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Singularity.AmpSeq
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Singularity.AmpSeq
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Bootstrap: debootstrap
OSVersion: bionic
MirrorURL: http://us.archive.ubuntu.com/ubuntu/
%labels
Maintainer Jonathan Fresnedo
AmpSeq Sigularity Container
%post
apt update
apt install -y apt-transport-https software-properties-common
apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9
add-apt-repository 'deb https://cloud.r-project.org/bin/linux/ubuntu bionic-cran35/'
apt update
apt install -y r-base
apt update
apt-add-repository universe
apt update
apt install -y git wget perl openjdk-8-jdk build-essential libtool libncurses5-dev libgtextutils-dev automake libbz2-dev liblzma-dev zlib1g-dev autoconf autogen cpanminus libgd-graph-perl libbio-samtools-perl git-lfs g++ cmake git-all pkg-config sed gnuplot-nox m4 libevent-dev gettext yaggo nano
export LC_ALL=C.UTF-8
export LANG=C.UTF-8
echo 'export LC_ALL=C.UTF-8' >> "$SINGULARITY_ENVIRONMENT"
echo 'export LANG=C.UTF-8' >> "$SINGULARITY_ENVIRONMENT"
echo "export PATH=/usr/local/bin:$PATH" >> "$SINGULARITY_ENVIRONMENT"
# Installing individual packages
make /home
cd home
git clone https://github.com/samtools/htslib.git
cd htslib
make
make install
cd ..
git clone https://github.com/samtools/samtools.git
cd samtools
make
make install
cd ..
git clone https://github.com/samtools/bcftools.git
cd bcftools
make
make install
cd ..
cpanm PerlIO::gzip
cpanm GD::Graph
cpanm GD::Graph::bars
cpanm Bio::SeqIO
cpanm Getopt::Std
git clone https://github.com/lh3/bwa.git
cd bwa
make
cp bwa /usr/local/bin
cd ..
git clone https://github.com/broadinstitute/picard.git
cd picard
./gradlew shadowJar
cd ..
cp -r picard /usr/local/bin
rm -r picard
git clone https://github.com/broadinstitute/gatk.git
cd gatk
./gradlew bundle
cd ..
cp -r gatk /usr/local/bin
rm -r gatk
wget http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/Trimmomatic-0.38.zip
unzip Trimmomatic-0.38.zip
cp -r Trimmomatic-0.38 /usr/local/bin
rm Trimmomatic-0.38.zip
rm -r Trimmomatic-0.38/
wget http://hannonlab.cshl.edu/fastx_toolkit/fastx_toolkit_0.0.13_binaries_Linux_2.6_amd64.tar.bz2
tar -xvjf fastx_toolkit_0.0.13_binaries_Linux_2.6_amd64.tar.bz2
cp bin/* /usr/local/bin
rm -r bin
rm fastx_toolkit_0.0.13_binaries_Linux_2.6_amd64.tar.bz2
wget ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast%2B/2.8.1/ncbi-blast-2.8.1%2B-x64-linux.tar.gz
tar -xvzf ncbi-blast-2.8.1+-x64-linux.tar.gz
cp ncbi-blast-2.8.1+/bin/* /usr/local/bin
rm -r ncbi-blast-2.8.1+
rm ncbi-blast-2.8.1+-x64-linux.tar.gz
wget https://sourceforge.net/projects/flashpage/files/FLASH-1.2.11.tar.gz
tar -xvzf FLASH-1.2.11.tar.gz
cd FLASH-1.2.11
make
cp flash /usr/local/bin
cd ..
rm FLASH-1.2.11.tar.gz
rm -r FLASH-1.2.11
wget http://www.clustal.org/download/current/clustalw-2.1.tar.gz
tar -xvzf clustalw-2.1.tar.gz
cd clustalw-2.1
./configure
make
make install
cd ..
rm -r clustalw-2.1
rm clustalw-2.1.tar.gz
wget http://www.clustal.org/omega/clustalo-1.2.4-Ubuntu-x86_64
chmod u+x clustalo-1.2.4-Ubuntu-x86_64
cp clustalo-1.2.4-Ubuntu-x86_64 /usr/local/bin/clustalo
rm clustalo-1.2.4-Ubuntu-x86_64
wget https://github.com/gmarcais/Jellyfish/releases/download/v2.2.10/jellyfish-2.2.10.tar.gz
tar -vxzf jellyfish-2.2.10.tar.gz
cd jellyfish-2.2.10/
./configure
make
make install
cd ..
rm -r jellyfish-2.2.10.tar.gz
rm -r jellyfish-2.2.10
git clone https://github.com/vcftools/vcftools.git
cd vcftools
./autogen.sh
./configure
make
make install
cd ..
rm -r vcftools
cd /usr/local/bin
git clone https://github.com/primer3-org/primer3.git
cd primer3/src
make
make install
# done