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| author | yating-l |
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| date | Wed, 12 Apr 2017 17:37:47 -0400 |
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| 1 Galaxy wrapper for SNAP | |
| 2 ======================== | |
| 3 | |
| 4 This wrapper is copyright 2016-2017 by Yating Liu | |
| 5 | |
| 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 | |
| 7 Parser. | |
| 8 | |
| 9 Reference | |
| 10 ---------------------- | |
| 11 | |
| 12 Korf I. Gene finding in novel Genomes. BMC Bioinformatics 2004, 5:59 | |
| 13 | |
| 14 Installation | |
| 15 ----------------------- | |
| 16 | |
| 17 To install SNAP, please download SNAP from | |
| 18 | |
| 19 http://korflab.ucdavis.edu/Software/snap-2013-11-29.tar.gz | |
| 20 | |
| 21 and follow the installation instractions. The software is routinely compiled and tested on Mac OS X. It should compile | |
| 22 fine on any Linux/Unix type operating systems. | |
| 23 The default compiler is gcc. If you have gcc installed, the easiest is to just compile as: | |
| 24 ``` | |
| 25 make | |
| 26 ``` | |
| 27 | |
| 28 The ZOE environment variable is used by SNAP to find the HMM files. Set this | |
| 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 | |
| 30 | |
| 31 ``` | |
| 32 setenv ZOE /usr/local/snap # csh, tcsh, etc | |
| 33 ``` | |
| 34 or | |
| 35 ``` | |
| 36 export ZOE=/usr/local/snap # sh, bash, etc | |
| 37 ``` | |
| 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: | |
| 39 ``` | |
| 40 <tool file="galaxy/tools/myTools/snap/snap.xml" /> | |
| 41 ``` | |
| 42 | |
| 43 | |
| 44 | |
| 45 | |
| 46 |