Mercurial > repos > iuc > trinity_contig_exn50_statistic

comparison README.rst @ 3:bc4e467da875 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 7f726b691ead726864f1b67230cb5d58e16b5f58
author iuc
date Fri, 15 Dec 2017 07:57:13 -0500
parents 570f2b1f3cd9
children 4687ecf0eb2d
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2:a482a374577d 3:bc4e467da875
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 TRINITY_MAX_MEMORY 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>
18 <plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner" workers="4"/> 18 <plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner" workers="4"/>
19 </plugins> 19 </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="TRINITY_MAX_MEMORY">1G</env>
26 </destination> 26 </destination>
27 </destinations> 27 </destinations>
28 </job_conf> 28 </job_conf>
29 29
30 30