Mercurial > repos > iuc > trinity_stats

annotate README.rst @ 0:ce94ad22e8c1 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit c6eab3b60743dfa415dc135d657267cc8a0a31ce
author iuc
date Tue, 08 Aug 2023 09:00:45 +0000
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
ce94ad22e8c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit c6eab3b60743dfa415dc135d657267cc8a0a31ce
iuc
parents:
diff changeset
1 Trinity memory usage
ce94ad22e8c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit c6eab3b60743dfa415dc135d657267cc8a0a31ce
iuc
parents:
diff changeset
2 ====================
ce94ad22e8c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit c6eab3b60743dfa415dc135d657267cc8a0a31ce
iuc
parents:
diff changeset
3
ce94ad22e8c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit c6eab3b60743dfa415dc135d657267cc8a0a31ce
iuc
parents:
diff changeset
4 As described on the official Trinity website
ce94ad22e8c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit c6eab3b60743dfa415dc135d657267cc8a0a31ce
iuc
parents:
diff changeset
5 `FAQ <http://trinityrnaseq.sourceforge.net/trinity_faq.html#ques_comp_resources_required>`_,
ce94ad22e8c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit c6eab3b60743dfa415dc135d657267cc8a0a31ce
iuc
parents:
diff changeset
6 trinity requires a large amount of memory to perform the assembly: "roughly
ce94ad22e8c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit c6eab3b60743dfa415dc135d657267cc8a0a31ce
iuc
parents:
diff changeset
7 ~1G of RAM per 1M reads to be assembled"
ce94ad22e8c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit c6eab3b60743dfa415dc135d657267cc8a0a31ce
iuc
parents:
diff changeset
8
ce94ad22e8c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit c6eab3b60743dfa415dc135d657267cc8a0a31ce
iuc
parents:
diff changeset
9 By default, this tool is configured to limit the memory consumption to 1G.
ce94ad22e8c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit c6eab3b60743dfa415dc135d657267cc8a0a31ce
iuc
parents:
diff changeset
10 You might need to lower this limit if the machine(s) executing the jobs have less memory available.
ce94ad22e8c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit c6eab3b60743dfa415dc135d657267cc8a0a31ce
iuc
parents:
diff changeset
11 If you have a lot of reads to assemble and a machine with enough memory, you can increase it.
ce94ad22e8c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit c6eab3b60743dfa415dc135d657267cc8a0a31ce
iuc
parents:
diff changeset
12
ce94ad22e8c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit c6eab3b60743dfa415dc135d657267cc8a0a31ce
iuc
parents:
diff changeset
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::
ce94ad22e8c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit c6eab3b60743dfa415dc135d657267cc8a0a31ce
iuc
parents:
diff changeset
14
ce94ad22e8c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit c6eab3b60743dfa415dc135d657267cc8a0a31ce
iuc
parents:
diff changeset
15 <destination id="cluster_high_mem" runner="slurm
ce94ad22e8c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit c6eab3b60743dfa415dc135d657267cc8a0a31ce
iuc
parents:
diff changeset
16 <param id="nativeSpecification">--mem=1024</param>
ce94ad22e8c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit c6eab3b60743dfa415dc135d657267cc8a0a31ce
iuc
parents:
diff changeset
17 </destination>
ce94ad22e8c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit c6eab3b60743dfa415dc135d657267cc8a0a31ce
iuc
parents:
diff changeset
18
ce94ad22e8c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit c6eab3b60743dfa415dc135d657267cc8a0a31ce
iuc
parents:
diff changeset
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)::
ce94ad22e8c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit c6eab3b60743dfa415dc135d657267cc8a0a31ce
iuc
parents:
diff changeset
20
ce94ad22e8c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit c6eab3b60743dfa415dc135d657267cc8a0a31ce
iuc
parents:
diff changeset
21 <?xml version="1.0"?>
ce94ad22e8c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit c6eab3b60743dfa415dc135d657267cc8a0a31ce
iuc
parents:
diff changeset
22 <!-- A sample job config that explicitly configures job running the way it is configured by default (if there is no explicit config). -->
ce94ad22e8c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit c6eab3b60743dfa415dc135d657267cc8a0a31ce
iuc
parents:
diff changeset
23 <job_conf>
ce94ad22e8c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit c6eab3b60743dfa415dc135d657267cc8a0a31ce
iuc
parents:
diff changeset
24 <plugins>
ce94ad22e8c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit c6eab3b60743dfa415dc135d657267cc8a0a31ce
iuc
parents:
diff changeset
25 <plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner" workers="4"/>
ce94ad22e8c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit c6eab3b60743dfa415dc135d657267cc8a0a31ce
iuc
parents:
diff changeset
26 </plugins>
ce94ad22e8c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit c6eab3b60743dfa415dc135d657267cc8a0a31ce
iuc
parents:
diff changeset
27 <handlers>
ce94ad22e8c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit c6eab3b60743dfa415dc135d657267cc8a0a31ce
iuc
parents:
diff changeset
28 <handler id="main"/>
ce94ad22e8c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit c6eab3b60743dfa415dc135d657267cc8a0a31ce
iuc
parents:
diff changeset
29 </handlers>
ce94ad22e8c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit c6eab3b60743dfa415dc135d657267cc8a0a31ce
iuc
parents:
diff changeset
30 <destinations>
ce94ad22e8c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit c6eab3b60743dfa415dc135d657267cc8a0a31ce
iuc
parents:
diff changeset
31 <destination id="local" runner="local">
ce94ad22e8c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit c6eab3b60743dfa415dc135d657267cc8a0a31ce
iuc
parents:
diff changeset
32 <env id="GALAXY_MEMORY_MB">1024</env>
ce94ad22e8c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit c6eab3b60743dfa415dc135d657267cc8a0a31ce
iuc
parents:
diff changeset
33 </destination>
ce94ad22e8c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit c6eab3b60743dfa415dc135d657267cc8a0a31ce
iuc
parents:
diff changeset
34 </destinations>
ce94ad22e8c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit c6eab3b60743dfa415dc135d657267cc8a0a31ce
iuc
parents:
diff changeset
35 </job_conf>
ce94ad22e8c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit c6eab3b60743dfa415dc135d657267cc8a0a31ce
iuc
parents:
diff changeset
36
ce94ad22e8c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit c6eab3b60743dfa415dc135d657267cc8a0a31ce
iuc
parents:
diff changeset
37