Mercurial > repos > yating-l > snap
changeset 2:b8d0fe342276 draft
planemo upload commit 0ba99fe246099cc1827f71f2722d253becee64ba
| author | yating-l |
|---|---|
| date | Thu, 21 Jul 2016 12:39:21 -0400 |
| parents | e177d8e95666 |
| children | f997ceb8bd37 |
| files | README.rst.md readme.md tool_dependencies.xml |
| diffstat | 3 files changed, 46 insertions(+), 64 deletions(-) [+] |
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--- /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: +``` +<tool file="galaxy/tools/myTools/snap/snap.xml" /> +``` + + + + +
--- 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 $GALAXY_ROOT/config/tool_conf.xml file to make the tool available to Galaxy. For example: -``` -<tool file="galaxy/tools/myTools/snap/snap.xml" /> -``` - - - - -
--- a/tool_dependencies.xml Thu Jul 21 11:55:35 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,18 +0,0 @@ -<?xml version="1.0"?> -<tool_dependency> - <package name="snap" version="0.1.0"> - <install version="0.1.0"> - <actions> - <action type="download_by_url">http://korflab.ucdavis.edu/Software/snap-2013-11-29.tar.gz</action> - <action type="shell_command">make</action> - <action type="set_environment"> - <environment_variable name="ZOE" action="set_to">$INSTALL_DIR</environment_variable> - </action> - </actions> - </install> - <readme>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. - </readme> - </package> -</tool_dependency>