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singularity.def
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Bootstrap: library
From: ubuntu:16.04
%files
.git /topmed_variant_calling/.git
.gitmodules /topmed_variant_calling/.gitmodules
apigenome /topmed_variant_calling/apigenome
bamUtil /topmed_variant_calling/bamUtil
bcftools /topmed_variant_calling/bcftools
cramore /topmed_variant_calling/cramore
htslib /topmed_variant_calling/htslib
invNorm /topmed_variant_calling/invNorm
king /topmed_variant_calling/king
libStatGen /topmed_variant_calling/libStatGen
libsvm /topmed_variant_calling/libsvm
samtools /topmed_variant_calling/samtools
scripts /topmed_variant_calling/scripts
vt-topmed /topmed_variant_calling/vt-topmed
%environment
export LC_ALL=C
%post
set -eu
apt-get update && apt-get install -y \
apt-utils \
automake \
autoconf \
build-essential \
cmake \
default-jre \
default-jdk \
gdb \
git \
ghostscript \
gnuplot \
groff \
libcurl4-gnutls-dev \
liblzma-dev \
libncurses5-dev \
libssl-dev \
libzstd-dev \
python3 \
r-base \
wget \
zlib1g-dev
cd /topmed_variant_calling
git submodule init
git submodule update
git clone https://github.com/samtools/htslib htslib-1.13
cd htslib-1.13
git checkout 1.13
git submodule update --init --recursive
autoreconf -i
./configure --disable-libcurl
make
cd ..
mkdir plink
cd plink/
wget http://s3.amazonaws.com/plink1-assets/plink_linux_x86_64_20190617.zip
unzip plink_linux_x86_64_20190617.zip
rm plink_linux_x86_64_20190617.zip
install -T plink /usr/local/bin/plink-1.9
cd ..
wget https://sourceforge.net/projects/snpeff/files/snpEff_v4_3t_core.zip/download
unzip download
rm download
rm -r clinEff/
cd libsvm/
make clean
make
cd ..
cd apigenome
git clean -fdx
autoreconf -vfi
./configure --prefix $PWD
make
make install
cd ..
cd libStatGen
git clean -fdx
make
cd ..
cd bamUtil
git clean -fdx
make
cd ..
cd invNorm
git clean -fdx
make
cd ..
cd htslib
git clean -fdx
autoheader
autoconf
./configure --disable-libcurl
make
install bgzip /usr/local/bin
install tabix /usr/local/bin
cd ..
cd vt-topmed
git clean -fdx
make
cd ..
cd cramore
git clean -fdx
mkdir build
cd build
cmake -DCMAKE_BUILD_TYPE=Release -DHTS_INCLUDE_DIRS=/topmed_variant_calling/htslib-1.13 -DHTS_LIBRARIES=/topmed_variant_calling/htslib-1.13/libhts.a ..
make
cd ../..
cd samtools
git clean -fdx
autoheader
autoconf -Wno-syntax
./configure
make
make install
cd ..
cd bcftools
git clean -fdx
make
make install
cd ..
cd king
rm -f king *.o
g++ -O3 -fopenmp -o king *.cpp -lm -lz
cd ..