Mercurial > repos > yhoogstrate > package_featurecounts_1_4_6

changeset 1:42796f06052f draft default tip

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planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit b05640a41e2106782ac7f88f858b0a256918fa6f
author yhoogstrate
date Thu, 10 Sep 2015 05:09:56 -0400
parents a4c247fdd71b
children
files tool_dependencies.xml
diffstat 1 files changed, 27 insertions(+), 29 deletions(-) [+]
line wrap: on
line diff
--- a/tool_dependencies.xml	Mon Jun 01 07:17:56 2015 -0400
+++ b/tool_dependencies.xml	Thu Sep 10 05:09:56 2015 -0400
@@ -1,32 +1,30 @@
 <?xml version="1.0"?>
 <tool_dependency>
-	<package name="featurecounts" version="1.4.6.p1">
-		<install version="1.0">
-			<actions>
-				<action type="shell_command">
-					wget http://garr.dl.sourceforge.net/project/subread/subread-1.4.6-p1/subread-1.4.6-p1-source.tar.gz	&amp;&amp;
-					tar -zxvf subread-1.4.6-p1-source.tar.gz															&amp;&amp;
-					cd subread-1.4.6-p1-source/src/																		&amp;&amp;
-					make -f Makefile.Linux																				&amp;&amp;
-					cd ../../
-				</action>
-				<action type="move_file">
-					<source>../subread-1.4.6-p1-source/bin/featureCounts</source>
-					<destination>$INSTALL_DIR/bin/</destination>
-				</action>
-				<action type="set_environment">
-					<environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
-					<!--<environment_variable name="PATH" action="prepend_to">$REPOSITORY_INSTALL_DIR</environment_variable>-->
-				</action>
-			</actions>
-		</install>
-		<readme>
-			Downloads and installs featureCounts.
-			
-			Prerequisites:
-			- wget
-			- gnu-autotools (make)
-			- tar
-		</readme>
-	</package>
+    <package name="featurecounts" version="1.4.6.p1">
+        <install version="1.0">
+            <actions>
+                <action type="download_by_url"
+                    sha256sum="48e0c516684c4771f965a0a3010fbc0ad55fb54cfd8f7090be3f55e7b5c09f36">http://sourceforge.net/projects/subread/files/subread-1.4.6-p1/subread-1.4.6-p1-source.tar.gz/download</action>
+                <action type="shell_command"><![CDATA[
+                    cd src/ &&
+                    make -f Makefile.Linux
+                ]]></action>
+                <action type="move_file">
+                    <source>bin/featureCounts</source>
+                    <destination>$INSTALL_DIR/bin/</destination>
+                </action>
+                <action type="set_environment">
+                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
+                </action>
+            </actions>
+        </install>
+        <readme>
+            Downloads and installs featureCounts.
+
+            Prerequisites:
+            - wget
+            - gnu-autotools (make)
+            - tar
+        </readme>
+    </package>
 </tool_dependency>