diff tool_dependencies.xml @ 7:fcadce4d9a06 draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
author bgruening
date Sat, 06 May 2017 13:18:09 -0400
parents 243e8f9fb75b
children
line wrap: on
line diff
--- a/tool_dependencies.xml	Wed Feb 11 16:21:51 2015 -0500
+++ b/tool_dependencies.xml	Sat May 06 13:18:09 2017 -0400
@@ -1,12 +1,17 @@
 <?xml version="1.0"?>
 <tool_dependency>
+	<!-- from test tool shed-->
+    <!--<package name="samtools" version="0.1.19">
+        <repository changeset_revision="a0ab0fae27e5" name="package_samtools_0_1_19" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    </package>-->
+    <!--from main tool shed-->
     <package name="samtools" version="0.1.19">
-        <repository changeset_revision="923adc89c666" name="package_samtools_0_1_19" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="c9bd782f5342" name="package_samtools_0_1_19" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
-    <set_environment version="1.0">
-        <environment_variable action="set_to" name="SCRIPT_PATH">$REPOSITORY_INSTALL_DIR</environment_variable>
-    </set_environment>
     <package name="bowtie2" version="2.1.0">
+         <repository changeset_revision="017a00c265f1" name="package_bowtie2_2_1_0" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" />
+     </package>
+    <!--<package name="bowtie2" version="2.1.0">
         <install version="1.0">
             <actions>
                 <action type="download_by_url">http://downloads.sourceforge.net/project/bowtie-bio/bowtie2/2.1.0/bowtie2-2.1.0-source.zip</action>
@@ -32,30 +37,5 @@
         <readme>
 Compiling bowtie2 requires zlib and libpthread to be present on your system.
         </readme>
-    </package>
-    <package name="bowtie" version="0.12.8">
-        <install version="1.0">
-            <actions>
-                <action type="download_by_url">http://downloads.sourceforge.net/project/bowtie-bio/bowtie/0.12.8/bowtie-0.12.8-src.zip</action>
-                <action type="shell_command">make</action>
-                <action type="move_file">
-                    <source>bowtie</source>
-                    <destination>$INSTALL_DIR/bin</destination>
-                </action>
-                <action type="move_file">
-                    <source>bowtie-inspect</source>
-                    <destination>$INSTALL_DIR/bin</destination>
-                </action>
-                <action type="move_file">
-                    <source>bowtie-build</source>
-                    <destination>$INSTALL_DIR/bin</destination>
-                </action>
-                <action type="set_environment">
-                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
-                </action>
-            </actions>
-        </install>
-        <readme>
-        </readme>
-    </package>
+    </package>-->
 </tool_dependency>