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annotate readme.rst @ 16:0e53fc7c15e7 draft

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author yating-l
date Fri, 22 Jul 2016 11:05:32 -0400
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1 Galaxy wrapper for SNAP
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2 ========================
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4 This wrapper is copyright 2016-2017 by Yating Liu
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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
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7 Parser.
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9 Reference
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10 ----------------------
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12 Korf I. Gene finding in novel Genomes. BMC Bioinformatics 2004, 5:59
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14 Installation
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15 -----------------------
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17 To install SNAP, please download SNAP from
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19 http://korflab.ucdavis.edu/Software/snap-2013-11-29.tar.gz
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21 and follow the installation instractions. The software is routinely compiled and tested on Mac OS X. It should compile
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22 fine on any Linux/Unix type operating systems.
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23 The default compiler is gcc. If you have gcc installed, the easiest is to just compile as:
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24 ```
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25 make
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26 ```
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28 The ZOE environment variable is used by SNAP to find the HMM files. Set this
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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
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31 ```
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32 setenv ZOE /usr/local/snap # csh, tcsh, etc
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33 ```
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34 or
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35 ```
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36 export ZOE=/usr/local/snap # sh, bash, etc
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37 ```
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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:
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39 ```
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40 <tool file="galaxy/tools/myTools/snap/snap.xml" />
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41 ```
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