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INSTALL
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## the detail command lines of installation of all the dependency softwares and GETA.
# All of below command lines were excuted on CentOS system with normal user "train" and super user "root".
## 1. Preparing folders
# switch user to "root"
mkdir /opt/biosoft/ /opt/sysoft/
chmod 1777 /opt/biosoft/ /opt/sysoft/
# switch user to a normal user "train"
mkdir ~/software
## 2. Installing NCBI-Blast+ and rmblastn
wget https://www.repeatmasker.org/rmblast/rmblast-2.14.1+-x64-linux.tar.gz -P ~/software
tar zxf ~/software/rmblast-2.14.1+-x64-linux.tar.gz -C /opt/biosoft
echo 'PATH=$PATH:/opt/biosoft/rmblast-2.14.1/bin' >> ~/.bashrc
source ~/.bashrc
## 3. Installing HMMER and Pfam database (http://www.hmmer.org/)
# exit user "train", and open a new terminal to load user "train", so as to load the default GCC with old version.
wget http://eddylab.org/software/hmmer/hmmer-3.3.2.tar.gz -P ~/software/
tar zxf ~/software/hmmer-3.3.2.tar.gz
cd hmmer-3.3.2/
./configure --prefix=/opt/biosoft/hmmer-3.3.2 && make -j 4 && make install
cd .. && rm -rf hmmer-3.3.2
echo 'PATH=/opt/biosoft/hmmer-3.3.2/bin/:$PATH' >> ~/.bashrc
source ~/.bashrc
wget http://ftp.ebi.ac.uk/pub/databases/Pfam/releases/Pfam37.0/Pfam-A.hmm.gz -O ~/software/Pfam-A_V37.0.hmm.gz
wget http://ftp.ebi.ac.uk/pub/databases/Pfam/releases/Pfam27.0/Pfam-B.hmm.gz -O ~/software/Pfam-B_V27.0.hmm.gz
mkdir -p /opt/biosoft/bioinfomatics_databases/Pfam
cd /opt/biosoft/bioinfomatics_databases/Pfam
gzip -dc ~/software/Pfam-A_V37.0.hmm.gz > PfamA
gzip -dc ~/software/Pfam-B_V27.0.hmm.gz > PfamB
hmmpress PfamA
hmmpress PfamB
## 4. Installing RepeatMasker (http://repeatmasker.org/RepeatMasker/)
wget http://repeatmasker.org/RepeatMasker/RepeatMasker-4.1.6.tar.gz -P ~/software
wget https://www.dfam.org/releases/Dfam_3.8/families/FamDB/dfam38_full.0.h5.gz -P ~/software
wget https://www.dfam.org/releases/Dfam_3.8/families/FamDB/dfam38_full.5.h5.gz -P ~/software
wget http://tandem.bu.edu/trf/downloads/trf409.linux64 -P ~/software/
tar zxf ~/software/RepeatMasker-4.1.6.tar.gz && mv RepeatMasker /opt/biosoft/RepeatMasker-4.1.6
cd /opt/biosoft/RepeatMasker-4.1.6
chmod 644 *.pm configure
echo 'PATH=$PATH:/opt/biosoft/RepeatMasker-4.1.6' >> ~/.bashrc
source ~/.bashrc
gzip -dc ~/software/dfam38_full.0.h5.gz > /opt/biosoft/RepeatMasker-4.1.6/Libraries/famdb/dfam38_full.0.h5
gzip -dc ~/software/dfam38_full.5.h5.gz > /opt/biosoft/RepeatMasker-4.1.6/Libraries/famdb/dfam38_full.5.h5
tar zxvf ~/software/RepBaseRepeatMaskerEdition-20181026.tar.gz -C /opt/biosoft/RepeatMasker-4.1.6/
cp ~/software/trf409.linux64 /opt/biosoft/RepeatMasker-4.1.6/trf
chmod 755 /opt/biosoft/RepeatMasker-4.1.6/trf
# Configuration of RepeatMasker
cd /opt/biosoft/RepeatMasker-4.1.6
perl ./configure
# /opt/biosoft/RepeatMasker-4.1.6/trf Enter
# 3 Enter
# /opt/biosoft/hmmer-3.3.2/bin Enter
# 2 Enter
# /opt/biosoft/rmblast-2.14.1/bin Enter
# N Enter
# 5 Enter
## 5. Installing RepeatModeler (http://www.repeatmasker.org/RepeatModeler/ | https://github.com/Dfam-consortium/RepeatModeler)
wget http://www.repeatmasker.org/RepeatModeler/RepeatModeler-2.0.5.tar.gz -P ~/software/
wget http://www.repeatmasker.org/RepeatModeler/RECON-1.08.tar.gz -P ~/software/
wget http://www.repeatmasker.org/RepeatScout-1.0.6.tar.gz -P ~/software/
wget http://genometools.org/pub/genometools-1.6.2.tar.gz -P ~/software/
wget https://github.com/oushujun/LTR_retriever/archive/v2.9.0.tar.gz -O ~/software/LTR_retriever-2.9.0.tar.gz
wget https://github.com/zhangrengang/TEsorter/archive/refs/tags/v1.4.6.tar.gz -O ~/software/TEsorter-1.4.6.tar.gz
wget https://mafft.cbrc.jp/alignment/software/mafft-7.505-without-extensions-src.tgz -P ~/software
wget https://github.com/weizhongli/cdhit/releases/download/V4.8.1/cd-hit-v4.8.1-2019-0228.tar.gz -P ~/software
wget https://github.com/TravisWheelerLab/NINJA/archive/0.95-cluster_only.tar.gz -O ~/software/NINJA-0.95-cluster_only.tar.gz
wget http://hgdownload.cse.ucsc.edu/admin/jksrc.v449.zip -P ~/software/
tar zxf ~/software/RECON-1.08.tar.gz -C /opt/biosoft/
cd /opt/biosoft/RECON-1.08/src/
make && make install
tar zxf ~/software/RepeatScout-1.0.6.tar.gz -C /opt/biosoft/
cd /opt/biosoft/RepeatScout-1.0.6
make
cd && tar zxf ~/software/genometools-1.6.2.tar.gz
cd genometools-1.6.2
perl -p -i -e 's/-Werror/-Wno-error/g' Makefile
make prefix=//opt/biosoft/genometools-1.6.2/ install -j 4
cd ../ && rm -rf genometools-1.6.2
tar zxf ~/software/LTR_retriever-2.9.0.tar.gz -C /opt/biosoft/
# install Python3
pip3 install xopen
unzip ~/software/TEsorter-1.4.6.zip
cd TEsorter-1.4.6
python setup.py install
cd .. && rm -rf TEsorter-1.4.6
tar zxf ~/software/mafft-7.505-without-extensions-src.tgz
cd mafft-7.505-without-extensions/core/
perl -p -i -e 's#PREFIX =.*#PREFIX = /opt/biosoft/mafft#' Makefile
perl -p -i -e 's#BINDIR =.*#BINDIR = /opt/biosoft/mafft/bin/#' Makefile
make -j 4
make install
cd ../../ && rm -rf mafft-7.505-without-extensions
echo 'PATH=$PATH:/opt/biosoft/mafft/bin/' >> ~/.bashrc
source ~/.bashrc
tar zxf ~/software/cd-hit-v4.8.1-2019-0228.tar.gz -C /opt/biosoft/
cd /opt/biosoft/cd-hit-v4.8.1-2019-0228
make -j 4
tar zxf ~/software/NINJA-0.95-cluster_only.tar.gz -C /opt/biosoft/
cd /opt/biosoft/NINJA-0.95-cluster_only/NINJA/
make -j 4
sudo dnf --disablerepo=* --enablerepo=media-* -y install libuuid libuuid-devel mariadb-connector-c-devel
unzip /home/train/software/jksrc.v449.zip -d /opt/biosoft/
cd /opt/biosoft/kent/src/
export MACHTYPE=x86_64
mkdir -p ~/bin/x86_64
make CXXFLAGS=-fPIC CFLAGS=-fPIC CPPFLAGS=-fPIC -j 4
cp ./lib/x86_64/jkweb.a ./lib/
mv ~/bin/x86_64/ ../bin/
mv ~/bin/scripts/ ../
tar zxf ~/software/RepeatModeler-2.0.5.tar.gz -C /opt/biosoft/
cd /opt/biosoft/RepeatModeler-2.0.5
perl configure
# Enter
# /usr/bin/perl Enter
# /opt/biosoft/RepeatMasker-4.1.6 Enter
# /opt/biosoft/RECON-1.08/bin Enter
# /opt/biosoft/RepeatScout-1.0.6 Enter
# /opt/biosoft/RepeatMasker-4.1.6 Enter
# /opt/biosoft/cd-hit-v4.8.1-2019-0228 Enter
# /opt/biosoft/kent/bin/ Enter
# /opt/biosoft/rmblast-2.14.1/bin Enter
# y Enter
# /opt/biosoft/genometools-1.6.2/bin Enter
# /opt/biosoft/LTR_retriever-2.9.4 Enter
# /opt/biosoft/mafft/bin Enter
# /opt/biosoft/NINJA-0.95-cluster_only/NINJA Enter
chmod 644 *.pm configure
echo 'PATH=$PATH:/opt/biosoft/RepeatModeler-2.0.1' >> ~/.bashrc
source ~/.bashrc
# Optimize the computational performance of RepeatMasker/RepeatModeler
perl -p -i -e 's/-num_threads \d+/-num_threads 32/' /opt/biosoft/RepeatMasker-4.1.6/NCBIBlastSearchEngine.pm
perl -p -i -e 's#^(.*Step 1)#\$options{"threads"} = 64;\n$1#' /opt/biosoft/RepeatModeler-2.0.5/RepeatClassifier
## 6. Installing Samtools and HTSlib (https://github.com/samtools/samtools/releases / https://www.htslib.org)
wget https://github.com/samtools/samtools/releases/download/1.17/samtools-1.17.tar.bz2 -P ~/software/
tar jxf ~/software/samtools-1.17.tar.bz2
cd samtools-1.17/
./configure --prefix=/opt/biosoft/samtools-1.17 && make -j 4 && make install
cd ../ && rm -rf samtools-1.17/
echo 'PATH=$PATH:/opt/biosoft/samtools-1.17/bin/' >> ~/.bashrc
source ~/.bashrc
wget https://sourceforge.net/projects/samtools/files/samtools/0.1.19/samtools-0.1.19.tar.bz2 -P ~/software
tar jxf ~/software/samtools-0.1.19.tar.bz2 -C /opt/biosoft
cd /opt/biosoft/samtools-0.1.19/
make -j 4
wget https://github.com/samtools/htslib/releases/download/1.17/htslib-1.17.tar.bz2 -P ~/software/
tar jxf ~/software/htslib-1.17.tar.bz2
cd htslib-1.17
./configure --prefix=/opt/biosoft/htslib-1.17 && make -j 4 && make install
cd .. && rm -rf htslib-1.17
echo 'export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/opt/biosoft/htslib-1.17/lib/' >> ~/.bashrc
echo 'export C_INCLUDE_PATH=$C_INCLUDE_PATH:/opt/biosoft/htslib-1.17/include/' >> ~/.bashrc
echo 'PATH=$PATH:/opt/biosoft/htslib-1.17/bin/' >> ~/.bashrc
source ~/.bashrc
## 7. Installing HISAT2 (https://daehwankimlab.github.io/hisat2/download/)
wget ftp://ftp.ccb.jhu.edu/pub/infphilo/hisat2/downloads/hisat2-2.1.0-Linux_x86_64.zip -P ~/software
unzip ~/software/hisat2-2.1.0-Linux_x86_64.zip -d /opt/biosoft/
echo "PATH=$PATH:/opt/biosoft/hisat2-2.1.0/" >> ~/.bashrc
source ~/.bashrc
## 8. Installing mmseqs2 (https://github.com/soedinglab/MMseqs2)
wget https://github.com/soedinglab/MMseqs2/archive/refs/tags/15-6f452.tar.gz -O ~/software/MMseqs2-15-6f452.tar.gz
tar zxf ~/software/MMseqs2-15-6f452.tar.gz
cd MMseqs2-15-6f452
mkdir build && cd build
cmake -DCMAKE_BUILD_TYPE=RELEASE -DCMAKE_INSTALL_PREFIX=/opt/biosoft/MMseqs2-15-6f452 -DHAVE_AVX2=1 ../
make -j 8
make install
cd ../../ && rm -rf MMseqs2-15-6f452
echo 'PATH=$PATH:/opt/biosoft/MMseqs2-15-6f452/bin' >> ~/.bashrc
source ~/.bashrc
## 9. Installing genewise (https://www.ebi.ac.uk/Tools/psa/genewise/ | https://www.ebi.ac.uk/~birney/wise2/)
wget http://www.ebi.ac.uk/~birney/wise2/wise2.4.1.tar.gz -P ~/software/
tar zxf ~/software/wise2.4.1.tar.gz -C /opt/biosoft/
cd /opt/biosoft/wise2.4.1/src/
find ./ -name makefile | xargs sed -i 's/glib-config/pkg-config --libs glib-2.0/'
perl -p -i -e 's/getline/get_line/g' ./HMMer2/sqio.c
perl -p -i -e 's/isnumber/isdigit/' models/phasemodel.c
perl -p -i -e 's/csh welcome.csh/sh welcome.csh/' makefile
make all -j 4
export WISECONFIGDIR=/opt/biosoft/wise2.4.1/wisecfg/
make test
echo 'PATH=$PATH:/opt/biosoft/wise2.4.1/src/bin/' >> ~/.bashrc
echo 'export WISECONFIGDIR=/opt/biosoft/wise2.4.1/wisecfg/' >> ~/.bashrc
source ~/.bashrc
## 10. Installing exonerate (https://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate)
wget http://ftp.ebi.ac.uk/pub/software/vertebrategenomics/exonerate/exonerate-2.2.0-x86_64.tar.gz -P ~/software/
tar zxf ~/software/exonerate-2.2.0-x86_64.tar.gz -C /opt/biosoft/
echo 'PATH=$PATH:/opt/biosoft/exonerate-2.2.0-x86_64/bin/' >> ~/.bashrc
source ~/.bashrc
# Installing SNAP (https://github.com/KorfLab/SNAP | http://korflab.ucdavis.edu/software.html)
#wget wget http://korflab.ucdavis.edu/Software/snap-2013-11-29.tar.gz -P ~/software/
tar zxf ~/software/snap-2013-11-29.tar.gz -C /opt/biosoft/
cd /opt/biosoft/snap/
perl -p -i -e 's/-Werror//g; s/Zoe; make;/Zoe;/' Makefile
perl -p -i -e 's/CC="gcc"/CC="gcc -fcommon"/' Makefile
make -j 4
echo 'PATH=$PATH:/opt/biosoft/snap' >> ~/.bashrc
source ~/.bashrc
# 11. Installing GenomeThreader (http://genomethreader.org/)
wget http://genomethreader.org/distributions/gth-1.7.3-Linux_x86_64-64bit.tar.gz -P ~/software/
tar zxf ~/software/gth-1.7.3-Linux_x86_64-64bit.tar.gz -C /opt/biosoft/
echo 'PATH=$PATH:/opt/biosoft/gth-1.7.3-Linux_x86_64-64bit/bin/' >> ~/.bashrc
source ~/.bashrc
## 12. Installing AUGUSTUS (http://bioinf.uni-greifswald.de/augustus/ | https://github.com/Gaius-Augustus/Augustus)
wget https://github.com/pezmaster31/bamtools/archive/v2.5.2.tar.gz -O ~/software/bamtools-2.5.2.tar.gz
wget https://boostorg.jfrog.io/artifactory/main/release/1.82.0/source/boost_1_82_0.tar.gz -P ~/software
wget https://sourceforge.net/projects/lpsolve/files/lpsolve/5.5.2.11/lp_solve_5.5.2.11_source.tar.gz -P ~/software
wget https://tangentsoft.com/mysqlpp/releases/mysql++-3.3.0.tar.gz -P ~/software/
wget https://github.com/Gaius-Augustus/Augustus/archive/refs/tags/v3.5.0.tar.gz -O ~/software/Augustus-3.5.0.tar.gz
# Installing bamtools (https://github.com/pezmaster31/bamtools)
tar zxf ~/software/bamtools-2.5.2.tar.gz
cd bamtools-2.5.2/
mkdir build
cd build/
cmake ../ -DCMAKE_INSTALL_PREFIX=/opt/biosoft/bamtools-2.5.2
make -j 4
make install
sudo cp -a /opt/biosoft/bamtools-2.5.2/include/bamtools/ /usr/include/
sudo cp -a /opt/biosoft/bamtools-2.5.2/lib64/* /usr/lib64/
cd ../../ && rm bamtools-2.5.2/ -rf
# Installing boost C++ Libraries (https://www.boost.org/)
tar zxf ~/software/boost_1_82_0.tar.gz
cd boost_1_82_0/
./bootstrap.sh --prefix=/opt/biosoft/boost_1_82_0
./b2 -j 4 install
cd .. && rm boost_1_82_0/ -rf
sudo ln -s /opt/biosoft/boost_1_82_0/include/boost /usr/include/
echo 'export LD_LIBRARY_PATH=/opt/biosoft/boost_1_82_0/lib:$LD_LIBRARY_PATH
export C_INCLUDE_PATH=/opt/biosoft/boost_1_82_0/include:$C_INCLUDE_PATH' >> ~/.bashrc
source ~/.bashrc
# Installing lpsolve (https://sourceforge.net/projects/lpsolve/)
tar zxf ~/software/lp_solve_5.5.2.11_source.tar.gz -C /opt/sysoft/
cd /opt/sysoft/lp_solve_5.5/lpsolve55
sh ccc
echo 'export LD_LIBRARY_PATH=/opt/sysoft/lp_solve_5.5/lpsolve55/bin/ux64:$LD_LIBRARY_PATH' >> ~/.bashrc
source ~/.bashrc
# Installing Mysql++ (https://tangentsoft.com/mysqlpp)
tar zxf ~/software/mysql++-3.3.0.tar.gz && cd mysql++-3.3.0
./configure --prefi=/opt/sysoft/mysql++-3.3.0 && make -j 4 && make install
cd .. && rm -rf mysql++-3.3.0
echo 'export LD_LIBRARY_PATH=/opt/sysoft/mysql++-3.3.0/lib:$LD_LIBRARY_PATH' >> ~/.bashrc
source ~/.bashrc
# Installing AUGUSTUS
sudo dnf --disablerepo=* --enablerepo=media-* -y install gsl gsl-devel sqlite sqlite-devel suitesparse mariadb mariadb-server
sudo dnf install suitesparse-devel
tar zxf ~/software/Augustus-3.5.0.tar.gz -C /opt/biosoft/
cd /opt/biosoft/Augustus-3.5.0/
perl -p -i -e 's#/usr/include/lpsolve#/opt/sysoft/lp_solve_5.5#' src/Makefile
perl -p -i -e 's#/usr/include/mysql#/opt/sysoft/mysql++-3.3.0/include -I/usr/include/mysql/#' src/Makefile export LIBRARY_PATH=/opt/biosoft/boost_1_82_0/lib:/opt/sysoft/lp_solve_5.5/lpsolve55/bin/ux64:/opt/sysoft/mysql++-3.3.0/lib/:/opt/biosoft/htslib-1.17/lib/:$LIBRARY_PATH
sudo ln -s /usr/lib64/libcolamd.so.2 /usr/lib64/libcolamd.so
make augustus -j 4
ln -s /opt/biosoft/htslib-1.17/include /opt/biosoft/htslib-1.17/htslib
ln -s /opt/biosoft/htslib-1.17/lib/* /opt/biosoft/htslib-1.17/htslib/
export TOOLDIR=/opt/biosoft/htslib-1.17/
make -j 4
chmod 777 /opt/biosoft/Augustus-3.5.0/config/species
echo 'PATH=$PATH:/opt/biosoft/Augustus-3.5.0/bin/' >> ~/.bashrc
echo 'PATH=$PATH:/opt/biosoft/Augustus-3.5.0/scripts/' >> ~/.bashrc
echo "export AUGUSTUS_CONFIG_PATH=/opt/biosoft/Augustus-3.5.0/config/" >> ~/.bashrc
source ~/.bashrc
## 13. Installing ParaFly
wget https://sourceforge.net/projects/parafly/files/parafly-r2013-01-21.tgz -P ~/software
tar zxf ~/software/parafly-r2013-01-21.tgz
cd parafly-r2013-01-21
./configure --prefix=/opt/sysoft/parafly-r2013-01-21 && make -j 8 && make install
cd .. && rm -rf parafly-r2013-01-21
echo 'PATH=/opt/sysoft/parafly-r2013-01-21/bin/:$PATH' >> ~/.bashrc
source ~/.bashrc
## 14. Installing Java
wget https://download.oracle.com/java/20/latest/jdk-20_linux-x64_bin.tar.gz -P ~/software/
tar zxf /home/train/software/jdk-20_linux-x64_bin.tar.gz -C /opt/sysoft/
echo 'PATH=/opt/sysoft/jdk-20.0.1/bin:$PATH' >> /home/train/.bashrc
## 15. Installing BUSCO (https://busco.ezlab.org/)
wget https://gitlab.com/ezlab/busco/-/archive/5.4.7/busco-5.4.7.tar.gz -P ~/software/
tar zxf ~/software/busco-5.4.7.tar.gz -C /opt/biosoft
# installing Python modules: biopython pandas
pip3 install biopython pandas -i https://pypi.tuna.tsinghua.edu.cn/simple
# installing BBTools (https://jgi.doe.gov/data-and-tools/software-tools/bbtools/)
wget https://sourceforge.net/projects/bbmap/files/BBMap_39.01.tar.gz -P ~/software/
tar zxf ~/software/BBMap_39.01.tar.gz -C /opt/biosoft
echo 'PATH=$PATH:/opt/biosoft/bbmap/' >> ~/.bashrc
source ~/.bashrc
# installing NCBI-Blast+, Augustus and R (Already satisfied)
# installing meaeuk (https://github.com/soedinglab/metaeuk)
wget https://github.com/soedinglab/metaeuk/releases/download/6-a5d39d9/metaeuk-linux-avx2.tar.gz -P ~/software/
tar zxf ~/software/metaeuk-linux-avx2.tar.gz -C /opt/biosoft/
echo 'PATH=$PATH:/opt/biosoft/metaeuk/bin/' >> ~/.bashrc
source ~/.bashrc
# installing Prodigal (https://github.com/hyattpd/Prodigal)
wget https://github.com/hyattpd/Prodigal/archive/refs/tags/v2.6.3.tar.gz -O ~/software/Prodigal-2.6.3.tar.gz
tar zxf ~/software/Prodigal-2.6.3.tar.gz -C /opt/biosoft
cd /opt/biosoft/Prodigal-2.6.3 && make -j 4
echo 'PATH=$PATH:/opt/biosoft/Prodigal-2.6.3/' >> ~/.bashrc
source ~/.bashrc
# installing sepp (https://github.com/smirarab/sepp/)
wget https://github.com/smirarab/sepp/archive/refs/tags/4.5.1.tar.gz -O ~/software/sepp-4.5.1.tar.gz
tar zxf ~/software/sepp-4.5.1.tar.gz && cd sepp-4.5.1
pip3 install dendropy
/opt/sysoft/Python-3.11.4/bin/python3 setup.py config
/opt/sysoft/Python-3.11.4/bin/python3 setup.py install
cd .. && rm -rf sepp-4.5.1
# configuring BUSCO
cd /opt/biosoft/busco-5.4.7
python3 setup.py install
perl -i -e '$/ = "\n\n"; while (<>) { if (m/command\s*=\s*(\S+)/) { my $path = `which $1`; $path =~ s/\s*$//; if ($path) { $path =~ s/(.*\/).*/$1/; s/path\s*=.*/path = $path/; } } print; }' config/config.ini
echo 'PATH=/opt/biosoft/busco-5.4.7/bin:$PATH
export BUSCO_CONFIG_FILE=/opt/biosoft/busco-5.4.7/config/config.ini' >> ~/.bashrc
source ~/.bashrc
# installing BUSCO Version 5 Databases
mkdir -p /opt/biosoft/bioinfomatics_databases/BUSCO_V5
cd /opt/biosoft/bioinfomatics_databases/BUSCO_V5
wget https://busco-data.ezlab.org/v5/data/information/lineages_list.2021-12-14.txt.tar.gz -P ~/software/
tar zxf ~/software/lineages_list.2021-12-14.txt.tar.gz
perl -e 'open IN, $ARGV[0]; while (<IN>) { last if m/^\s*eukaryota_odb10/; } $info{"eukaryota_odb10"} = 1; while (<IN>) { $info{$1} = 1 if m/-\s*(\S+)/; } my $curl = `curl https://busco-data.ezlab.org/v5/data/lineages/`; foreach (keys %info) { print "wget -c https://busco-data.ezlab.org/v5/data/lineages/$1\n" if $curl =~ m/href=\"($_.*?.tar.gz)/;; }' lineages_list.2021-12-14.txt > command.wget.list
ParaFly -c command.wget.list -CPU 5
for i in `ls *.tar.gz`
do
tar zxf $i
done