Mercurial > repos > iuc > trinity_align_and_estimate_abundance

comparison README.rst @ 9:cb5f0dde2aa8 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 5098e1bf7037e204f24fa1cbf7c3749bf0779550
author iuc
date Mon, 22 Jan 2018 11:26:51 -0500
parents 4c929a15a0b8
children 983552d5822d
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8:4c929a15a0b8 9:cb5f0dde2aa8
7 ~1G of RAM per 1M reads to be assembled" 7 ~1G of RAM per 1M reads to be assembled"
8 8
9 By default, this tool is configured to limit the memory consumption to 1G. 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. 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. 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 TRINITY_MAX_MEMORY environmental variable in the destination section of the job_conf.xml file:: 12 In both cases, you can set the GALAXY_MEMORY_MB environmental variable in the destination section of the job_conf.xml file::
13 13
14 <?xml version="1.0"?> 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). --> 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> 16 <job_conf>
17 <plugins> 17 <plugins>
20 <handlers> 20 <handlers>
21 <handler id="main"/> 21 <handler id="main"/>
22 </handlers> 22 </handlers>
23 <destinations> 23 <destinations>
24 <destination id="local" runner="local"> 24 <destination id="local" runner="local">
25 <env id="TRINITY_MAX_MEMORY">1G</env> 25 <env id="GALAXY_MEMORY_MB">1G</env>
26 </destination> 26 </destination>
27 </destinations> 27 </destinations>
28 </job_conf> 28 </job_conf>
29 29
30 30