Mercurial > repos > yating-l > snap

annotate README.rst @ 19:a7f57cf408e8 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit ff6c810cf2b46e59b45738700e68431743e4b83d
author yating-l
date Fri, 12 Aug 2016 12:03:46 -0400
parents f997ceb8bd37
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
3
f997ceb8bd37 planemo upload commit 0ba99fe246099cc1827f71f2722d253becee64ba
yating-l
parents:
diff changeset
1 Galaxy wrapper for SNAP
f997ceb8bd37 planemo upload commit 0ba99fe246099cc1827f71f2722d253becee64ba
yating-l
parents:
diff changeset
2 ========================
f997ceb8bd37 planemo upload commit 0ba99fe246099cc1827f71f2722d253becee64ba
yating-l
parents:
diff changeset
3
f997ceb8bd37 planemo upload commit 0ba99fe246099cc1827f71f2722d253becee64ba
yating-l
parents:
diff changeset
4 This wrapper is copyright 2016-2017 by Yating Liu
f997ceb8bd37 planemo upload commit 0ba99fe246099cc1827f71f2722d253becee64ba
yating-l
parents:
diff changeset
5
f997ceb8bd37 planemo upload commit 0ba99fe246099cc1827f71f2722d253becee64ba
yating-l
parents:
diff changeset
6 This is a wrapper for the gene prediction tool SNAP. SNAP is a general purpose gene finding program suitable for both eukaryotic and prokaryotic genomes. SNAP is an acroynm for Semi-HMM-based Nucleic Acid
f997ceb8bd37 planemo upload commit 0ba99fe246099cc1827f71f2722d253becee64ba
yating-l
parents:
diff changeset
7 Parser.
f997ceb8bd37 planemo upload commit 0ba99fe246099cc1827f71f2722d253becee64ba
yating-l
parents:
diff changeset
8
f997ceb8bd37 planemo upload commit 0ba99fe246099cc1827f71f2722d253becee64ba
yating-l
parents:
diff changeset
9 Reference
f997ceb8bd37 planemo upload commit 0ba99fe246099cc1827f71f2722d253becee64ba
yating-l
parents:
diff changeset
10 ----------------------
f997ceb8bd37 planemo upload commit 0ba99fe246099cc1827f71f2722d253becee64ba
yating-l
parents:
diff changeset
11
f997ceb8bd37 planemo upload commit 0ba99fe246099cc1827f71f2722d253becee64ba
yating-l
parents:
diff changeset
12 Korf I. Gene finding in novel Genomes. BMC Bioinformatics 2004, 5:59
f997ceb8bd37 planemo upload commit 0ba99fe246099cc1827f71f2722d253becee64ba
yating-l
parents:
diff changeset
13
f997ceb8bd37 planemo upload commit 0ba99fe246099cc1827f71f2722d253becee64ba
yating-l
parents:
diff changeset
14 Installation
f997ceb8bd37 planemo upload commit 0ba99fe246099cc1827f71f2722d253becee64ba
yating-l
parents:
diff changeset
15 -----------------------
f997ceb8bd37 planemo upload commit 0ba99fe246099cc1827f71f2722d253becee64ba
yating-l
parents:
diff changeset
16
f997ceb8bd37 planemo upload commit 0ba99fe246099cc1827f71f2722d253becee64ba
yating-l
parents:
diff changeset
17 To install SNAP, please download SNAP from
f997ceb8bd37 planemo upload commit 0ba99fe246099cc1827f71f2722d253becee64ba
yating-l
parents:
diff changeset
18
f997ceb8bd37 planemo upload commit 0ba99fe246099cc1827f71f2722d253becee64ba
yating-l
parents:
diff changeset
19 http://korflab.ucdavis.edu/Software/snap-2013-11-29.tar.gz
f997ceb8bd37 planemo upload commit 0ba99fe246099cc1827f71f2722d253becee64ba
yating-l
parents:
diff changeset
20
f997ceb8bd37 planemo upload commit 0ba99fe246099cc1827f71f2722d253becee64ba
yating-l
parents:
diff changeset
21 and follow the installation instractions. The software is routinely compiled and tested on Mac OS X. It should compile
f997ceb8bd37 planemo upload commit 0ba99fe246099cc1827f71f2722d253becee64ba
yating-l
parents:
diff changeset
22 fine on any Linux/Unix type operating systems.
f997ceb8bd37 planemo upload commit 0ba99fe246099cc1827f71f2722d253becee64ba
yating-l
parents:
diff changeset
23 The default compiler is gcc. If you have gcc installed, the easiest is to just compile as:
f997ceb8bd37 planemo upload commit 0ba99fe246099cc1827f71f2722d253becee64ba
yating-l
parents:
diff changeset
24 ```
f997ceb8bd37 planemo upload commit 0ba99fe246099cc1827f71f2722d253becee64ba
yating-l
parents:
diff changeset
25 make
f997ceb8bd37 planemo upload commit 0ba99fe246099cc1827f71f2722d253becee64ba
yating-l
parents:
diff changeset
26 ```
f997ceb8bd37 planemo upload commit 0ba99fe246099cc1827f71f2722d253becee64ba
yating-l
parents:
diff changeset
27
f997ceb8bd37 planemo upload commit 0ba99fe246099cc1827f71f2722d253becee64ba
yating-l
parents:
diff changeset
28 The ZOE environment variable is used by SNAP to find the HMM files. Set this
f997ceb8bd37 planemo upload commit 0ba99fe246099cc1827f71f2722d253becee64ba
yating-l
parents:
diff changeset
29 to the directory containing this file. For example, if you unpackaged the tar-ball in /usr/local/snap, set the ZOE environment variable to /usr/local/snap
f997ceb8bd37 planemo upload commit 0ba99fe246099cc1827f71f2722d253becee64ba
yating-l
parents:
diff changeset
30
f997ceb8bd37 planemo upload commit 0ba99fe246099cc1827f71f2722d253becee64ba
yating-l
parents:
diff changeset
31 ```
f997ceb8bd37 planemo upload commit 0ba99fe246099cc1827f71f2722d253becee64ba
yating-l
parents:
diff changeset
32 setenv ZOE /usr/local/snap # csh, tcsh, etc
f997ceb8bd37 planemo upload commit 0ba99fe246099cc1827f71f2722d253becee64ba
yating-l
parents:
diff changeset
33 ```
f997ceb8bd37 planemo upload commit 0ba99fe246099cc1827f71f2722d253becee64ba
yating-l
parents:
diff changeset
34 or
f997ceb8bd37 planemo upload commit 0ba99fe246099cc1827f71f2722d253becee64ba
yating-l
parents:
diff changeset
35 ```
f997ceb8bd37 planemo upload commit 0ba99fe246099cc1827f71f2722d253becee64ba
yating-l
parents:
diff changeset
36 export ZOE=/usr/local/snap # sh, bash, etc
f997ceb8bd37 planemo upload commit 0ba99fe246099cc1827f71f2722d253becee64ba
yating-l
parents:
diff changeset
37 ```
f997ceb8bd37 planemo upload commit 0ba99fe246099cc1827f71f2722d253becee64ba
yating-l
parents:
diff changeset
38 To install the wrapper copy the snap folder in the galaxy tools and modify the $GALAXY_ROOT/config/tool_conf.xml file to make the tool available to Galaxy. For example:
f997ceb8bd37 planemo upload commit 0ba99fe246099cc1827f71f2722d253becee64ba
yating-l
parents:
diff changeset
39 ```
f997ceb8bd37 planemo upload commit 0ba99fe246099cc1827f71f2722d253becee64ba
yating-l
parents:
diff changeset
40 <tool file="galaxy/tools/myTools/snap/snap.xml" />
f997ceb8bd37 planemo upload commit 0ba99fe246099cc1827f71f2722d253becee64ba
yating-l
parents:
diff changeset
41 ```
f997ceb8bd37 planemo upload commit 0ba99fe246099cc1827f71f2722d253becee64ba
yating-l
parents:
diff changeset
42
f997ceb8bd37 planemo upload commit 0ba99fe246099cc1827f71f2722d253becee64ba
yating-l
parents:
diff changeset
43
f997ceb8bd37 planemo upload commit 0ba99fe246099cc1827f71f2722d253becee64ba
yating-l
parents:
diff changeset
44
f997ceb8bd37 planemo upload commit 0ba99fe246099cc1827f71f2722d253becee64ba
yating-l
parents:
diff changeset
45
f997ceb8bd37 planemo upload commit 0ba99fe246099cc1827f71f2722d253becee64ba
yating-l
parents:
diff changeset
46