trinity-software
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| Both sides previous revisionPrevious revisionNext revision | Previous revision | ||
| trinity-software [2018/03/27 16:00] – aorth | trinity-software [2020/10/28 11:28] (current) – aorth | ||
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| ===== Information ===== | ===== Information ===== | ||
| - | * Latest Version: v2.6.6 | + | * Latest Version: v2.11.0 |
| * Added: March, 2015 | * Added: March, 2015 | ||
| - | * Updated: | + | * Updated: |
| * Link: https:// | * Link: https:// | ||
| Line 14: | Line 14: | ||
| Load one version into your environment and run it: | Load one version into your environment and run it: | ||
| - | < | + | < |
| $ Trinity</ | $ Trinity</ | ||
| - | **Notes about running 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 | + | * Please use the '' |
| * Trinity creates millions of small files, which is inefficient and causes problems on the HPC storage server, so you please direct the output from these jobs to a directory inside /// | * Trinity creates millions of small files, which is inefficient and causes problems on the HPC storage server, so you please direct the output from these jobs to a directory inside /// | ||
| * For example: | * For example: | ||
| Line 40: | Line 40: | ||
| < | < | ||
| - | $ wget https:// | + | $ wget https:// |
| - | $ tar xf Trinityrnaseq-v2.6.6.wExtSampleData.tar.gz | + | $ tar xf trinityrnaseq-v2.11.0.FULL.tar.gz |
| - | $ cd Trinityrnaseq-v2.6.6 | + | $ cd trinityrnaseq-v2.11.0 |
| + | $ sed -i ' | ||
| $ make | $ make | ||
| $ make plugins | $ make plugins | ||
| - | $ sudo yum install numpy | + | $ sudo yum install |
| - | $ sudo mkdir / | + | $ sudo mkdir -p / |
| - | $ make test_trinity | + | $ sudo cp -r . / |
| - | $ sudo cp -r . / | + | $ export TRINITY_HOME=/ |
| + | $ module load samtools/ | ||
| + | $ cd sample_data/ | ||
| + | $ ./runMe.sh</ | ||
| - | Consult the [[https:// | + | Consult the [[https:// |
trinity-software.1522166428.txt.gz · Last modified: by aorth