trinity-software
Differences
This shows you the differences between two versions of the page.
Both sides previous revisionPrevious revisionNext revision | Previous revisionNext revisionBoth sides next revision | ||
trinity-software [2015/03/24 07:56] – joguya | trinity-software [2016/01/28 10:31] – joguya | ||
---|---|---|---|
Line 4: | Line 4: | ||
===== Information ===== | ===== Information ===== | ||
- | * Version: v2.0.6 | + | * Latest |
+ | * Updated: January, 2016 | ||
* Added: March, 2015 | * Added: March, 2015 | ||
* Link: https:// | * Link: https:// | ||
Line 10: | Line 11: | ||
===== Usage ===== | ===== Usage ===== | ||
- | === See versions of trinity which are available | + | See versions of trinity which are available: |
- | < | + | |
- | **Note:** Trinity creates millions of small files -- which causes problems on the HPC storage server -- so you must direct output from these jobs to /// | + | < |
- | < | + | **Note:** |
+ | * You should use the **−−full_cleanup** option so that Trinity can clean up after itself by removing all the intermediary files it has created except for the final Trinity.fasta results file. | ||
+ | * Trinity creates millions of small files -- which causes problems on the HPC storage server -- so you must direct output from these jobs to /// | ||
#SBATCH -p highmem | #SBATCH -p highmem | ||
#SBATCH -J trinity | #SBATCH -J trinity | ||
- | #SBATCH -n 10 | + | #SBATCH -n 8 |
- | module load trinity/v2.0.3 | + | module load trinity/v2.1.1 |
module load bowtie/ | module load bowtie/ | ||
module load samtools/ | module load samtools/ | ||
# cd to working dir just in case | # cd to working dir just in case | ||
- | export WORKDIR=$SLURM_JOBID | + | export WORKDIR=/ |
+ | mkdir -p $WORKDIR | ||
cd $WORKDIR | cd $WORKDIR | ||
# match CPUs to amount requested in SBATCH options! | # match CPUs to amount requested in SBATCH options! | ||
- | Trinity --seqType fq --max_memory 10G --left fish_R1.fastq --right fish_R2.fastq --CPU 10 --output trinity-fish2</ | + | Trinity --seqType fq --max_memory 10G --left fish_R1.fastq --right fish_R2.fastq --CPU 8 --output trinity-fish2 |
===== Installation ====== | ===== Installation ====== | ||
Notes from the sysadmin during installation: | Notes from the sysadmin during installation: | ||
- | < | + | < |
- | $ wget https:// | + | $ wget "https:// |
- | $ tar xf v2.0.3.tar.gz | + | $ tar -xvf v2.1.1.tar.gz |
- | $ cd trinityrnaseq-2.0.3 | + | $ cd trinityrnaseq-2.1.1 |
- | $ sudo mkdir / | + | |
- | $ sudo chown aorth / | + | |
- | $ cp -r * / | + | |
$ scl enable devtoolset-2 bash | $ scl enable devtoolset-2 bash | ||
- | $ make | + | $ CC=clang |
- | $ make plugins | + | $ CC=clang |
- | $ sudo chown -R root: | + | $ sudo mkdir / |
+ | $ sudo cp -r . / | ||
+ | </ |
trinity-software.txt · Last modified: 2020/10/28 11:28 by aorth