Start an interactive job, with a walltime of 12 hours, 2000MB of memory. Load related modules:
srun --pty -p interactive -t 0-12:0:0 --mem 3G -c 2 /bin/bash
Create a directory in home, download and compile trinity:
mkdir -p ~/pub/trinity cd ~/pub/trinity wget https://github.com/trinityrnaseq/trinityrnaseq/archive/Trinity-v2.6.6.tar.gz tar xvzf Trinity-v2.6.6.tar.gz cd trinityrnaseq-Trinity-v2.6.6/ module load gcc/6.2.0 python/2.7.12 java/jdk-1.8u112 make make plugins
Create a directory in home and download salmon. Note: this a binary, does not need to compile
mkdir -p ~/pub/salmon cd ~/pub/salmon wget https://github.com/COMBINE-lab/salmon/releases/download/v0.10.0/salmon-0.10.0_linux_x86_64.tar.gz tar xvzf salmon-0.10.0_linux_x86_64.tar.gz
Test run Trinity using test data
module load gcc/6.2.0 python/2.7.12 java/jdk-1.8u112 samtools/1.3.1 jellyfish/2.2.6 bowtie2/2.2.9 export PATH=~/pub/salmon/salmon-0.10.0_linux_x86_64/bin:~/pub/trinity/trinityrnaseq-Trinity-v2.6.6:$PATH cd ~/pub/trinity/trinityrnaseq-Trinity-v2.6.6/sample_data/test_Trinity_Assembly/ Trinity --seqType fq --max_memory 2G --left reads.left.fq.gz --right reads.right.fq.gz --SS_lib_type RF --CPU 2 export TRINITY_HOME=~/pub/trinity/trinityrnaseq-Trinity-v2.6.6 module load blat/35 $TRINITY_HOME/Analysis/FL_reconstruction_analysis/FL_trans_analysis_pipeline.pl --query trinity_out_dir/Trinity.fasta \ --target __indiv_ex_sample_derived/refSeqs.fa --no_reuse
For downstream analysis, please visit: https://github.com/trinityrnaseq/trinityrnaseq/wiki