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changeset 9:006081904eec draft

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planemo upload commit d1ae46c18d1157b3dd74ac799911f5f232a53931-dirty
author yating-l
date Thu, 21 Jul 2016 19:07:30 -0400
parents 7107b7be52da
children 5a894cccfcd0
files README.rst readme.rst snap.xml tool_dependencies.xml
diffstat 4 files changed, 67 insertions(+), 48 deletions(-) [+]
line wrap: on
line diff
--- a/README.rst	Thu Jul 21 17:25:04 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" />
-```
-
-
-
-
-
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/readme.rst	Thu Jul 21 19:07:30 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 $GALAXY_ROOT/config/tool_conf.xml file to make the tool available to Galaxy. For example:
+```
+<tool file="galaxy/tools/myTools/snap/snap.xml" />
+```
+
+
+
+
+
--- a/snap.xml	Thu Jul 21 17:25:04 2016 -0400
+++ b/snap.xml	Thu Jul 21 19:07:30 2016 -0400
@@ -1,6 +1,6 @@
 <tool id="snap" name="Semi-HMM-based Nucleic Acid Parser (SNAP)" version="0.1.0">
     <requirements>
-	<requirement type="package" version="0.1.0">snap</requirement>
+        <requirement type="package" version="0.1.0">snap</requirement>
     </requirements>
     <stdio>
         <exit_code range="1:" />
--- a/tool_dependencies.xml	Thu Jul 21 17:25:04 2016 -0400
+++ b/tool_dependencies.xml	Thu Jul 21 19:07:30 2016 -0400
@@ -1,6 +1,25 @@
 <?xml version="1.0"?>
 <tool_dependency>
     <package name="snap" version="0.1.0">
-        <repository changeset_revision="9b410d18d689" name="package_snap_0_1_0" owner="yating-l" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+        <install version="0.1.0">
+            <actions_group>
+                <actions>
+                    <action type="download_by_url">http://korflab.ucdavis.edu/Software/snap-2013-11-29.tar.gz</action>
+                    <action type="move_directory_files">
+                            <source_directory>.</source_directory>
+                            <destination_directory>$INSTALL_DIR</destination_directory>
+                    </action>
+                    <action type="shell_command">make</action>
+                    <action type="set_environment">
+                        <environment_variable name="ZOE" action="set_to">$INSTALL_DIR/HMM</environment_variable>
+                        <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR</environment_variable>
+                    </action>
+                </actions>
+            </actions_group>
+        </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>