trinity-software
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trinity-software [2015/03/20 15:28] – [Usage] aorth | trinity-software [2018/03/27 16:00] – aorth | ||
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===== Information ===== | ===== Information ===== | ||
- | * Version: v2.0.3 | + | * Latest |
- | * Added: | + | * Added: |
+ | * 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</ | ||
+ | |||
+ | **Notes about running Trinity: | ||
+ | * Please 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 fasta results | ||
+ | * Trinity creates millions of small files, | ||
+ | * For example: | ||
+ | | ||
+ | #SBATCH -p highmem | ||
+ | #SBATCH -J trinity | ||
+ | #SBATCH -n 8 | ||
+ | |||
+ | module | ||
+ | |||
+ | # 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 | ||
- | **Note:** Trinity creates millions of small files -- which causes problems on the HPC storage server -- so you must direct output from these jobs to /// | ||
===== 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 xf Trinityrnaseq-v2.6.6.wExtSampleData.tar.gz |
- | $ cd trinityrnaseq-2.0.3 | + | $ cd Trinityrnaseq-v2.6.6 |
- | $ sudo mkdir / | + | |
- | $ sudo chown aorth / | + | |
- | $ cp -r * / | + | |
- | $ scl enable devtoolset-2 bash | + | |
$ make | $ make | ||
$ make plugins | $ make plugins | ||
- | $ sudo chown -R root: | + | $ sudo yum install numpy |
+ | $ sudo mkdir / | ||
+ | $ make test_trinity | ||
+ | $ sudo cp -r . / | ||
+ | |||
+ | Consult the [[https:// |
trinity-software.txt · Last modified: 2020/10/28 11:28 by aorth