trinity-software
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trinity-software [2017/08/22 12:20] – aorth | trinity-software [2020/10/28 11:28] (current) – aorth | ||
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===== Information ===== | ===== Information ===== | ||
- | * Latest Version: v2.4.0 | + | * Latest Version: v2.11.0 |
* Added: March, 2015 | * Added: March, 2015 | ||
- | * Updated: | + | * Updated: |
* Link: https:// | * Link: https:// | ||
===== Usage ===== | ===== Usage ===== | ||
- | |||
See versions of trinity which are available: | See versions of trinity which are available: | ||
- | |||
< | < | ||
- | **Note:** | + | Load one version into your environment and run it: |
- | * You should | + | < |
- | * Trinity creates millions of small files -- which causes problems on the HPC storage server | + | $ Trinity</ |
+ | |||
+ | Notes about running Trinity: | ||
+ | * Please | ||
+ | * 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/v2.4.0 | + | module load trinity/v2.6.6 |
# create and change to a working directory on the compute node | # create and change to a working directory on the compute node | ||
Line 36: | Line 40: | ||
< | < | ||
- | $ wget https:// | + | $ wget https:// |
- | $ unzip Trinity-v2.4.0.zip | + | $ tar xf trinityrnaseq-v2.11.0.FULL.tar.gz |
- | $ cd trinityrnaseq-Trinity-v2.4.0 | + | $ cd trinityrnaseq-v2.11.0 |
- | $ scl enable devtoolset-4 bash | + | $ sed -i ' |
$ make | $ make | ||
$ make plugins | $ make plugins | ||
- | $ sudo mkdir / | + | $ sudo yum install python36-numpy.x86_64 |
- | $ make test_trinity | + | $ sudo mkdir -p / |
- | $ sudo cp -r . / | + | $ sudo cp -r . / |
+ | $ export TRINITY_HOME=/ | ||
+ | $ module load samtools/ | ||
+ | $ cd sample_data/ | ||
+ | $ ./runMe.sh</ | ||
+ | |||
+ | Consult the [[https:// |
trinity-software.1503404455.txt.gz · Last modified: 2017/08/22 12:20 by aorth