安装pasa

#1.安装依赖软件

# installing GMAP
#wget http://research-pub.gene.com/gmap/src/gmap-gsnap-2017-11-15.tar.gz -P ~/software/
tar zxf /opt/software/gmap-gsnap-2017-11-15.tar.gz 
cd gmap-2017-11-15
./configure --prefix=/opt/biosoft/gmap-2017-11-15/ && make -j 4 && make install
cd .. && rm -rf gmap-2017-11-15/
echo 'PATH=$PATH:/opt/biosoft/gmap-2017-11-15/bin/' >> ~/.bashrc.14
source ~/.bashrc.14

# installing blat 
#wget http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/blat/blat -P ~/software/
mkdir /opt/biosoft/blat
cp /opt/software/blat /opt/biosoft/blat
chmod 755 /opt/biosoft/blat/blat
echo 'PATH=$PATH:/opt/biosoft/blat/' >> ~/.bashrc.14
source ~/.bashrc.14

# installing FASTA ()
#wget http://faculty.virginia.edu/wrpearson/fasta/fasta36/fasta-36.3.8g.tar.gz -P ~/software/
tar zxf /opt/software/fasta-36.3.8g.tar.gz -C /opt/biosoft/
cd /opt/biosoft/fasta-36.3.8g/src/
make -f ../make/Makefile.linux_sse2 all
ln -s /opt/biosoft/fasta-36.3.8g/bin/fasta36 /opt/biosoft/fasta-36.3.8g/bin/fasta
echo 'PATH=$PATH:/opt/biosoft/fasta-36.3.8g/bin/' >> ~/.bashrc.14
source ~/.bashrc.14

#2.安装pasa

# installing PASA
#wget https://github.com/PASApipeline/PASApipeline/releases/download/pasa-v2.3.3/PASApipeline-v2.3.3.tar.gz -P ~/software/
tar zxf /opt/software/PASApipeline-v2.3.3.tar.gz -C /opt/biosoft/
cd /opt/biosoft/PASApipeline-v2.3.3
make -j 4
echo 'PATH=$PATH:/opt/biosoft/PASApipeline-v2.3.3/bin/' >> ~/.bashrc.14
source ~/.bashrc.14

#3.EVM和UniVec库

# installing EVidenceModeler-1.1.1
tar zxf ~/software/EVidenceModeler-1.1.1.tar.gz -C /opt/biosoft/
tar zxf ~/software/EVM_r2012-06-25.tgz -C /opt/biosoft/

# installing UniVec database for seqclean (https://www.ncbi.nlm.nih.gov/tools/vecscreen/univec/)
# install ncbi-blast fistly (ftp://ftp.ncbi.nih.gov/blast/executables/legacy.NOTSUPPORTED/2.2.26/)
#wget ftp://ftp.ncbi.nih.gov/blast/executables/legacy.NOTSUPPORTED/2.2.26/blast-2.2.26-x64-linux.tar.gz -P ~/software/
tar zxf /opt/software/blast-2.2.26-x64-linux.tar.gz -C /opt/biosoft/
echo 'PATH=$PATH:/opt/biosoft/blast-2.2.26/bin/' >> ~/.bashrc.14
source ~/.bashrc.14
#wget ftp://ftp.ncbi.nlm.nih.gov/pub/UniVec/UniVec -P ~/software/
mkdir /opt/biosoft/PASApipeline-v2.3.3/UniVec
cd /opt/biosoft/PASApipeline-v2.3.3/UniVec
cp /opt/software/UniVec ./
formatdb -t UniVec -i UniVec -p F -o T

#4.配置mysql

# modify pasa configure file
cd /opt/biosoft/PASApipeline-v2.3.3/pasa_conf/
cp pasa.CONFIG.template conf.txt
perl -p -i -e 's/MYSQLSERVER=.*/MYSQLSERVER=localhost/' conf.txt
perl -p -i -e 's/MYSQL_RW_USER=.*/MYSQL_RW_USER=train/' conf.txt
perl -p -i -e 's/MYSQL_RW_PASSWORD=.*/MYSQL_RW_PASSWORD=java31password/' conf.txt
perl -p -i -e 's/MYSQL_RO_USER=.*/MYSQL_RO_USER=train/' conf.txt
perl -p -i -e 's/MYSQL_RO_PASSWORD=.*/MYSQL_RO_PASSWORD=java31password/' conf.txt
perl -p -i -e 's#BASE_PASA_URL=.*#BASE_PASA_URL=http://localhost/pasa/cgi-bin/#' conf.txt
perl -p -i -e 's#VECTOR_DB=.*#VECTOR_DB=/opt/biosoft/PASApipeline-v2.3.3/UniVec/UniVec#' conf.txt

#5.http，gcc版本问题

# installing lighttpd (https://www.lighttpd.net/) 是启用PASA网页工具所依赖的
#wget https://download.lighttpd.net/lighttpd/releases-1.4.x/lighttpd-1.4.54.tar.gz -P ~/software/
tar zxf /opt/software/lighttpd-1.4.54.tar.gz
cd lighttpd-1.4.54/
./configure --prefix /opt/sysoft/lighttpd-1.4.54
make -j 4
make install
cd ../ && rm -rf lighttpd-1.4.54
echo 'PATH=$PATH:/opt/sysoft/lighttpd-1.4.54/sbin/' >> ~/.bashrc.14


#libstdc++.so.6: version `GLIBCXX_3.4.20' not found
#/opt/biosoft/PASApipeline-v2.3.3/bin/pasa: /public/software/compiler/gnu/4.8.5/lib64/libstdc++.so.6: version `GLIBCXX_3.4.20' not found (required by /opt/biosoft/PASApipeline-v2.3.3/bin/pasa)
# ls -l | grep libstdc++.so.6
# strings /usr/lib64/libstdc++.so.6  | grep GLIBCXX
#sudo locate libstdc++.so.6
rm /public/software/compiler/gnu/4.8.5/lib64/libstdc++.so.6
ln -s /public/software/compiler/gnu/5.5.0/lib64/libstdc++.so.6.0.21 /public/software/compiler/gnu/4.8.5/lib64/libstdc++.so.6