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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit bc4ea54f0deec4ddec8e6cf79fd547491e165686
author iuc
date Mon, 28 Aug 2017 16:55:02 -0400
parents a29741290660
children 35c9616aaef8
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5bb8e7dcc404 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 95f3e6a69bf939326c73a98e3306bccae8414ecd
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1 Trinity memory usage
5bb8e7dcc404 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 95f3e6a69bf939326c73a98e3306bccae8414ecd
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2 ====================
5bb8e7dcc404 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 95f3e6a69bf939326c73a98e3306bccae8414ecd
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5bb8e7dcc404 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 95f3e6a69bf939326c73a98e3306bccae8414ecd
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4 As described on the official Trinity website
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5 `FAQ <http://trinityrnaseq.sourceforge.net/trinity_faq.html#ques_comp_resources_required>`_,
5bb8e7dcc404 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 95f3e6a69bf939326c73a98e3306bccae8414ecd
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6 trinity requires a large amount of memory to perform the assembly: "roughly
5bb8e7dcc404 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 95f3e6a69bf939326c73a98e3306bccae8414ecd
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7 ~1G of RAM per 1M reads to be assembled"
5bb8e7dcc404 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 95f3e6a69bf939326c73a98e3306bccae8414ecd
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9 By default, this tool is configured to limit the memory consumption to 1G.
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5bb8e7dcc404 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 95f3e6a69bf939326c73a98e3306bccae8414ecd
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10 You might need to lower this limit if the machine(s) executing the jobs have less memory available.
5bb8e7dcc404 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 95f3e6a69bf939326c73a98e3306bccae8414ecd
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11 If you have a lot of reads to assemble and a machine with enough memory, you can increase it.
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a29741290660 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 7efdf3224552d113a01043ee5bf4517d770df933
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12 In both cases, you can set the TRINITY_MAX_MEMORY environmental variable in the destination section of the job_conf.xml file:
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14 <?xml version="1.0"?>
a29741290660 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 7efdf3224552d113a01043ee5bf4517d770df933
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15 <!-- A sample job config that explicitly configures job running the way it is configured by default (if there is no explicit config). -->
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16 <job_conf>
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17 <plugins>
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18 <plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner" workers="4"/>
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19 </plugins>
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20 <handlers>
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21 <handler id="main"/>
a29741290660 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 7efdf3224552d113a01043ee5bf4517d770df933
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22 </handlers>
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23 <destinations>
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24 <destination id="local" runner="local">
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25 <env id="TRINITY_MAX_MEMORY">1G</env>
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26 </destination>
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27 </destinations>
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28 </job_conf>
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