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comparison README.rst @ 3:24d072085816 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 7efdf3224552d113a01043ee5bf4517d770df933
author iuc
date Fri, 31 Mar 2017 11:37:35 -0400
parents d4128a4e49ca
children 96be11bb913d
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2:cfd497973b88 3:24d072085816
4 As described on the official Trinity website 4 As described on the official Trinity website
5 `FAQ <http://trinityrnaseq.sourceforge.net/trinity_faq.html#ques_comp_resources_required>`_, 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 6 trinity requires a large amount of memory to perform the assembly: "roughly
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 30G. 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 edit the TRINITY_MEM_OPTIONS in the 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 <tool_dependency_dir>/environment_settings/TRINITY_MEM_OPTIONS/iuc/trinity/<hash_string>/env.sh 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="TRINITY_MAX_MEMORY">1G</env>
26 </destination>
27 </destinations>
28 </job_conf>
15 29
16 to lower the maximum memory usage to 2G for example:
17 30
18 TRINITY_MEM_OPTIONS='--max_memory 2G --bflyHeapSpaceMax 2G'