Mercurial > repos > artbio > trinity
comparison README.rst @ 0:b3fe7c4ca5aa draft default tip
planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/trinity commit bfb22f460d6f3825ff1bd3eed924a5760c99c96d
| author | artbio |
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| date | Sat, 17 Mar 2018 17:43:58 -0400 |
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| -1:000000000000 | 0:b3fe7c4ca5aa |
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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 1G. | |
| 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 set the GALAXY_MEMORY_MB environmental variable in the destination section of the job_conf.xml file:: | |
| 13 | |
| 14 <?xml version="1.0"?> | |
| 15 <!-- A sample job config that explicitly configures job running the way it is configured by default (if there is no explicit config). --> | |
| 16 <job_conf> | |
| 17 <plugins> | |
| 18 <plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner" workers="4"/> | |
| 19 </plugins> | |
| 20 <handlers> | |
| 21 <handler id="main"/> | |
| 22 </handlers> | |
| 23 <destinations> | |
| 24 <destination id="local" runner="local"> | |
| 25 <env id="GALAXY_MEMORY_MB">1G</env> | |
| 26 </destination> | |
| 27 </destinations> | |
| 28 </job_conf> | |
| 29 | |
| 30 |