The file is an example of the command lines used to run Trinity and PASA, at the time of the original work (“LincRNAs landscape in human lymphocytes highlights modulation of T cell differentiation by linc-MAF-4” by Ranzani V. et al.) Recently Trinity and PASA were updated, the current command lines and options can differ.

trinity-pipeline-template.pbs

#!/bin/bash

# Copyright (C) 2015 INGM

# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.

# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
# GNU General Public License for more details.

# You should have received a copy of the GNU General Public License
# along with this program.  If not, see <http://www.gnu.org/licenses/>.

BAM_NAME=$1
JOB_NAME=$2
FASTAREFERENCE=$3
FASTAREFERENCENAME=`basename ${FASTAREFERENCE}`
HOSTDB=$4
TRINITYTMPDIR=$5
CPUS=$6
NODE=1

    qsub -N $JOB_NAME  -j eo -v NODE=$NODE,BAM_NAME=$BAM_NAME,JOB_NAME=$JOB_NAME,FASTAREFERENCE=$FASTAREFERENCE,FASTAREFERENCENAME=$FASTAREFERENCENAME,HOSTDB=$HOSTDB,TRINITYTMPDIR=$TRINITYTMPDIR,CPUS=$CPUS <<EOS
    #!/bin/bash
    #PBS -l nodes=$NODE:ppn=${CPUS}
    #PBS -S /bin/bash
    if [[ -z \$TMPDIR || ! -d \$TMPDIR ]]; then
      TMPDIR=\`mktemp -d --tmpdir=${TRINITYTMPDIR} --suffix=\$JOB_NAME\`
    fi
    ORGDIR=\`pwd\`
    cd \$TMPDIR
    SAM_NAME=\`basename \${BAM_NAME}\`.sam
    samtools view -h -o \$SAM_NAME \$BAM_NAME
    /opt/trinityrnaseq/util/prep_rnaseq_alignments_for_genome_assisted_assembly.pl --coord_sorted_SAM \$SAM_NAME -I 589824 —jaccard_clip
    find Dir_* -name "*reads" > read_files.list
    /opt/trinityrnaseq/util/GG_write_trinity_cmds.pl --reads_list_file read_files.list --paired  > trinity_GG.cmds
    /opt/trinityrnaseq/Inchworm/bin/ParaFly -c trinity_GG.cmds -CPU ${CPUS} -failed_cmds trinity_GG.cmds.failed -v
    find Dir_*  -name "*inity.fasta" -exec cat {} + | /opt/trinityrnaseq/util/inchworm_accession_incrementer.pl > Trinity_GG.fasta
    cp ${FASTAREFERENCE} .
    generate_alignAssembly_config.sh \$TMPDIR \$JOB_NAME
    /opt/PASA/scripts/Launch_PASA_pipeline.pl -c alignAssembly.config -C -R -g ${FASTAREFERENCENAME} -t Trinity_GG.fasta --MAX_INTRON_LENGTH 589824
    mysqldump --host=${HOSTDB} -upasamaster -ppasamaster \$JOB_NAME > \${JOB_NAME}.sql
    cd ..
EOS