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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
cd /home/train/
wget http://www.repeatmasker.org/rmblast-2.10.0+-x64-linux.tar.gz -P ~/software
tar zxf ~/software/rmblast-2.10.0+-x64-linux.tar.gz -C /opt/biosoft
mv /opt/biosoft/rmblast-2.10.0 /opt/biosoft/ncbi-rmblast-2.10.0+
echo 'PATH=/opt/biosoft/ncbi-rmblast-2.10.0+/bin/:$PATH' >> ~/.bashrc
source ~/.bashrc
## 3. Installing HMMER and Pfam database
# exit user "train", and open a new terminal to load user "train", so as to load the default GCC with old version.
cd /home/train/
wget http://eddylab.org/software/hmmer/hmmer-3.3.2.tar.gz -P ~/software/
tar zxf ~/software/hmmer-3.3.2.tar.gz
cd hmmer-3.3.2/
./configure --prefix=/opt/biosoft/hmmer-3.3.2 && make -j 4 && make install
cd .. && rm -rf hmmer-3.3.2
echo 'PATH=/opt/biosoft/hmmer-3.3.2/bin/:$PATH' >> ~/.bashrc
source ~/.bashrc
wget ftp://ftp.ebi.ac.uk/pub/databases/Pfam/releases/Pfam27.0/Pfam-A.hmm.gz -P ~/software
wget ftp://ftp.ebi.ac.uk/pub/databases/Pfam/releases/Pfam27.0/Pfam-B.hmm.gz -P ~/software
cd /opt/biosoft/hmmer-3.3.2/
gzip -dc ~/software/Pfam-A.hmm.gz > Pfam-AB.hmm
gzip -dc ~/software/Pfam-B.hmm.gz >> Pfam-AB.hmm
hmmpress Pfam-AB.hmm
## 4. Installing RepeatMasker
wget http://www.repeatmasker.org/RepeatMasker-4.1.0.tar.gz -P ~/software
wget --http-user=chenlianfu_china --http-password=u2o7rn https://www.girinst.org/server/RepBase/protected/repeatmaskerlibraries/RepBaseRepeatMaskerEdition-20181026.tar.gz -P ~/software/
wget http://tandem.bu.edu/trf/downloads/trf409.linux64 -P ~/software/
tar zxf ~/software/RepeatMasker-4.1.0.tar.gz -C /opt/biosoft/
cd /opt/biosoft/RepeatMasker/
chmod 644 *.pm configure
echo 'PATH=$PATH:/opt/biosoft/RepeatMasker' >> ~/.bashrc
source ~/.bashrc
tar zxf ~/software/RepBaseRepeatMaskerEdition-20181026.tar.gz -C /opt/biosoft/RepeatMasker/
cp ~/software/trf409.linux64 /opt/biosoft/RepeatMasker/trf
chmod 755 /opt/biosoft/RepeatMasker/trf
# Configuration of RepeatMasker
cd /opt/biosoft/RepeatMasker/
perl ./configure
# /opt/biosoft/RepeatMasker/trf Enter
# 2 Enter
# /opt/biosoft/ncbi-rmblast-2.10.0+/bin Enter
# Y Enter
# 5 Enter
## 5. Installing RepeatModeler
wget http://www.repeatmasker.org/RepeatModeler/RepeatModeler-2.0.1.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-1.5.9.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://mafft.cbrc.jp/alignment/software/mafft-7.407-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
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-1.5.9.tar.gz
cd genometools-1.5.9
perl -p -i -e 's/-Werror/-Wno-error/g' Makefile
make prefix=//opt/biosoft/genometools-1.5.9/ install -j 4
cd ../ && rm -rf genometools-1.5.9
tar zxf ~/software/LTR_retriever-2.9.0.tar.gz -C /opt/biosoft/
tar zxf ~/software/mafft-7.407-without-extensions-src.tgz
cd mafft-7.407-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-7.407-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
tar zxf ~/software/RepeatModeler-2.0.1.tar.gz -C /opt/biosoft/
cd /opt/biosoft/RepeatModeler-2.0.1
perl configure
# Enter
# /usr/bin/perl Enter
# /opt/biosoft/RepeatMasker Enter
# /opt/biosoft/RECON-1.08/bin Enter
# /opt/biosoft/RepeatScout-1.0.6 Enter
# /opt/biosoft/RepeatMasker/trf Enter
# 1 Enter
# /opt/biosoft/ncbi-rmblast-2.10.0+/bin Enter
# 3 Enter
# y Enter
# /opt/biosoft/genometools-1.5.9/bin Enter
# /opt/biosoft/LTR_retriever-2.9.0 Enter
# /opt/biosoft/mafft/bin Enter
# /opt/biosoft/NINJA-0.95-cluster_only/NINJA Enter
# /opt/biosoft/cd-hit-v4.8.1-2019-0228 Enter
chmod 644 *.pm configure RepModelConfig.pm.tmpl
echo 'PATH=$PATH:/opt/biosoft/RepeatModeler-2.0.1' >> ~/.bashrc
source ~/.bashrc
## 6. Installing Samtools
cd /home/train/
wget https://github.com/samtools/samtools/releases/download/1.11/samtools-1.11.tar.bz2 -P ~/software
tar jxf ~/software/samtools-1.11.tar.bz2 -C /opt/biosoft/
cd /opt/biosoft/samtools-1.11
./configure --prefix=/opt/biosoft/samtools-1.11
make -j 8 && make install
echo 'PATH=/opt/biosoft/samtools-1.11/bin/:$PATH' >> ~/.bashrc
source ~/.bashrc
## 7. Installing HISAT2
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=$PATH:/opt/biosoft/hisat2-2.1.0/" >> ~/.bashrc
source ~/.bashrc
## 8. Installing genewise
wget http://www.ebi.ac.uk/~birney/wise2/wise2.4.1.tar.gz
tar zxf ~/software/wise2.4.1.tar.gz -C /opt/biosoft/
cd /opt/biosoft/wise2.4.1/src/
# switch user to "root"
yum install *glib*
# switch user to "train"
find ./ -name makefile | xargs sed -i 's/glib-config/pkg-config --libs glib-2.0/'
export C_INCLUDE_PATH=/usr/include/glib-2.0/:/usr/lib64/glib-2.0/include/:$C_INCLUDE_PATH
perl -p -i -e 's/getline/get_line/g' ./HMMer2/sqio.c
perl -p -i -e 's/isnumber/isdigit/' models/phasemodel.c
make all
export WISECONFIGDIR=/opt/biosoft/wise2.4.1/wisecfg/
make test
echo 'PATH=$PATH:/opt/biosoft/wise2.4.1/src/bin/' >> ~/.bashrc
echo 'export WISECONFIGDIR=/opt/biosoft/wise2.4.1/wisecfg/' >> ~/.bashrc
source ~/.bashrc
## 9. Installing AUGUSTUS
wget https://github.com/pezmaster31/bamtools/archive/v2.5.1.tar.gz -O ~/software/bamtools-2.5.1.tar.gz
wget http://bioinf.uni-greifswald.de/augustus/binaries/augustus-3.3.3.tar.gz -P ~/software
tar zxf ~/software/bamtools-2.5.1.tar.gz
cd bamtools-2.5.1/
mkdir build
cd build/
#cmake ../ -DCMAKE_INSTALL_PREFIX=/opt/biosoft/bamtools-2.5.1
cmake ../
make -j 4
sudo make install
sudo cp /usr/local/include/bamtools/ /usr/include/ -rf
cd ../../
rm bamtools-2.5.1/ -rf
tar zxf ~/software/augustus-3.3.3.tar.gz -C /opt/biosoft/
cd /opt/biosoft/augustus-3.3.3/
make clean
perl -p -i.bak -e 's#^SAMTOOLS=.*#SAMTOOLS=/opt/biosoft/samtools-1.11#; s#^HTSLIB=.*#HTSLIB=/opt/biosoft/samtools-1.11/htslib-1.11#;' auxprogs/bam2wig/Makefile
make -j 4
chmod 777 /opt/biosoft/augustus-3.3.3/config/species
echo 'PATH=$PATH:/opt/biosoft/augustus-3.3.3/bin/' >> ~/.bashrc
echo 'PATH=$PATH:/opt/biosoft/augustus-3.3.3/scripts/' >> ~/.bashrc
echo "export AUGUSTUS_CONFIG_PATH=/opt/biosoft/augustus-3.3.3/config/" >> ~/.bashrc
source ~/.bashrc
## 10. Installing ParaFly
wget https://sourceforge.net/projects/parafly/files/parafly-r2013-01-21.tgz -P ~/software
tar zxf ~/software/parafly-r2013-01-21.tgz
cd parafly-r2013-01-21
./configure --prefix=/opt/sysoft/parafly-r2013-01-21 && make -j 8 && make install
cd .. && rm -rf parafly-r2013-01-21
echo 'PATH=/opt/sysoft/parafly-r2013-01-21/bin/:$PATH' >> ~/.bashrc
source ~/.bashrc
## 11. Installing Java
wget https://javadl.oracle.com/webapps/download/AutoDL?BundleId=244058_89d678f2be164786b292527658ca1605 -O ~/software/jre-8u281-linux-x64.tar.gz
tar zxf ~/software/jre-8u281-linux-x64.tar.gz -C /opt/sysoft/
echo 'PATH=/opt/sysoft/jre1.8.0_281/bin:$PATH' >> ~/.bashrc
source ~/.bashrc