Mercurial > repos > iuc > trinity_analyze_diff_expr
diff README.rst @ 0:d4128a4e49ca draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 30192223eeb60f33a42046921351c6ba3c80c90c
author | iuc |
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date | Mon, 21 Nov 2016 11:59:35 -0500 |
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children | 24d072085816 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.rst Mon Nov 21 11:59:35 2016 -0500 @@ -0,0 +1,18 @@ +Trinity memory usage +==================== + +As described on the official Trinity website +`FAQ <http://trinityrnaseq.sourceforge.net/trinity_faq.html#ques_comp_resources_required>`_, +trinity requires a large amount of memory to perform the assembly: "roughly +~1G of RAM per 1M reads to be assembled" + +By default, this tool is configured to limit the memory consumption to 30G. +You might need to lower this limit if the machine(s) executing the jobs have less memory available. +If you have a lot of reads to assemble and a machine with enough memory, you can increase it. +In both cases, you can edit the TRINITY_MEM_OPTIONS in the file: + +<tool_dependency_dir>/environment_settings/TRINITY_MEM_OPTIONS/iuc/trinity/<hash_string>/env.sh + +to lower the maximum memory usage to 2G for example: + +TRINITY_MEM_OPTIONS='--max_memory 2G --bflyHeapSpaceMax 2G'