trinity-software
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trinity-software [2015/07/31 11:59] – joguya | trinity-software [2018/03/27 16:00] – aorth | ||
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===== Information ===== | ===== Information ===== | ||
- | * Version: v2.0.6 | + | * Latest |
* Added: March, 2015 | * Added: March, 2015 | ||
+ | * Updated: March, 2018 | ||
* Link: https:// | * Link: https:// | ||
===== Usage ===== | ===== Usage ===== | ||
- | |||
See versions of trinity which are available: | See versions of trinity which are available: | ||
+ | < | ||
- | < | + | Load one version into your environment and run it: |
+ | < | ||
+ | $ Trinity</ | ||
- | **Note:** | + | **Notes about running Trinity:** |
- | * You should always | + | * Please |
- | * Trinity creates millions of small files -- which causes problems on the HPC storage server | + | * Trinity creates millions of small files, which is inefficient and causes problems on the HPC storage server, so you please |
- | + | * For example: | |
- | < | + | |
#SBATCH -p highmem | #SBATCH -p highmem | ||
#SBATCH -J trinity | #SBATCH -J trinity | ||
#SBATCH -n 8 | #SBATCH -n 8 | ||
- | module load trinity/v2.0.6 | + | module load trinity/v2.6.6 |
- | module load bowtie/ | + | |
- | module load samtools/ | + | |
- | # cd to working | + | # create and change |
export WORKDIR=/ | export WORKDIR=/ | ||
mkdir -p $WORKDIR | mkdir -p $WORKDIR | ||
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# 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 8 --output trinity-fish2</ | + | Trinity --seqType fq --max_memory 10G --left fish_R1.fastq --right fish_R2.fastq --CPU 8 --output trinity-fish2 |
===== Installation ====== | ===== Installation ====== | ||
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< | < | ||
- | $ wget "https:// | + | $ wget https:// |
- | $ tar -xvf trinity-v2.0.6.tar.gz | + | $ tar xf Trinityrnaseq-v2.6.6.wExtSampleData.tar.gz |
- | $ cd trinityrnaseq-2.0.6/ | + | $ cd Trinityrnaseq-v2.6.6 |
- | $ scl enable devtoolset-2 bash | + | $ make |
- | $ CC=clang | + | $ make plugins |
- | $ CC=clang | + | $ sudo yum install numpy |
- | $ sudo mkdir / | + | $ sudo mkdir / |
- | $ cp -r * / | + | $ make test_trinity |
- | $ sudo chown -R root:root /export/apps/trinity/v2.0.6</code> | + | $ sudo cp -r . / |
+ | |||
+ | Consult the [[https://github.com/trinityrnaseq/trinityrnaseq/wiki/ |
trinity-software.txt · Last modified: 2020/10/28 11:28 by aorth