Mercurial > repos > iuc > trinity_analyze_diff_expr

annotate README.rst @ 12:de949e8c076d draft

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 f3d9db3063d2cba26e6fbe82a3eee4e1a6fe0bd5"
author iuc
date Thu, 14 Nov 2019 04:07:10 -0500
parents c5f02e00d596
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
d4128a4e49ca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 30192223eeb60f33a42046921351c6ba3c80c90c
iuc
parents:
diff changeset
1 Trinity memory usage
d4128a4e49ca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 30192223eeb60f33a42046921351c6ba3c80c90c
iuc
parents:
diff changeset
2 ====================
d4128a4e49ca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 30192223eeb60f33a42046921351c6ba3c80c90c
iuc
parents:
diff changeset
3
d4128a4e49ca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 30192223eeb60f33a42046921351c6ba3c80c90c
iuc
parents:
diff changeset
4 As described on the official Trinity website
d4128a4e49ca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 30192223eeb60f33a42046921351c6ba3c80c90c
iuc
parents:
diff changeset
5 `FAQ <http://trinityrnaseq.sourceforge.net/trinity_faq.html#ques_comp_resources_required>`_,
d4128a4e49ca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 30192223eeb60f33a42046921351c6ba3c80c90c
iuc
parents:
diff changeset
6 trinity requires a large amount of memory to perform the assembly: "roughly
d4128a4e49ca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 30192223eeb60f33a42046921351c6ba3c80c90c
iuc
parents:
diff changeset
7 ~1G of RAM per 1M reads to be assembled"
d4128a4e49ca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 30192223eeb60f33a42046921351c6ba3c80c90c
iuc
parents:
diff changeset
8
3
24d072085816 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 7efdf3224552d113a01043ee5bf4517d770df933
iuc
parents: 0
diff changeset
9 By default, this tool is configured to limit the memory consumption to 1G.
0
d4128a4e49ca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 30192223eeb60f33a42046921351c6ba3c80c90c
iuc
parents:
diff changeset
10 You might need to lower this limit if the machine(s) executing the jobs have less memory available.
d4128a4e49ca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 30192223eeb60f33a42046921351c6ba3c80c90c
iuc
parents:
diff changeset
11 If you have a lot of reads to assemble and a machine with enough memory, you can increase it.
12
de949e8c076d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit f3d9db3063d2cba26e6fbe82a3eee4e1a6fe0bd5"
iuc
parents: 6
diff changeset
12
de949e8c076d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit f3d9db3063d2cba26e6fbe82a3eee4e1a6fe0bd5"
iuc
parents: 6
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::
de949e8c076d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit f3d9db3063d2cba26e6fbe82a3eee4e1a6fe0bd5"
iuc
parents: 6
diff changeset
14
de949e8c076d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit f3d9db3063d2cba26e6fbe82a3eee4e1a6fe0bd5"
iuc
parents: 6
diff changeset
15 <destination id="cluster_high_mem" runner="slurm
de949e8c076d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit f3d9db3063d2cba26e6fbe82a3eee4e1a6fe0bd5"
iuc
parents: 6
diff changeset
16 <param id="nativeSpecification">--mem=1024</param>
de949e8c076d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit f3d9db3063d2cba26e6fbe82a3eee4e1a6fe0bd5"
iuc
parents: 6
diff changeset
17 </destination>
de949e8c076d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit f3d9db3063d2cba26e6fbe82a3eee4e1a6fe0bd5"
iuc
parents: 6
diff changeset
18
de949e8c076d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit f3d9db3063d2cba26e6fbe82a3eee4e1a6fe0bd5"
iuc
parents: 6
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)::
0
d4128a4e49ca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 30192223eeb60f33a42046921351c6ba3c80c90c
iuc
parents:
diff changeset
20
5
96be11bb913d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 7f726b691ead726864f1b67230cb5d58e16b5f58
iuc
parents: 3
diff changeset
21 <?xml version="1.0"?>
96be11bb913d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 7f726b691ead726864f1b67230cb5d58e16b5f58
iuc
parents: 3
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). -->
96be11bb913d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 7f726b691ead726864f1b67230cb5d58e16b5f58
iuc
parents: 3
diff changeset
23 <job_conf>
96be11bb913d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 7f726b691ead726864f1b67230cb5d58e16b5f58
iuc
parents: 3
diff changeset
24 <plugins>
96be11bb913d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 7f726b691ead726864f1b67230cb5d58e16b5f58
iuc
parents: 3
diff changeset
25 <plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner" workers="4"/>
96be11bb913d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 7f726b691ead726864f1b67230cb5d58e16b5f58
iuc
parents: 3
diff changeset
26 </plugins>
96be11bb913d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 7f726b691ead726864f1b67230cb5d58e16b5f58
iuc
parents: 3
diff changeset
27 <handlers>
96be11bb913d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 7f726b691ead726864f1b67230cb5d58e16b5f58
iuc
parents: 3
diff changeset
28 <handler id="main"/>
96be11bb913d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 7f726b691ead726864f1b67230cb5d58e16b5f58
iuc
parents: 3
diff changeset
29 </handlers>
96be11bb913d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 7f726b691ead726864f1b67230cb5d58e16b5f58
iuc
parents: 3
diff changeset
30 <destinations>
96be11bb913d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 7f726b691ead726864f1b67230cb5d58e16b5f58
iuc
parents: 3
diff changeset
31 <destination id="local" runner="local">
12
de949e8c076d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit f3d9db3063d2cba26e6fbe82a3eee4e1a6fe0bd5"
iuc
parents: 6
diff changeset
32 <env id="GALAXY_MEMORY_MB">1024</env>
5
96be11bb913d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 7f726b691ead726864f1b67230cb5d58e16b5f58
iuc
parents: 3
diff changeset
33 </destination>
96be11bb913d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 7f726b691ead726864f1b67230cb5d58e16b5f58
iuc
parents: 3
diff changeset
34 </destinations>
96be11bb913d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 7f726b691ead726864f1b67230cb5d58e16b5f58
iuc
parents: 3
diff changeset
35 </job_conf>
0
d4128a4e49ca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 30192223eeb60f33a42046921351c6ba3c80c90c
iuc
parents:
diff changeset
36
3
24d072085816 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 7efdf3224552d113a01043ee5bf4517d770df933
iuc
parents: 0
diff changeset
37