Mercurial > repos > iuc > trinity_contig_exn50_statistic
comparison README.rst @ 0:1e8a2c87461a draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit ed037d83415937b11a45a4611584e71e99ad1da0
| author | iuc |
|---|---|
| date | Thu, 23 Mar 2017 10:18:11 -0400 |
| parents | |
| children | 570f2b1f3cd9 |
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| -1:000000000000 | 0:1e8a2c87461a |
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| 1 Trinity memory usage | |
| 2 ==================== | |
| 3 | |
| 4 As described on the official Trinity website | |
| 5 `FAQ <http://trinityrnaseq.sourceforge.net/trinity_faq.html#ques_comp_resources_required>`_, | |
| 6 trinity requires a large amount of memory to perform the assembly: "roughly | |
| 7 ~1G of RAM per 1M reads to be assembled" | |
| 8 | |
| 9 By default, this tool is configured to limit the memory consumption to 30G. | |
| 10 You might need to lower this limit if the machine(s) executing the jobs have less memory available. | |
| 11 If you have a lot of reads to assemble and a machine with enough memory, you can increase it. | |
| 12 In both cases, you can edit the TRINITY_MEM_OPTIONS in the file: | |
| 13 | |
| 14 <tool_dependency_dir>/environment_settings/TRINITY_MEM_OPTIONS/iuc/trinity/<hash_string>/env.sh | |
| 15 | |
| 16 to lower the maximum memory usage to 2G for example: | |
| 17 | |
| 18 TRINITY_MEM_OPTIONS='--max_memory 2G --bflyHeapSpaceMax 2G' |