Mercurial > repos > iuc > trinity_stats
comparison README.rst @ 0:b2ce45417d9e draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit c6eab3b60743dfa415dc135d657267cc8a0a31ce
| author | iuc |
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| date | Tue, 08 Aug 2023 09:12:09 +0000 |
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| -1:000000000000 | 0:b2ce45417d9e |
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| 1 Trinity memory usage | |
| 2 ==================== | |
| 3 | |
| 4 As described on the official Trinity website | |
| 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 | |
| 7 ~1G of RAM per 1M reads to be assembled" | |
| 8 | |
| 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. | |
| 11 If you have a lot of reads to assemble and a machine with enough memory, you can increase it. | |
| 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):: | |
| 20 | |
| 21 <?xml version="1.0"?> | |
| 22 <!-- A sample job config that explicitly configures job running the way it is configured by default (if there is no explicit config). --> | |
| 23 <job_conf> | |
| 24 <plugins> | |
| 25 <plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner" workers="4"/> | |
| 26 </plugins> | |
| 27 <handlers> | |
| 28 <handler id="main"/> | |
| 29 </handlers> | |
| 30 <destinations> | |
| 31 <destination id="local" runner="local"> | |
| 32 <env id="GALAXY_MEMORY_MB">1024</env> | |
| 33 </destination> | |
| 34 </destinations> | |
| 35 </job_conf> | |
| 36 | |
| 37 |