Pseudo-PR: First code review

.travis.yml

@@ -11,9 +11,9 @@ before_install:
   # PRs to master are only ok if coming from dev branch
   - '[ $TRAVIS_PULL_REQUEST = "false" ] || [ $TRAVIS_BRANCH != "master" ] || ([ $TRAVIS_PULL_REQUEST_SLUG = $TRAVIS_REPO_SLUG ] && [ $TRAVIS_PULL_REQUEST_BRANCH = "dev" ])'
   # Pull the docker image first so the test doesn't wait for this
-  - docker pull nfcore/lncpipe
+  - docker pull nfcore/lncpipe:dev
   # Fake the tag locally so that the pipeline runs properly
-  - docker tag nfcore/lncpipe nfcore/lncpipe:latest
+  - docker tag nfcore/lncpipe:dev nfcore/lncpipe:dev
 
 install:
   # Install Nextflow
@@ -27,10 +27,14 @@ install:
 
 env:
   - NXF_VER='0.32.0' # Specify a minimum NF version that should be tested and work
-  - NXF_VER='' # Plus: get the latest NF version and check that it works
+  # - NXF_VER='' # Plus: get the latest NF version and check that it works
 
 script:
   # Lint the pipeline code
   - nf-core lint ${TRAVIS_BUILD_DIR}
+  # download the test data 
+  - wget http://cancerbio.info/pub/lncpipe/testdata.tar.gz
+  - tar -xvzf testdata.tar.gz
+  - cd testdata
   # Run the pipeline with the test profile
   - nextflow run ${TRAVIS_BUILD_DIR} -profile test,docker

CHANGELOG.md

@@ -2,3 +2,5 @@
 
 ## v1.0dev - <date>
 Initial release of nf-core/lncpipe, created with the [nf-core](http://nf-co.re/) template.
+  * add rename the process name that solved the duplicated processed error by update Nextflow version 
+  * fix typos.

Dockerfile

@@ -1,135 +1,10 @@
-FROM ubuntu LABEL authors="[email protected],[email protected]" \
-	description="Docker image containing all requirements for LncPipe"
-# Update OS # DEBIAN_FRONTEND=noninteractive is for relieving the dependence of readline perl library by prohibiting interactive frontend # default-jre is for NextFlow (run groovy) # gcc and g++ is for compiling CPAT, PLEK as well as some R packages # gfortran is for compiling R package hexbin (required by plotly) # make is for executing makefiles for several tools # Cython provides C header files like Python.h for CPAT compiling # DO NOT use pip for installing Cython, which will cause missing .h files # zlib1g-dev is for CPAT compiling dependency # libncurses5-dev for samtools (may be used later) # libssl-dev is for R package openssl # libcurl4-openssl-dev is for R package curl # perl brings us FindBin module, which is required by FastQC # ca-certificates is required by aria2 RUN export DEBIAN_FRONTEND=noninteractive && \
-	apt-get -qq update && \
-	apt-get -qq install -y --no-install-recommends \
-	default-jre \
-	unzip \
-	pbzip2 \
-	pigz \
-	aria2 \
-	gcc \
-	g++ \
-	gfortran \
-	make \
-	python-dev \
-	cython \
-	zlib1g-dev \
-	libssl-dev \
-	libcurl4-openssl-dev \
-	perl \
-	ca-certificates
-# Install latest pip WITHOUT wheel and setuptools # DO NOT use apt-get python-pip in ubuntu for preventing from complicated related tools and libraries # Setuptools is required by CPAT during its installation RUN aria2c https://bootstrap.pypa.io/get-pip.py -q -o /opt/get-pip.py && \
-	python /opt/get-pip.py --no-wheel && \
-	rm /opt/get-pip.py
-# Install required python packages	RUN pip -qqq install numpy
-# Install nextflow RUN aria2c https://github.com/nextflow-io/nextflow/releases/download/v0.25.6/nextflow -q -o /opt/nextflow && \
-	chmod 777 /opt/nextflow && \
-	ln -s /opt/nextflow /usr/local/bin
-# Install STAR RUN aria2c https://raw.githubusercontent.com/alexdobin/STAR/master/bin/Linux_x86_64/STAR -q -o /opt/STAR && \
-	chmod 777 /opt/STAR && \
-	ln -s /opt/STAR /usr/local/bin
-# Install cufflinks	RUN aria2c https://github.com/bioinformatist/cufflinks/releases/download/v2.2.1/cufflinks-2.2.1.Linux_x86_64.tar.gz -q -o /opt/cufflinks-2.2.1.Linux_x86_64.tar.gz && \
-	tar xf /opt/cufflinks-2.2.1.Linux_x86_64.tar.gz --use-compress-prog=pigz -C /opt/ && \
-	rm /opt/cufflinks-2.2.1.Linux_x86_64/README && \
-	ln -s /opt/cufflinks-2.2.1.Linux_x86_64/* /usr/local/bin/ && \
-	rm /opt/cufflinks-2.2.1.Linux_x86_64.tar.gz
-# Install PLEK # Remove documents, demo files, source files, object files and R scripts # dos2unix in perl one-liner: remove BOM head and deal with \r problem RUN aria2c https://ncu.dl.sourceforge.net/project/plek/PLEK.1.2.tar.gz -q -o /opt/PLEK.1.2.tar.gz && \
-	tar xf /opt/PLEK.1.2.tar.gz --use-compress-prog=pigz -C /opt/ && \
-	cd /opt/PLEK.1.2/ && \
-	python PLEK_setup.py || : && \
-	rm *.pdf *.txt *.h *.c *.fa *.cpp *.o *.R *.doc PLEK_setup.py && \
-	chmod 777 * && \
-	perl -CD -pi -e'tr/\x{feff}//d && s/[\r\n]+/\n/' *.py && \
-	ln -s /opt/PLEK.1.2/PLEK* /usr/local/bin/ && \
-	ln -s /opt/PLEK.1.2/svm* /usr/local/bin/ && \
-	rm /opt/PLEK.1.2.tar.gz
-# Use bash instead for shopt only works with bash SHELL ["/bin/bash", "-c"] # Install CNCI # Enable the extglob shell option # Parentheses and the pipe symbol should be escaped RUN aria2c https://codeload.github.com/www-bioinfo-org/CNCI/zip/master -q -o /opt/CNCI-master.zip && \
-	unzip -qq /opt/CNCI-master.zip -d /opt/ && \
-	rm /opt/CNCI-master.zip && \
-	unzip -qq /opt/CNCI-master/libsvm-3.0.zip -d /opt/CNCI-master/ && \
-	rm /opt/CNCI-master/libsvm-3.0.zip && \
-	cd /opt/CNCI-master/libsvm-3.0 && \
-	make > /dev/null 2>&1 && \
-	shopt -s extglob && \
-	rm -rfv !\("svm-predict"\|"svm-scale"\) && \
-	cd .. && \
-	rm draw_class_pie.R LICENSE README.md && \
-	chmod -R 777 * && \
-	ln -s /opt/CNCI-master/*.py /usr/local/bin/
-# Install CPAT # DO NOT use absolute path when setup, and changing directory is necessary. Python interpreter will check current directory for dependencies # Remove line 21 from setup.py: distribute_setup::use_setuptools() for: https://stackoverflow.com/questions/46967488/getting-error-403-while-installing-package-with-pip/46979531#46979531 RUN aria2c https://nchc.dl.sourceforge.net/project/rna-cpat/v1.2.3/CPAT-1.2.3.tar.gz -q -o /opt/CPAT-1.2.3.tar.gz && \
-	tar xf /opt/CPAT-1.2.3.tar.gz --use-compress-prog=pigz -C /opt/ && \
-	cd /opt/CPAT-1.2.3/ && \
-	perl -i -lanE'say unless $. == 21' setup.py && \
-	python setup.py install && \
-	rm -rfv !"dat" && \
-	chmod -R 777 *
-# Set back to default shell SHELL ["/bin/sh", "-c"] # Install StringTie RUN aria2c http://ccb.jhu.edu/software/stringtie/dl/stringtie-1.3.3b.Linux_x86_64.tar.gz -q -o /opt/stringtie-1.3.3b.Linux_x86_64.tar.gz && \
-	tar xf /opt/stringtie-1.3.3b.Linux_x86_64.tar.gz --use-compress-prog=pigz -C /opt/ && \
-	rm /opt/stringtie-1.3.3b.Linux_x86_64/README && \
-	ln -s /opt/stringtie-1.3.3b.Linux_x86_64/stringtie /usr/local/bin/stringtie && \
-	rm /opt/stringtie-1.3.3b.Linux_x86_64.tar.gz
-# Install Hisat2	RUN aria2c ftp://ftp.ccb.jhu.edu/pub/infphilo/hisat2/downloads/hisat2-2.1.0-Linux_x86_64.zip -q -o /opt/hisat2-2.1.0-Linux_x86_64.zip && \
-	unzip -qq /opt/hisat2-2.1.0-Linux_x86_64.zip -d /opt/ && \
-	rm /opt/hisat2-2.1.0-Linux_x86_64.zip && \
-	cd /opt/hisat2-2.1.0 && \
-	rm -rf doc example *debug MANUAL* NEWS TUTORIAL && \
-	ln -s /opt/hisat2-2.1.0/hisat2* /usr/local/bin/ && \
-	ln -sf /opt/hisat2-2.1.0/*.py /usr/local/bin/
-# Install Kallisto # There's some trashy pointers in Kallisto tarball archieve RUN aria2c https://github.com/pachterlab/kallisto/releases/download/v0.43.1/kallisto_linux-v0.43.1.tar.gz -q -o  /opt/kallisto_linux-v0.43.1.tar.gz && \
-	tar xf /opt/kallisto_linux-v0.43.1.tar.gz --use-compress-prog=pigz -C /opt/ && \
-	cd /opt && \
-	rm ._* kallisto_linux-v0.43.1.tar.gz && \
-	cd kallisto_linux-v0.43.1 && \
-	rm -rf ._* 	README.md test && \
-	ln -s /opt/kallisto_linux-v0.43.1/kallisto /usr/local/bin/
-# Install Microsoft-R-Open with MKL, you must use MRO v3.4.2 or later # For more, see this GitHub issue comment: https://github.com/Microsoft/microsoft-r-open/issues/26#issuecomment-340276347 RUN aria2c https://mran.blob.core.windows.net/install/mro/3.4.2/microsoft-r-open-3.4.2.tar.gz -q -o /opt/microsoft-r-open-3.4.2.tar.gz && \
-	tar xf /opt/microsoft-r-open-3.4.2.tar.gz --use-compress-prog=pigz -C /opt/ && \
-	cd /opt/microsoft-r-open && \
-	./install.sh -as && \
-	rm -rf /opt/microsoft-r*
-# Cleaning up the apt cache helps keep the image size down (must be placed here, since MRO installation need the cache) RUN rm -rf /var/lib/apt/lists/*
-# Install cpanminus # RUN aria2c https://cpanmin.us/ -q -o /opt/cpanm && \ #	chmod +x /opt/cpanm && \ #	ln -s /opt/cpanm /usr/local/bin/ # Install Perl module FindBin, which is required by FastQC # RUN cpanm FindBin # Install FastQC RUN aria2c https://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v0.11.5.zip -q -o /opt/fastqc_v0.11.5.zip && \
-	unzip -qq /opt/fastqc_v0.11.5.zip -d /opt/ && \
-	rm /opt/fastqc_v0.11.5.zip && \
-	cd /opt/FastQC && \
-	shopt -s extglob && \
-	rm -rfv !\("fastqc"\|*.jar\) && \
-	chmod 777 * && \
-	ln -s /opt/FastQC/fastqc /usr/local/bin/
-# Install Pandoc (required by reporter) RUN aria2c https://github.com/jgm/pandoc/releases/download/1.19.2.1/pandoc-1.19.2.1-1-amd64.deb -q -o /opt/pandoc-1.19.2.1-1-amd64.deb && \
-	dpkg -i /opt/pandoc-1.19.2.1-1-amd64.deb && \
-	rm /opt/pandoc-1.19.2.1-1-amd64.deb
-# Install PyPy RUN aria2c https://bitbucket.org/squeaky/portable-pypy/downloads/pypy-5.9-linux_x86_64-portable.tar.bz2 -q -o /opt/pypy-5.9-linux_x86_64-portable.tar.bz2 && \
-	tar xf /opt/pypy-5.9-linux_x86_64-portable.tar.bz2 --use-compress-prog=pbzip2 -C /opt/ && \
-	rm /opt/pypy-5.9-linux_x86_64-portable/README.rst /opt/pypy-5.9-linux_x86_64-portable.tar.bz2 && \
-	ln -s /opt/pypy-5.9-linux_x86_64-portable/bin/pypy /usr/local/bin/
-# Install BEDOPS RUN aria2c https://github.com/bedops/bedops/releases/download/v2.4.29/bedops_linux_x86_64-v2.4.29.tar.bz2 -q -o /opt/bedops_linux_x86_64-v2.4.29.tar.bz2 && \
-	tar xf /opt/bedops_linux_x86_64-v2.4.29.tar.bz2 --use-compress-prog=pbzip2 -C /opt/ && \
-	ln -s /opt/bin/* /usr/local/bin/ && \
-	rm /opt/bedops_linux_x86_64-v2.4.29.tar.bz2
-# Install AfterQC # Use PyPy to run AfterQC as default RUN aria2c https://github.com/OpenGene/AfterQC/archive/v0.9.7.tar.gz -q -o /opt/AfterQC-0.9.7.tar.gz && \
-	tar xf /opt/AfterQC-0.9.7.tar.gz --use-compress-prog=pigz -C /opt/ && \
-	cd /opt/AfterQC-0.9.7 && \
-	make && \
-	perl -i -lape's/python/pypy/ if $. == 1' after.py && \
-	rm -rf Dockerfile Makefile README.md testdata report_sample && \
-	rm editdistance/*.cpp editdistance/*.h && \
-	ln -s /opt/AfterQC-0.9.7/*.py /usr/local/bin/ && \
-	rm /opt/AfterQC-0.9.7.tar.gz
-# Install R package LncPipeReporter（via GitHub) RUN Rscript -e "source('http://bioconductor.org/biocLite.R'); install.packages(c('curl', 'httr')); install.packages('devtools'); devtools::install_github('bioinformatist/LncPipeReporter')"
-# Install GffCompare RUN aria2c https://github.com/gpertea/gffcompare/archive/master.zip -q -o /opt/gffcompare-master.zip && \
-	aria2c https://github.com/gpertea/gclib/archive/master.zip -q -o /opt/gclib-master.zip && \
-	unzip -qq /opt/gffcompare-master.zip -d /opt/ && \
-	unzip -qq /opt/gclib-master.zip -d /opt/ && \
-	rm /opt/gffcompare-master.zip /opt/gclib-master.zip && \
-	mv /opt/gclib-master /opt/gclib && \
-	cd /opt/gffcompare-master && \
-	make release && \
-	rm Makefile README.md gtf_tracking.h *.o *.cpp *.sh && \
-	ln -s /opt/gffcompare-master/gffcompare /usr/local/bin/
-# Install sambamba RUN aria2c https://github.com/biod/sambamba/releases/download/v0.6.7/sambamba_v0.6.7_linux.tar.bz2 -q -o /opt/sambamba_v0.6.7_linux.tar.bz2 && \
-	tar xf /opt/sambamba_v0.6.7_linux.tar.bz2 --use-compress-prog=pbzip2 -C /opt/ && \
-	ln -s /opt/sambamba /usr/local/bin/ && \
-	rm /opt/sambamba_v0.6.7_linux.tar.bz2
+
+FROM nfcore/base
+LABEL maintainer="[email protected]"
+LABEL authors="[email protected]" \
+    description="Docker image containing all requirements for the nfcore/lncpipe pipeline"
+
+COPY environment.yml /
+RUN conda env create -f /environment.yml && conda clean -a
+ENV PATH /opt/conda/envs/nf-core-lncpipe-1.0dev/bin:$PATH