Mercurial > repos > iuc > trinity_gene_to_trans_map

comparison README.rst @ 13:460090d15f6f draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit f3d9db3063d2cba26e6fbe82a3eee4e1a6fe0bd5"
author iuc
date Thu, 14 Nov 2019 04:08:47 -0500
parents c2c039e421af
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12:9267b878862e 13:460090d15f6f
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 GALAXY_MEMORY_MB environmental variable in the destination section of the job_conf.xml file:: 12
13 This tool uses the GALAXY_MEMORY_MB environmental variable to limit the its memory usage. If you use a supported cluster type, you just need to limit the memory in the destination section of the job_conf.xml file to the amount of available memory (in MB), for example with a Slurm cluster::
14
15 <destination id="cluster_high_mem" runner="slurm
16 <param id="nativeSpecification">--mem=1024</param>
17 </destination>
18
19 If you cluster type does not support memory limit detection, you can also set manually the GALAXY_MEMORY_MB environmental variable in the destination section of the job_conf.xml file to the amount of available memory (in MB)::
13 20
14 <?xml version="1.0"?> 21 <?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). --> 22 <!-- 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> 23 <job_conf>
17 <plugins> 24 <plugins>
20 <handlers> 27 <handlers>
21 <handler id="main"/> 28 <handler id="main"/>
22 </handlers> 29 </handlers>
23 <destinations> 30 <destinations>
24 <destination id="local" runner="local"> 31 <destination id="local" runner="local">
25 <env id="GALAXY_MEMORY_MB">1G</env> 32 <env id="GALAXY_MEMORY_MB">1024</env>
26 </destination> 33 </destination>
27 </destinations> 34 </destinations>
28 </job_conf> 35 </job_conf>
29 36
30 37