trinity-software
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| trinity-software [2015/02/12 11:37] – created aorth | trinity-software [2017/08/22 12:20] – aorth | ||
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| ===== Information ===== | ===== Information ===== | ||
| - | * Version: v2.0.3 | + | * Latest |
| - | * Added: | + | * Added: |
| + | * Updated: August, 2017 | ||
| * Link: https:// | * Link: https:// | ||
| ===== Usage ===== | ===== Usage ===== | ||
| - | === See versions of trinity which are available | + | See versions of trinity which are available: |
| - | < | + | |
| + | < | ||
| + | |||
| + | **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 -J trinity | ||
| + | #SBATCH -n 8 | ||
| + | |||
| + | module load trinity/ | ||
| + | |||
| + | # create and change to a working directory on the compute node | ||
| + | export WORKDIR=/ | ||
| + | mkdir -p $WORKDIR | ||
| + | cd $WORKDIR | ||
| + | |||
| + | # match CPUs to amount requested in SBATCH options! | ||
| + | Trinity --seqType fq --max_memory 10G --left fish_R1.fastq --right fish_R2.fastq --CPU 8 --output trinity-fish2 --full_cleanup</ | ||
| ===== 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 | + | $ unzip Trinity-v2.4.0.zip |
| - | $ cd trinityrnaseq-2.0.3 | + | $ cd trinityrnaseq-Trinity-v2.4.0 |
| - | $ sudo mkdir / | + | $ scl enable devtoolset-4 bash |
| - | $ sudo chown aorth / | + | |
| - | $ cp -r * / | + | |
| - | $ scl enable devtoolset-2 bash | + | |
| $ make | $ make | ||
| $ make plugins | $ make plugins | ||
| - | $ sudo chown -R root: | + | $ sudo mkdir / |
| + | $ make test_trinity | ||
| + | $ sudo cp -r . / | ||
trinity-software.txt · Last modified: 2020/10/28 11:28 by aorth