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feat: update REAT singularity definition file
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@gemygk
gemygk committed Nov 11, 2024
1 parent 7063181 commit 3494464
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146 changes: 76 additions & 70 deletions singularity/reat_singularity.def
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Bootstrap: docker
From: ubuntu:18.04
From: ubuntu:20.04

%environment
export PATH=$PATH:/opt/software/hisat2-2.2.1
export PATH=$PATH:/opt/software/TransDecoder-TransDecoder-v5.5.0:/opt/software/TransDecoder-TransDecoder-v5.5.0/util
export PATH=$PATH:/opt/software/repeatmasker/RepeatMasker:/opt/software/repeatmasker/RepeatModeler
export PATH=$PATH:/opt/software/spaln/bin
export LD_LIBRARY_PATH=/usr/local/lib:$LD_LIBRARY_PATH
export PYTHONPATH=$PYTHONPATH:/usr/local/lib/python3.6/dist-packages/
export ALN_DBS=/opt/software/spaln/seqdb
export ALN_TAB=/opt/software/spaln/table
export PATH=$PATH:/opt/software/hisat2-2.2.1
export PATH=$PATH:/opt/software/TransDecoder-TransDecoder-v5.5.0:/opt/software/TransDecoder-TransDecoder-v5.5.0/util
export PATH=$PATH:/opt/software/repeatmasker/RepeatMasker:/opt/software/repeatmasker/RepeatModeler
export PATH=$PATH:/opt/software/spaln/bin
export LD_LIBRARY_PATH=/usr/local/lib:$LD_LIBRARY_PATH
export PYTHONPATH=$PYTHONPATH:/usr/local/lib/python3.6/dist-packages/
export ALN_DBS=/opt/software/spaln/seqdb
export ALN_TAB=/opt/software/spaln/table

%post
mkdir /jic
mkdir /nbi
mkdir /tgac
mkdir /ei
mkdir /tsl
mkdir /opt/software

### Install your packages ###
cd /opt/software/
apt -y update
apt -y install software-properties-common build-essential zlib1g-dev libbz2-dev libncurses5-dev libgdbm-dev libnss3-dev libssl-dev \
DEBIAN_FRONTEND=noninteractive apt -y update
DEBIAN_FRONTEND=noninteractive apt -y install software-properties-common build-essential zlib1g-dev libbz2-dev libncurses5-dev libgdbm-dev libnss3-dev libssl-dev \
libreadline-dev libffi-dev wget lzma lzma-dev liblzma-dev tk-dev libsqlite3-dev python3 ruby-full libidn11-dev libidn11 \
default-jdk git libcurl4-openssl-dev curl cmake libcairo2-dev libcogl-pango-dev unzip python python3-pip python-pip \
default-jdk git libcurl4-openssl-dev curl cmake libcairo2-dev libcogl-pango-dev unzip python python3-pip \
libboost-all-dev make libssl-dev libghc-zlib-dev libexpat1-dev gettext unzip gnuplot cpanminus bison

java -version
python3 --version
python --version

# DIAMOND - 2.0.7
wget https://github.com/bbuchfink/diamond/archive/v2.0.7.tar.gz
tar xf v2.0.7.tar.gz
cd diamond-2.0.7
# DIAMOND - 2.0.11
wget https://github.com/bbuchfink/diamond/archive/v2.0.11.tar.gz
tar xf v2.0.11.tar.gz
cd diamond-2.0.11
mkdir build
cd build
cmake ../
make
make install
cd ../../
rm -rf diamond-2.0.7 v2.0.7.tar.gz
rm -rf diamond-2.0.11 v2.0.11.tar.gz
diamond --help

# BioPerl
cpanm -i XML::DOM::XPath --force
cpanm -i Parallel::ForkManager File::Which Scalar::Util::Numeric URI::Escape Data::Dumper URI::Escape Bio::SeqIO Text::Soundex JSON
cpanm -i Parallel::ForkManager File::Which Scalar::Util::Numeric URI::Escape Data::Dumper URI::Escape Bio::SeqIO Text::Soundex JSON --force

# FullLengtherNext - 1.0.1
gem install -q -f full_lengther_next -v 1.0.1 -N
full_lengther_next --help

# Install BLAST - 2.7.1 NEEDS UPDATE
wget ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.7.1/ncbi-blast-2.7.1+-x64-linux.tar.gz
tar xf ncbi-blast-2.7.1+-x64-linux.tar.gz
cp ncbi-blast-2.7.1+/bin/* /usr/local/bin
# Install BLAST - 2.16.0
wget ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.16.0/ncbi-blast-2.16.0+-x64-linux.tar.gz
tar xf ncbi-blast-2.16.0+-x64-linux.tar.gz
cp ncbi-blast-2.16.0+/bin/* /usr/local/bin
blastx -help

# Install MagicBlast - 1.5.0
Expand All @@ -68,46 +63,47 @@ magicblast -help
cd /opt/software/
git clone https://github.com/ebiggers/libdeflate.git
cd libdeflate
git checkout tags/v1.14
make -j 20
make install
cd ../
rm -rf libdeflate

# HTSLib - 1.11
wget https://github.com/samtools/htslib/releases/download/1.11/htslib-1.11.tar.bz2
tar xaf htslib-1.11.tar.bz2
mv htslib-1.11 htslib # Necessary for augustus
# HTSLib - 1.18
wget https://github.com/samtools/htslib/releases/download/1.18/htslib-1.18.tar.bz2
tar xaf htslib-1.18.tar.bz2
mv htslib-1.18 htslib # Necessary for augustus
cd htslib
./configure --enable-libcurl --enable-plugins --enable-s3 --with-libdeflate
make -j 20
make install
htsfile --help 2>&1 | head
cd ../
rm htslib-1.11.tar.bz2
rm htslib-1.18.tar.bz2

# Samtools - 1.11
wget https://github.com/samtools/samtools/releases/download/1.11/samtools-1.11.tar.bz2
tar xaf samtools-1.11.tar.bz2
mv samtools-1.11 samtools # Necessary for augustus
# Samtools - 1.18
wget https://github.com/samtools/samtools/releases/download/1.18/samtools-1.18.tar.bz2
tar xaf samtools-1.18.tar.bz2
mv samtools-1.18 samtools # Necessary for augustus
cd samtools # and similarly for bcftools and htslib
./configure --enable-libcurl --enable-plugins --enable-s3
make -j 20
make install
samtools --help 2>&1 | head
cd ../
rm samtools-1.11.tar.bz2
rm samtools-1.18.tar.bz2

# BCFTools - 1.11
wget https://github.com/samtools/bcftools/releases/download/1.11/bcftools-1.11.tar.bz2
tar xaf bcftools-1.11.tar.bz2
mv bcftools-1.11 bcftools
# BCFTools - 1.18
wget https://github.com/samtools/bcftools/releases/download/1.18/bcftools-1.18.tar.bz2
tar xaf bcftools-1.18.tar.bz2
mv bcftools-1.18 bcftools
cd bcftools
./configure --enable-libcurl --enable-plugins --enable-s3
make -j 20
make install
bcftools --help 2>&1 | head
cd /opt/software/
rm -rf bcftools-1.11.tar.bz2
rm -rf bcftools-1.18.tar.bz2

# BAMtools - 2.5.1
wget https://github.com/pezmaster31/bamtools/archive/v2.5.1.tar.gz -O bamtools-v2.5.1.tar.gz
Expand Down Expand Up @@ -140,10 +136,10 @@ cd /opt/software/
gffread --help 2>&1 | head
rm -rf gffread gclib

# GMAP - 2021-02-12
wget http://research-pub.gene.com/gmap/src/gmap-gsnap-2021-02-12.tar.gz
tar xaf gmap-gsnap-2021-02-12.tar.gz
cd gmap-2021-02-12
# GMAP - 2021-03-08
wget http://research-pub.gene.com/gmap/src/gmap-gsnap-2021-03-08.tar.gz
tar xaf gmap-gsnap-2021-03-08.tar.gz
cd gmap-2021-03-08
for i in sse2 ssse3 sse41 sse42;
do
./configure --with-simd-level=$i --enable-zlib --enable-bzlib
Expand All @@ -154,26 +150,26 @@ done;
gmap --help
gsnap --help
cd /opt/software/
rm -rf gmap-gsnap-2021-02-12.tar.gz
rm -rf gmap-gsnap-2021-03-08.tar.gz

# MiniMap2 - 2.17
wget https://github.com/lh3/minimap2/releases/download/v2.17/minimap2-2.17_x64-linux.tar.bz2
tar xaf minimap2-2.17_x64-linux.tar.bz2
cd minimap2-2.17_x64-linux
# MiniMap2 - 2.18
wget https://github.com/lh3/minimap2/releases/download/v2.18/minimap2-2.18_x64-linux.tar.bz2
tar xaf minimap2-2.18_x64-linux.tar.bz2
cd minimap2-2.18_x64-linux
mv k8 minimap2 paftools.js -t /usr/local/bin/
minimap2 --help
cd /opt/software/
rm -rf minimap2-2.17_x64-linux.tar.bz2 minimap2-2.17_x64-linux
rm -rf minimap2-2.18_x64-linux.tar.bz2 minimap2-2.18_x64-linux

# GenomeTools - 1.5.10
# GenomeTools - 1.6.5
cd /opt/software/
wget https://github.com/genometools/genometools/archive/v1.5.10.tar.gz -O genometools-1.5.10.tar.gz
tar xaf genometools-1.5.10.tar.gz
cd genometools-1.5.10
wget https://github.com/genometools/genometools/archive/v1.6.5.tar.gz -O genometools-1.6.5.tar.gz
tar xaf genometools-1.6.5.tar.gz
cd genometools-1.6.5
make 64bit=yes opt=yes cairo=no errorcheck=yes useshared=no -j 20
make install
cd /opt/software/
rm -rf genometools-1.5.10.tar.gz genometools-1.5.10
rm -rf genometools-1.6.5.tar.gz genometools-1.6.5


# HISAT2 - 2.2.1
Expand Down Expand Up @@ -209,8 +205,8 @@ cp bioawk /usr/local/bin

cd /opt/software

# Stringtie2 - v2.1.4
git clone -b v2.1.4 https://github.com/gpertea/stringtie.git
# Stringtie2 - v2.2.3
git clone -b v2.2.3 https://github.com/gpertea/stringtie.git
cd stringtie
make -j 4 release
cp stringtie /usr/local/bin
Expand Down Expand Up @@ -257,23 +253,33 @@ wget https://github.com/TransDecoder/TransDecoder/archive/TransDecoder-v5.5.0.ta
tar xf TransDecoder-v5.5.0.tar.gz

## Prepare python dependencies for Mikado and Portcullis
pip3 install pandas matplotlib setuptools sphinx tabulate cython scipy
pip3 install "pandas<=1.5.0" matplotlib setuptools sphinx tabulate "cython<=0.29.32" "scipy<=1.11.1"

# Portcullis - 1.2.2
wget https://github.com/maplesond/portcullis/archive/1.2.2.tar.gz
tar xf 1.2.2.tar.gz
cd portcullis-1.2.2
# Portcullis - 1.2.4
wget https://github.com/EI-CoreBioinformatics/portcullis/archive/refs/tags/Release-1.2.4.tar.gz
tar xf Release-1.2.4.tar.gz
mv portcullis-Release-1.2.4 portcullis-1.2.4
cd portcullis-1.2.4
./autogen.sh
./configure
make -j 8
make install
cd /opt/software

# Gotoh's SPALN

wget https://github.com/ogotoh/spaln/archive/refs/tags/ver.2.4.4.tar.gz
tar xf ver.2.4.4.tar.gz
cd spaln-ver.2.4.4/src
# Gotoh's SPALN - 2.4.7
wget https://github.com/ogotoh/spaln/archive/refs/tags/ver.2.4.7.tar.gz
tar xf ver.2.4.7.tar.gz
cd spaln-ver.2.4.7/src
./configure -e /opt/software/spaln/bin -t /opt/software/spaln/table -d /opt/software/spaln/seqdbs
make -j 4
make install
make install
cd /opt/software

# miniprot - 0.12
wget https://github.com/lh3/miniprot/releases/download/v0.12/miniprot-0.12_x64-linux.tar.bz2
tar xaf miniprot-0.12_x64-linux.tar.bz2
cd miniprot-0.12_x64-linux
mv miniprot -t /usr/local/bin/
minimap2 --help
cd /opt/software/
rm -rf miniprot-0.12_x64-linux.tar.bz2 miniprot-0.12_x64-linux

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