botaoliuphd/singularitysc:latest
$ singularity pull shub://botaoliuphd/singularitysc:latest
Singularity Recipe
BootStrap: docker
From: ubuntu:16.04
%labels
AUTHOR Onur Yukselen <onur.yukselen@umassmed.edu>
Version v1.0
Botao Liu added splicing packages
%environment
PATH=$PATH:/bin:/sbin:/usr/local/bin/dolphin-bin:/usr/bin/bcl2fastq2-v2.17.1.14/bin:/usr/local/bin/dolphin-bin/tophat-2.0.14.Linux_x86_64:/usr/local/bin/julia/bin:/usr/local/bin/sratoolkit/bin:/home/botaoliu/.cargo/bin:/usr/local/bin/matt
export PATH
%post
apt-get update
apt-get -y upgrade
apt-get dist-upgrade
apt-get -y install unzip libsqlite3-dev libbz2-dev libssl-dev python python-dev \
python-pip git libxml2-dev software-properties-common wget tree vim \
subversion g++ gcc gfortran libcurl4-openssl-dev curl zlib1g-dev build-essential libffi-dev python-lzo
###################
## Python modules
###################
export LC_ALL=C
pip install --upgrade pip==9.0.3
pip install pysam
pip install numpy scipy biopython
###################
## JAVA
###################
echo oracle-java8-installer shared/accepted-oracle-license-v1-1 select true | debconf-set-selections && \
add-apt-repository -y ppa:webupd8team/java && \
apt-get update && \
apt-get install -y oracle-java8-installer && \
rm -rf /var/lib/apt/lists/* && \
rm -rf /var/cache/oracle-jdk8-installer
apt-get -y autoremove
###################
## NEXTFLOW
###################
export JAVA_HOME=/usr/lib/jvm/java-8-oracle
mkdir /data && cd /data
curl -s https://get.nextflow.io | bash
mv /data/nextflow /usr/bin/.
mkdir /project /nl /share /.nextflow
#################
## Dolphin-bin ##
#################
export GITUSER=UMMS-Biocore
git clone https://github.com/${GITUSER}/dolphin-bin /usr/local/bin/dolphin-bin
pip install -U boto
pip install --upgrade pip
pip install RSeQC
cd /usr/local/bin/dolphin-bin/MACS2 && python setup.py install
make -C /usr/local/bin/dolphin-bin/RSEM-1.2.29
###tophat-2.0.14
cd /tmp
wget https://ccb.jhu.edu/software/tophat/downloads/tophat-2.0.14.Linux_x86_64.tar.gz
tar -xvzf tophat-2.0.14.Linux_x86_64.tar.gz
rm -rf /usr/local/bin/dolphin-bin/tophat2_2.0.12
mv tophat-2.0.14.Linux_x86_64/ /usr/local/bin/dolphin-bin/.
###bowtie
# wget -N --no-check-certificate https://sourceforge.net/projects/bowtie-bio/files/bowtie2/2.1.0/bowtie2-2.1.0-linux-x86_64.zip
# unzip bowtie2-2.1.0-linux-x86_64.zip
# rm -rf /usr/local/bin/dolphin-bin/bowtie2*
# mv bowtie2-2.1.0/bowtie2* /usr/local/bin/dolphin-bin/.
#################
## BCL2FASTQ v2.17.1.14
#################
add-apt-repository universe
apt-get update
apt-get -y install zip unzip zlibc libc6 libboost-all-dev cmake
export TMP=/tmp/singularity/programs
export SOURCE=${TMP}/bcl2fastq
export BUILD=${TMP}/bcl2fastq2-v2.17.1.14-build
export INSTALL_DIR=/usr/bin/bcl2fastq2-v2.17.1.14
git clone https://github.com/onuryukselen/singularity /tmp/singularity
cd ${TMP}
# wget ftp://webdata2:webdata2@ussd-ftp.illumina.com/downloads/Software/bcl2fastq/bcl2fastq2-v2.17.1.14.tar.zip
unzip bcl2fastq2-v2.17.1.14.tar.zip
tar -xvzf bcl2fastq2-v2.17.1.14.tar.gz
mkdir ${BUILD}
cd ${BUILD}
sed -i 's@HINTS ENV C_INCLUDE_PATH ENV CPATH ENV CPLUS_INCLUDE_PATH@HINTS ENV C_INCLUDE_PATH ENV CPATH ENV CPLUS_INCLUDE_PATH /usr/include/x86_64-linux-gnu/@g' ${SOURCE}/src/cmake/macros.cmake
sed -i 's@boost::property_tree::xml_writer_make_settings@boost::property_tree::xml_writer_make_settings<ptree::key_type>@g' ${SOURCE}/src/cxx/lib/io/Xml.cpp
${SOURCE}/src/configure --prefix=${INSTALL_DIR}
make
make install
#################
## UMI-TOOLS
#################
pip install umi_tools
#################
## R ##
#################
NPROCS=`awk '/^processor/ {s+=1}; END{print s}' /proc/cpuinfo`
cd /tmp
wget http://security.ubuntu.com/ubuntu/pool/main/i/icu/libicu52_52.1-3ubuntu0.8_amd64.deb
dpkg -i libicu52_52.1-3ubuntu0.8_amd64.deb
wget https://cran.rstudio.com/src/base/R-3/R-3.5.1.tar.gz
tar xvf R-3.5.1.tar.gz
cd /tmp/R-3.5.1
apt-get update
apt-get install -y libblas3 libblas-dev liblapack-dev liblapack3 ghostscript libicu52
apt-get install -y libgmp10 libgmp-dev
apt-get install -y fort77 aptitude
aptitude install -y xorg-dev
aptitude install -y libreadline-dev
apt install -y libpcre3-dev liblzma-dev
apt-get update
apt-get install -y bioperl
apt-get update
./configure --enable-R-static-lib --with-blas --with-lapack --enable-R-shlib=yes
echo "Will use make with $NPROCS cores."
make -j${NPROCS}
make install
## The following package are added by Botao ##
#################
## whippet ##
#################
cd /tmp
wget https://julialang-s3.julialang.org/bin/linux/x64/0.6/julia-0.6.4-linux-x86_64.tar.gz
tar -xvzf julia-0.6.4-linux-x86_64.tar.gz
mkdir /usr/local/bin/julia
mv julia-9d11f62bcb/* /usr/local/bin/julia
# Haven't figure out how to install julia package from command line.
#################
## dexseq ##
#################
apt-get install -y build-essential python-matplotlib python-htseq
pip install 'HTSeq==0.11.0'
#################
## majiq 2.0 ##
#################
cd /tmp
wget "https://github.com/samtools/htslib/releases/download/1.9/htslib-1.9.tar.bz2"
tar -vxjf htslib-1.9.tar.bz2
cd htslib-1.9
make
make install
apt-get install -y python3-dev python3-pip
pip3 install virtualenv awscli
pip3 install pip
pip3 install wheel setuptools
pip3 install cython numpy GitPython
pip3 install git+https://bitbucket.org/biociphers/majiq_stable.git#egg=majiq
#################
## sratoolkit ###
#################
cd /tmp
wget "https://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/2.9.2/sratoolkit.2.9.2-ubuntu64.tar.gz"
tar -xvzf sratoolkit.2.9.2-ubuntu64.tar.gz
mkdir /usr/local/bin/sratoolkit
mv sratoolkit.2.9.2-ubuntu64/* /usr/local/bin/sratoolkit
#################
##### rMATS #####
#################
cd /tmp
wget "http://mirrors.kernel.org/ubuntu/pool/main/g/gsl/libgsl0ldbl_1.16+dfsg-1ubuntu1_amd64.deb"
dpkg -i libgsl0ldbl_1.16+dfsg-1ubuntu1_amd64.deb
#################
##### Matt #####
#################
cd /usr/local/bin
mkdir matt
cd matt
wget matt.crg.eu/matt.tar.gz
tar -xvzf matt.tar.gz
./INSTALL
Collection
- Name: botaoliuphd/singularitysc
- License: None
View on Datalad
Metrics
key | value |
---|---|
id | /containers/botaoliuphd-singularitysc-latest |
collection name | botaoliuphd/singularitysc |
branch | master |
tag | latest |
commit | 1aaebdb4a22d8985dd5062f2fdf9af897a782669 |
version (container hash) | e1dd6de3633e1fb5f035577f08a503cb |
build date | 2019-04-03T00:18:34.678Z |
size (MB) | 6319 |
size (bytes) | 2103107615 |
SIF | Download URL (please use pull with shub://) |
Datalad URL | View on Datalad |
Singularity Recipe | Singularity Recipe on Datalad |
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