trinity-software
Differences
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| Both sides previous revisionPrevious revisionNext revision | Previous revisionNext revisionBoth sides next revision | ||
| trinity-software [2015/03/24 07:56] – joguya | trinity-software [2015/03/24 17:04] – aorth | ||
|---|---|---|---|
| Line 18: | Line 18: | ||
| #SBATCH -p highmem | #SBATCH -p highmem | ||
| #SBATCH -J trinity | #SBATCH -J trinity | ||
| - | #SBATCH -n 10 | + | #SBATCH -n 8 |
| - | module load trinity/ | + | module load trinity/ |
| 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 trinity-v2.0.6.tar.gz |
| - | $ cd trinityrnaseq-2.0.3 | + | $ cd trinityrnaseq-2.0.6/ |
| - | $ 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:root / | + | $ sudo mkdir / |
| + | $ cp -r * / | ||
| + | $ sudo chown -R root:root / | ||
trinity-software.txt · Last modified: 2020/10/28 11:28 by aorth