====== Install Trinity ======
* Install extra packages: bowtie, ncurses and PerlIO layer to gzip/gunzip
root@rachaelx:~# apt-get install bowtie libncurses-dev libperlio-gzip-perl
* Download and compile Trinity
root@rachaelx:~# cd /root
root@rachaelx:~# wget http://garr.dl.sourceforge.net/project/trinityrnaseq/trinityrnaseq_r2012-10-05.tgz
root@rachaelx:~# tar xzf trinityrnaseq_r2012-10-05.tgz
root@rachaelx:~# cd trinityrnaseq_r2012-10-05/
root@rachaelx:~# make
* Install Trinity
root@rachaelx:~# mkdir /usr/share/trinity
root@rachaelx:~# cp -R trinityrnaseq_r2012-10-05/* /usr/share/trinity/
root@rachaelx:~# chown -R root:root /usr/share/trinity/*
root@rachaelx:~# chmod -R 755 /usr/share/trinity/*
* Upgrade Trinity (with support for java 1.7)
cd /root/
wget http://garr.dl.sourceforge.net/project/trinityrnaseq/trinityrnaseq_r2013-02-25.tgz
tar xzf trinityrnaseq_r2013-02-25.tgz
cd trinityrnaseq_r2013-02-25/
make
cd ..
mv /usr/share/trinity /usr/share/trinityOLD
mv trinityrnaseq_r2013-02-25 /usr/share/trinity
chown -R root:root /usr/share/trinity
chmod -R 755 /usr/share/trinity
* User script to activate Trinity
export PATH=/usr/share/trinity:/usr/share/trinity/util:/usr/share/trinity/util/RSEM_util:$PATH
ulimit -s unlimited
* Test installation
\\
\\
Logon and activate Trinity
user@rachaelx:~$ source trinityactivate.sh
Copy sample directory
user@rachaelx:~$ cp -R /usr/share/trinity/sample_data ~/
Edit test script and remove script path
user@rachaelx:~$ cd sample_data/test_Trinity_Assembly/
user@rachaelx:~/sample_data/test_Trinity_Assembly$ nano -w runMe.sh
#!/bin/bash -ve
if [ -e reads.left.fq.gz ] && ! [ -e reads.left.fq ]
then
gunzip -c reads.left.fq.gz > reads.left.fq
fi
if [ -e reads.right.fq.gz ] && ! [ -e reads.right.fq ]
then
gunzip -c reads.right.fq.gz > reads.right.fq
fi
#######################################################
## Run Trinity to Generate Transcriptome Assemblies ##
#######################################################
## use jellyfish
Trinity.pl --seqType fq --JM 2G --left reads.left.fq.gz --right reads.right.fq.gz --SS_lib_type RF --CPU 4 --no_cleanup
##### Done Running Trinity #####
if [ ! $* ]; then
exit 0
fi
sleep 2
######################################################
## align reads back to the transcripts using Bowtie ##
######################################################
sleep 2
alignReads.pl --left reads.left.fq --right reads.right.fq --target trinity_out_dir/Trinity.fasta --aligner bowtie --seqType fq --SS_lib_type RF
##### Done aligning reads #######
sleep 2
###########################################
# use RSEM to estimate read abundance ####
###########################################
sleep 2
run_RSEM.pl --transcripts trinity_out_dir/Trinity.fasta --name_sorted_bam bowtie_out/bowtie_out.nameSorted.sam.+.sam.PropMapPairsForRSEM.bam --paired
###### Done running RSEM ########
Exec test
user@rachaelx:~/sample_data/test_Trinity_Assembly$ ./runMe.sh
Result
...
##### Done Running Trinity #####
Clean test dirs
user@rachaelx:~/sample_data/test_Trinity_Assembly$ ./cleanme.pl