# HG changeset patch # User yating-l # Date 1469119161 14400 # Node ID b8d0fe34227685a86e6b41ed08e97d039c765208 # Parent e177d8e95666d6d0dbf0f51a506ae2c84efd3971 planemo upload commit 0ba99fe246099cc1827f71f2722d253becee64ba diff -r e177d8e95666 -r b8d0fe342276 README.rst.md --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.rst.md Thu Jul 21 12:39:21 2016 -0400 @@ -0,0 +1,46 @@ +Galaxy wrapper for SNAP +======================== + +This wrapper is copyright 2016-2017 by Yating Liu + +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 +Parser. + +Reference +---------------------- + + Korf I. Gene finding in novel Genomes. BMC Bioinformatics 2004, 5:59 + +Installation +----------------------- + +To install SNAP, please download SNAP from + +http://korflab.ucdavis.edu/Software/snap-2013-11-29.tar.gz + +and follow the installation instractions. The software is routinely compiled and tested on Mac OS X. It should compile +fine on any Linux/Unix type operating systems. +The default compiler is gcc. If you have gcc installed, the easiest is to just compile as: +``` + make +``` + +The ZOE environment variable is used by SNAP to find the HMM files. Set this +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 + +``` + setenv ZOE /usr/local/snap # csh, tcsh, etc +``` + or +``` + export ZOE=/usr/local/snap # sh, bash, etc +``` +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: +``` + +``` + + + + + diff -r e177d8e95666 -r b8d0fe342276 readme.md --- a/readme.md Thu Jul 21 11:55:35 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,46 +0,0 @@ -Galaxy wrapper for SNAP -======================== - -This wrapper is copyright 2016-2017 by Yating Liu - -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 -Parser. - -Reference ----------------------- - - Korf I. Gene finding in novel Genomes. BMC Bioinformatics 2004, 5:59 - -Installation ------------------------ - -To install SNAP, please download SNAP from - -http://korflab.ucdavis.edu/Software/snap-2013-11-29.tar.gz - -and follow the installation instractions. The software is routinely compiled and tested on Mac OS X. It should compile -fine on any Linux/Unix type operating systems. -The default compiler is gcc. If you have gcc installed, the easiest is to just compile as: -``` - make -``` - -The ZOE environment variable is used by SNAP to find the HMM files. Set this -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 - -``` - setenv ZOE /usr/local/snap # csh, tcsh, etc -``` - or -``` - export ZOE=/usr/local/snap # sh, bash, etc -``` -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: -``` - -``` - - - - - diff -r e177d8e95666 -r b8d0fe342276 tool_dependencies.xml --- a/tool_dependencies.xml Thu Jul 21 11:55:35 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,18 +0,0 @@ - - - - - - http://korflab.ucdavis.edu/Software/snap-2013-11-29.tar.gz - make - - $INSTALL_DIR - - - - 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 - Parser. - - -