Mercurial > repos > iuc > trinity_abundance_estimates_to_matrix
view README.rst @ 10:13ab393ba794 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
author | iuc |
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date | Thu, 14 Jun 2018 03:12:12 -0400 |
parents | 67906d99d3c0 |
children | 08326e2e82f1 |
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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 GALAXY_MEMORY_MB 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="GALAXY_MEMORY_MB">1G</env> </destination> </destinations> </job_conf>