trinity-software
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trinity-software [2015/03/24 08:00] – joguya | trinity-software [2015/06/11 12:55] – aorth | ||
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===== 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:** Trinity creates millions of small files -- which causes problems on the HPC storage server -- so you must direct output from these jobs to /// | ||
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#SBATCH -p highmem | #SBATCH -p highmem | ||
#SBATCH -J trinity | #SBATCH -J trinity | ||
- | #SBATCH -n 10 | + | #SBATCH -n 8 |
module load trinity/ | module load trinity/ | ||
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# 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: | ||
- | < | + | < |
- | $ sudo su - provisioning | + | |
- | $ cd src | + | |
$ wget " | $ wget " | ||
$ tar -xvf trinity-v2.0.6.tar.gz | $ tar -xvf trinity-v2.0.6.tar.gz | ||
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$ CC=clang make plugins | $ CC=clang make plugins | ||
$ sudo mkdir / | $ sudo mkdir / | ||
- | $ sudo chown -R provisioning: | ||
$ cp -r * / | $ cp -r * / | ||
- | $ sudo chown -R root:root / | + | $ sudo chown -R root:root / |
- | </ | + |
trinity-software.txt · Last modified: 2020/10/28 11:28 by aorth