linux_x86_64.zip && \
-  cp -r hisat2-2.1.0/. /usr/local/bin/. && \
-  rm -rf hisat2-2.1.0-Linux_x86_64.zip hisat2-2.1.0 && \
-
-  # Install RSeQC
-  pip install RSeQC && \
-
-  # Install samblaster specific version manually
-  wget https://github.com/GregoryFaust/samblaster/releases/download/v.0.1.24/samblaster-v.0.1.24.tar.gz && \
-  tar -xzf samblaster-v.0.1.24.tar.gz && \
-  cd samblaster-v.0.1.24 && \
-  make && \
-  cp samblaster /usr/local/bin/. && \
-  cd .. && \
-  rm -rf samblaster-v.0.1.24.tar.gz samblaster-v.0.1.24 && \
-
-  # Install sambamba specific version manually
-  wget https://github.com/lomereiter/sambamba/releases/download/v0.6.6/sambamba_v0.6.6_linux.tar.bz2 && \
-  tar -jxf sambamba_v0.6.6_linux.tar.bz2 && \
-  cp sambamba_v0.6.6 /usr/local/bin/sambamba && \
-  rm -rf sambamba_v0.6.6_linux.tar.bz2 && \
+################## MAINTAINER ######################
+MAINTAINER **nalcala** <**alcalan@fellows.iarc.fr**>
 
-  # Remove unnecessary dependences
-  DEBIAN_FRONTEND=noninteractive apt-get remove -y \
-  make \
-  g++ \
-  wget \
-  bzip2 \
-  git \
-  zlib1g-dev \
-  libncurses5-dev && \
 
-  # Clean
-  DEBIAN_FRONTEND=noninteractive apt-get autoremove -y && \
-  apt-get clean
+#RUN mkdir -p /var/cache/apt/archives/partial && \
+#	touch /var/cache/apt/archives/lock && \
+#	chmod 640 /var/cache/apt/archives/lock && \
+#	apt-get update -y &&\
+#	apt-get install -y gnupg2
+#	RUN	apt-key adv --keyserver keyserver.ubuntu.com --recv-keys F76221572C52609D && \
+#	apt-get clean && \
+#	apt-get update -y && \
+
+################## INSTALLATION ######################
+COPY environment.yml /
+RUN conda env create -n rnaseq-nf -f /environment.yml && conda clean -a
+ENV PATH /opt/conda/envs/rnaseq-nf/bin:$PATH
+#RUN echo ". /opt/conda/etc/profile.d/conda.sh"  >> ~/.bashrc