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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit baff3f60cf4a039a74091e24b3453f4499cfaf02
author iuc
date Wed, 27 Jul 2016 08:42:42 -0400
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d02ec0323dda planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit baff3f60cf4a039a74091e24b3453f4499cfaf02
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1 Trinity memory usage
d02ec0323dda planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit baff3f60cf4a039a74091e24b3453f4499cfaf02
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2 ====================
d02ec0323dda planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit baff3f60cf4a039a74091e24b3453f4499cfaf02
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d02ec0323dda planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit baff3f60cf4a039a74091e24b3453f4499cfaf02
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4 As described on the official Trinity website
d02ec0323dda planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit baff3f60cf4a039a74091e24b3453f4499cfaf02
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5 `FAQ <http://trinityrnaseq.sourceforge.net/trinity_faq.html#ques_comp_resources_required>`_,
d02ec0323dda planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit baff3f60cf4a039a74091e24b3453f4499cfaf02
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6 trinity requires a large amount of memory to perform the assembly: "roughly
d02ec0323dda planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit baff3f60cf4a039a74091e24b3453f4499cfaf02
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7 ~1G of RAM per 1M reads to be assembled"
d02ec0323dda planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit baff3f60cf4a039a74091e24b3453f4499cfaf02
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d02ec0323dda planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit baff3f60cf4a039a74091e24b3453f4499cfaf02
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9 By default, this tool is configured to limit the memory consumption to 30G.
d02ec0323dda planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit baff3f60cf4a039a74091e24b3453f4499cfaf02
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10 You might need to lower this limit if the machine(s) executing the jobs have less memory available.
d02ec0323dda planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit baff3f60cf4a039a74091e24b3453f4499cfaf02
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11 If you have a lot of reads to assemble and a machine with enough memory, you can increase it.
d02ec0323dda planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit baff3f60cf4a039a74091e24b3453f4499cfaf02
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12 In both cases, you can edit the TRINITY_MEM_OPTIONS in the file:
d02ec0323dda planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit baff3f60cf4a039a74091e24b3453f4499cfaf02
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d02ec0323dda planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit baff3f60cf4a039a74091e24b3453f4499cfaf02
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14 <tool_dependency_dir>/environment_settings/TRINITY_MEM_OPTIONS/iuc/trinity/<hash_string>/env.sh
d02ec0323dda planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit baff3f60cf4a039a74091e24b3453f4499cfaf02
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d02ec0323dda planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit baff3f60cf4a039a74091e24b3453f4499cfaf02
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16 to lower the maximum memory usage to 2G for example:
d02ec0323dda planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit baff3f60cf4a039a74091e24b3453f4499cfaf02
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d02ec0323dda planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit baff3f60cf4a039a74091e24b3453f4499cfaf02
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18 TRINITY_MEM_OPTIONS='--max_memory 2G --bflyHeapSpaceMax 2G'