Mercurial > repos > iuc > trinity_align_and_estimate_abundance
view README.rst @ 7:3baf18bcf03e draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 6d3a6d130b58b15190bf286b9840caa162a2bea1
author | iuc |
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date | Thu, 14 Dec 2017 10:22:11 -0500 |
parents | be3607a306af |
children | 4c929a15a0b8 |
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Trinity memory usage ==================== As described on the official Trinity website `FAQ <http://trinityrnaseq.sourceforge.net/trinity_faq.html#ques_comp_resources_required>`_, trinity requires a large amount of memory to perform the assembly: "roughly ~1G of RAM per 1M reads to be assembled" By default, this tool is configured to limit the memory consumption to 1G. You might need to lower this limit if the machine(s) executing the jobs have less memory available. If you have a lot of reads to assemble and a machine with enough memory, you can increase it. In both cases, you can set the TRINITY_MAX_MEMORY environmental variable in the destination section of the job_conf.xml file: <?xml version="1.0"?> <!-- A sample job config that explicitly configures job running the way it is configured by default (if there is no explicit config). --> <job_conf> <plugins> <plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner" workers="4"/> </plugins> <handlers> <handler id="main"/> </handlers> <destinations> <destination id="local" runner="local"> <env id="TRINITY_MAX_MEMORY">1G</env> </destination> </destinations> </job_conf>