onuryukselen/piPipes_singularity:latest
$ singularity pull shub://onuryukselen/piPipes_singularity:latest
Singularity Recipe
BootStrap: shub
From: shub://onuryukselen/singularity
%labels
AUTHOR Onur Yukselen <onur.yukselen@umassmed.edu>
Version v1.0
%environment
PATH=$PATH:/Software/piPipes/bin:/Software/brew/bin:/Software/sratoolkit.2.9.0-ubuntu64/bin
export PATH
%apprun R
exec R "$@"
%apprun Rscript
exec Rscript "$@"
%runscript
exec R "$@"
%post
############
### piPipes
############
mkdir -p /Software
cd /Software
chmod 777 /Software
## clone piPipes_singularity
git clone https://github.com/onuryukselen/piPipes_singularity
## copy forked piPipes
git clone https://github.com/onuryukselen/piPipes.git /Software/piPipes
cd /Software/piPipes
ln -s $PWD/piPipes /usr/local/bin/piPipes
ln -s $PWD/piPipes_debug /usr/local/bin/piPipes_debug
#################
### Genome data
#################
mkdir -p /Software/piPipes/common/hg19/rmsk
cd /Software/piPipes_singularity/genome_data
cat rmsk.txt.gz* > rmsk.txt.gz
rsync -vazu /Software/piPipes_singularity/genome_data/rmsk.txt.gz /Software/piPipes/common/hg19/rmsk/.
# wget --timestamping 'ftp://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/rmsk.txt.gz' -O rmsk.txt.gz
## commented out related download scripts from the piPipes/bin/piPipes_install_genomes.sh
sed -i 's/rsync -a -P/#rsync -a -P/g' /Software/piPipes/bin/piPipes_install_genomes.sh
mkdir -p /Software/piPipes/common/dm3
rsync -vazu /Software/piPipes_singularity/genome_data/chrU.fa.gz /Software/piPipes/common/dm3/.
# wget ftp://hgdownload.cse.ucsc.edu/goldenPath/dm3/chromosomes/chrU.fa.gz
#### 1. 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-3.4.3.tar.gz
tar xvf R-3.4.3.tar.gz
cd /tmp/R-3.4.3
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
pip install fastcluster
echo install.packages\(\"fastcluster\"\, dependencies = TRUE, repos\=\'https://cloud.r-project.org\'\, Ncpus\=${NPROCS}\) | R --slave
echo install.packages\(\"stringi\"\, dependencies = TRUE, repos\=\'https://cloud.r-project.org\'\, Ncpus\=${NPROCS}\) | R --slave
echo install.packages\(\"RColorBrewer\"\, dependencies = TRUE, repos\=\'https://cloud.r-project.org\'\, Ncpus\=${NPROCS}\) | R --slave
echo install.packages\(\"ggplot2\"\, dependencies = TRUE, repos\=\'https://cloud.r-project.org\'\, Ncpus\=${NPROCS}\) | R --slave
echo install.packages\(\"grid\"\, dependencies = TRUE, repos\=\'https://cloud.r-project.org\'\, Ncpus\=${NPROCS}\) | R --slave
echo install.packages\(\"ggthemes\"\, dependencies = TRUE, repos\=\'https://cloud.r-project.org/\'\, Ncpus\=${NPROCS}\) | R --slave
echo install.packages\(\"gplots\"\, dependencies = TRUE, repos\=\'https://cloud.r-project.org/\'\, Ncpus\=${NPROCS}\) | R --slave
echo install.packages\(\"parallel\"\, dependencies = TRUE, repos\=\'https://cloud.r-project.org/\'\, Ncpus\=${NPROCS}\) | R --slave
echo install.packages\(\"scales\"\, dependencies = TRUE, repos\=\'https://cloud.r-project.org/\'\, Ncpus\=${NPROCS}\) | R --slave
echo install.packages\(\"reshape\"\, dependencies = TRUE, repos\=\'https://cloud.r-project.org/\'\, Ncpus\=${NPROCS}\) | R --slave
echo install.packages\(\"gridExtra\"\, dependencies = TRUE, repos\=\'https://cloud.r-project.org/\'\, Ncpus\=${NPROCS}\) | R --slave
echo install.packages\(\"gdata\"\, dependencies = TRUE, repos\=\'https://cloud.r-project.org/\'\, Ncpus\=${NPROCS}\) | R --slave
echo install.packages\(\"labeling\"\, dependencies = TRUE, repos\=\'https://cloud.r-project.org/\'\, Ncpus\=${NPROCS}\) | R --slave
echo install.packages\(\"RCircos\"\, dependencies = TRUE, repos\=\'https://cloud.r-project.org/\'\, Ncpus\=${NPROCS}\) | R --slave
echo install.packages\(\"reshape2\"\, dependencies = TRUE, repos\=\'https://cloud.r-project.org/\'\, Ncpus\=${NPROCS}\) | R --slave
yes | apt-get install libmariadb-client-lgpl-dev
R --slave -e "source('https://bioconductor.org/biocLite.R'); biocLite()"
R --slave -e "source('https://bioconductor.org/biocLite.R'); biocLite('cummeRbund')"
# 2. HTSeq-count
pip install HTSeq
which htseq-count
# 3. MACS2
pip install macs2
which macs2
# 4. Perl Module Statistics::Descriptive;
yes | cpan Statistics::Descriptive
perl -MStatistics::Descriptive -e "print \"Installed.\\n\";"
# 5. Install Gawk with Linuxbrew
locale-gen "en_US.UTF-8"
dpkg-reconfigure locales
export LANGUAGE="en_US.UTF-8"
echo 'LANGUAGE="en_US.UTF-8"' >> /etc/default/locale
echo 'LC_ALL="en_US.UTF-8"' >> /etc/default/locale
cd /Software
chmod 777 /tmp
chmod +t /tmp
apt-get install -y apt-transport-https build-essential libsm6 libxrender1 libfontconfig1 ruby
useradd -m singularity
su -c 'cd /Software && git clone https://github.com/Linuxbrew/brew.git /Software/brew' singularity
su -c '/Software/brew/bin/brew install gawk' singularity
ln -s /Software/brew/bin/gawk /Software/piPipes/bin/awk
##6. NCBI SRA and cutadapt
cd /Software
#curl -O https://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/2.9.0/sratoolkit.2.9.0-ubuntu64.tar.gz
#tar xvf sratoolkit.2.9.0-ubuntu64.tar.gz
pip install cutadapt
##7. RSeQC
pip install RSeQC
Collection
- Name: onuryukselen/piPipes_singularity
- License: None
View on Datalad
Metrics
key | value |
---|---|
id | /containers/onuryukselen-piPipes_singularity-latest |
collection name | onuryukselen/piPipes_singularity |
branch | master |
tag | latest |
commit | c965c33604043f354e398d00247e18c16c767342 |
version (container hash) | aac9c0ce0162c500f61ced2461d2b6fd |
build date | 2018-09-20T19:10:30.884Z |
size (MB) | 7142 |
size (bytes) | 3676807199 |
SIF | Download URL (please use pull with shub://) |
Datalad URL | View on Datalad |
Singularity Recipe | Singularity Recipe on Datalad |
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