mirror of
https://github.com/MillironX/singularity-builds.git
synced 2024-11-23 18:09:55 +00:00
Add Sanger Pathogens' Assembly Improvement
This commit is contained in:
parent
0c3b4ccb06
commit
f05c179091
GPG key ID:
139C07724802BC5D
1 changed files with 173 additions and 0 deletions
173
assembly_improvement/assembly_improvement.def
Normal file
173
assembly_improvement/assembly_improvement.def
Normal file
|
|
@ -0,0 +1,173 @@
|
|||
Bootstrap: library
|
||||
From: default/centos:latest
|
||||
|
||||
%post
|
||||
# Quiet perl down
|
||||
export LC_ALL=C
|
||||
|
||||
# Install package files: repositories
|
||||
dnf install dnf-plugins-core -y
|
||||
dnf install epel-release -y
|
||||
dnf config-manager --set-enabled PowerTools
|
||||
|
||||
# Operating dependencies
|
||||
dnf --setopt=install_weak_deps=False install procps perl python3 -y
|
||||
|
||||
# Building dependencies
|
||||
dnf groupinstall 'Development Tools' -y
|
||||
dnf install perl-App-cpanminus boost-devel cmake jsoncpp-devel jemalloc-devel expat-devel -y
|
||||
|
||||
# Install SSPACE
|
||||
cd /opt || exit 1
|
||||
git clone https://github.com/nsoranzo/sspace_basic.git
|
||||
cd sspace_basic || exit 1
|
||||
git checkout 4fe5c # Not available as release tarball
|
||||
cd || exit 1
|
||||
export PATH=$PATH:/opt/sspace_basic
|
||||
|
||||
# Install GapFiller
|
||||
curl -L https://downloads.sourceforge.net/project/gapfiller/v2.1.2/gapfiller-2.1.2.tar.gz | tar xvz
|
||||
cd gapfiller-2.1.2
|
||||
./configure
|
||||
make && make install
|
||||
cd .. || exit 1
|
||||
rm -rf gapfiller-2.1.2
|
||||
|
||||
# Install khmer
|
||||
pip3 install khmer
|
||||
|
||||
# Install MUMmer
|
||||
curl -L https://github.com/mummer4/mummer/releases/download/v4.0.0rc1/mummer-4.0.0rc1.tar.gz | tar xvz
|
||||
cd mummer-4.0.0rc1 || exit 1
|
||||
./configure
|
||||
make && make install
|
||||
cd .. || exit 1
|
||||
rm -rf mummer-4.0.0rc1
|
||||
|
||||
# SGA uses an old C++ standard, so all of its dependencies must be compiled
|
||||
# against that standard, too
|
||||
export CFLAGS=-std=gnu++03
|
||||
export CXXFLAGS=-std=gnu++03
|
||||
export CPPFLAGS=-std=gnu++03
|
||||
|
||||
# Install Google sparsehash (dependency for SGA)
|
||||
curl -L https://github.com/sparsehash/sparsehash/archive/refs/tags/sparsehash-2.0.4.tar.gz | tar xvz
|
||||
cd sparsehash-sparsehash-2.0.4 || exit 1
|
||||
./configure
|
||||
make && make install
|
||||
cd .. || exit 1
|
||||
rm -rf sparsehash-sparsehash-2.0.4
|
||||
|
||||
# Install bamtools library (dependency for SGA)
|
||||
curl -L https://github.com/pezmaster31/bamtools/archive/refs/tags/v2.5.2.tar.gz | tar xvz
|
||||
cd bamtools-2.5.2 || exit 1
|
||||
mkdir build && cd build || exit 1
|
||||
# Dependency issue unique to RHEL/CentOS 8: https://github.com/ComplianceAsCode/content/issues/7016#issuecomment-845066366
|
||||
dnf upgrade libarchive -y
|
||||
cmake ..
|
||||
make && make install
|
||||
cd ../.. || exit 1
|
||||
rm -rf bamtools-2.5.2
|
||||
|
||||
# Install ruffus (dependency for SGA)
|
||||
pip3 install ruffus --upgrade
|
||||
|
||||
# Install pysam (dependency for SGA)
|
||||
pip3 install pysam
|
||||
|
||||
# Install SGA
|
||||
git clone https://github.com/jts/sga.git
|
||||
cd sga/src || exit 1
|
||||
git checkout 229293b # Contains compiler-blocking bug fixes that are not in the release tarball
|
||||
./autogen.sh
|
||||
./configure --with-bamtools=/usr/local
|
||||
make && make install
|
||||
cd ../.. || exit 1
|
||||
rm -rf sga
|
||||
|
||||
# Unset the compiler flags
|
||||
export CFLAGS=''
|
||||
export CXXFLAGS=''
|
||||
export CPPFLAGS=''
|
||||
|
||||
# QUASR is nowhere to be found, so skip installing it
|
||||
|
||||
# Install assembly_improvement's dependencies
|
||||
cpanm -f Bio::AssemblyImprovement
|
||||
|
||||
# Install an up-to-date version of assembly_improvement
|
||||
cd /opt || exit 1
|
||||
curl -L https://github.com/sanger-pathogens/assembly_improvement/releases/download/v2021.01.04.08.24.00.726/Bio_AssemblyImprovement-2021.01.04.08.24.00.726.tar.gz | tar xvz
|
||||
export PATH=$PATH:/opt/Bio_AssemblyImprovement-2021.01.04.08.24.00.726/bin
|
||||
cd || exit 1
|
||||
|
||||
# Shim preloaded arguments into PATH
|
||||
IMPROVE_PREFIX=/opt/Bio_AssemblyImprovement-2021.01.04.08.24.00.726/bin
|
||||
SSPACE_PATH=/opt/sspace_basic/SSPACE_Basic.pl
|
||||
GF_PATH=/usr/local/bin/GapFiller
|
||||
ABACAS_PATH=/usr/local/bin/abacas.pl
|
||||
SGA_PATH=/usr/local/bin/sga
|
||||
cd /opt || exit 1
|
||||
mkdir shims && cd shims || exit 1
|
||||
echo "$IMPROVE_PREFIX/improve_assembly -s $SSPACE_PATH -g $GF_PATH -b $ABACAS_PATH \"\$@\"" > improve_assembly
|
||||
echo "$IMPROVE_PREFIX/diginorm_with_khmer -py /usr/bin/python3 \"\$@\"" > diginorm_with_khmer
|
||||
echo "$IMPROVE_PREFIX/fill_gaps_with_gapfiller -s $GF_PATH \"\$@\"" > fill_gaps_with_gapfiller
|
||||
echo "$IMPROVE_PREFIX/order_contigs_with_abacas -b $ABACAS_PATH \"\$@\"" > order_contigs_with_abacas
|
||||
echo "$IMPROVE_PREFIX/read_correction_with_sga -s $SGA_PATH \"\$@\"" > read_correction_with_sga
|
||||
echo "$IMPROVE_PREFIX/scaffold_with_sspace -s $SSPACE_PATH \"\$@\"" > scaffold_with_sspace
|
||||
echo "echo 'Error! QUASR is discontinued and not available in this container.'; exit 1" > remove_primers_with_quasr
|
||||
chmod +x ./*
|
||||
cd || exit 1
|
||||
export PATH=/opt/shims:$PATH
|
||||
|
||||
# Clean up
|
||||
dnf groupremove 'Development Tools' -y
|
||||
dnf remove perl-App-cpanminus boost-devel cmake jsoncpp-devel jemalloc-devel expat-devel -y
|
||||
dnf autoremove -y
|
||||
dnf clean all
|
||||
|
||||
%environment
|
||||
export LC_ALL=C
|
||||
export PATH=$PATH:/opt/sspace_basic
|
||||
export PATH=$PATH:/opt/Bio_AssemblyImprovement-2021.01.04.08.24.00.726/bin
|
||||
export PATH=/opt/shims:$PATH
|
||||
|
||||
%test
|
||||
# We can use bash notation here, since /bin/sh is symlinked to bash in CentOS
|
||||
CMDS=('bash' 'ps' 'SSPACE_Basic.pl' 'GapFiller' 'abacas.pl' 'sga' 'improve_assembly' 'diginorm_with_khmer' 'fill_gaps_with_gapfiller' 'order_contigs_with_abacas' 'read_correction_with_sga' 'scaffold_with_sspace')
|
||||
for CMD in "${CMDS[@]}"; do
|
||||
if ! command -v "$CMD"; then
|
||||
echo "command $CMD not found!"
|
||||
FAILED_TESTS=1
|
||||
fi
|
||||
done
|
||||
# Abort if a test failed
|
||||
if [ -n "$FAILED_TESTS" ]; then
|
||||
exit 1
|
||||
fi
|
||||
|
||||
%runscript
|
||||
/opt/Bio_AssemblyImprovement-2021.01.04.08.24.00.726/bin/improve_assembly -s /opt/sspace_basic/SSPACE_Basic.pl -g /usr/local/bin/GapFiller -b /usr/local/bin/abacas.pl "$@"
|
||||
|
||||
%labels
|
||||
Author 25492070+MillironX@users.noreply.github.com
|
||||
SoftwareVersion 1.160490
|
||||
SingularityDefinitionVersion 1
|
||||
|
||||
%help
|
||||
Assembly Improvement
|
||||
====================
|
||||
|
||||
Take in an assembly in FASTA format, reads in FASTQ format, and make the
|
||||
assembly better by scaffolding and gap filling.
|
||||
|
||||
**NOTE:** When using this container, **do not** use options that point to the
|
||||
paths of binaries. These have already been included in the container, and
|
||||
shims are setup to point to the containerized binaries already.
|
||||
E.g. `improve_assembly` is shimmed to execute
|
||||
`improve_assembly -s /opt/sspace_basic/SSPACE_Basic.pl -g /usr/local/bin/GapFiller -b /usr/local/bin/abacas.pl "$@"`,
|
||||
so providing `-s`, `-g`, or `-b` will break the usage.
|
||||
|
||||
For more help, see
|
||||
- <https://github.com/sanger-pathogens/assembly_improvement>
|
||||
- <https://github.com/MillironX/singularity-builds>
|
||||
Loading…
Reference in a new issue