Mercurial > repos > iuc > package_fastqc_0_11_4

changeset 2:a8f485b2efd9 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_fastqc_0_11_4 commit b'67cff25a50ba173b0468819204d0999496f68ea9'
author iuc
date Tue, 19 Jan 2016 09:37:46 -0500
parents a288b8869b7b
children
files tool_dependencies.xml
diffstat 1 files changed, 12 insertions(+), 7 deletions(-) [+]
line wrap: on
line diff
--- a/tool_dependencies.xml	Tue Jan 19 06:56:53 2016 -0500
+++ b/tool_dependencies.xml	Tue Jan 19 09:37:46 2016 -0500
@@ -8,22 +8,27 @@
                     <action type="move_directory_files">
                         <source_directory>../FastQC</source_directory>
                         <destination_directory>$INSTALL_DIR</destination_directory>
-                        <action type="shell_command">chmod ugo+x $INSTALL_DIR/fastqc</action>
+                    </action>
+                    <action type="chmod">
+                        <file mode="755">$INSTALL_DIR/fastqc</file>
+                    </action>
+                    <action type="set_environment">
+                        <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR</environment_variable>
+                        <environment_variable name="FASTQC_JAR_PATH" action="set_to">$INSTALL_DIR</environment_variable>
                     </action>
                 </actions>
                 <actions os="darwin" architecture="x86_64">
                     <action type="download_by_url" sha256sum="bd4089397cfa1086d81e7b29508542d2478917df8d1ef1fb494616da1b8e651a">https://depot.galaxyproject.org/software/fastqc/fastqc_0.11.4_darwin_all.dmg</action>
                     <action type="shell_command">
-                        hdiutil attach fastqc_v0.11.4.dmg &amp;&amp;
+                        hdiutil attach fastqc_0.11.4_darwin_all.dmg &amp;&amp;
                         cp -R /Volumes/FastQC/FastQC.app $INSTALL_DIR &amp;&amp;
                         hdiutil detach /Volumes/FastQC
                     </action>
-                    <action type="shell_command">chmod ugo+x $INSTALL_DIR/fastqc</action>
+                    <action type="set_environment">
+                        <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/FastQC.app/Contents/MacOS</environment_variable>
+                        <environment_variable name="FASTQC_JAR_PATH" action="set_to">$INSTALL_DIR/FastQC.app/Contents/MacOS</environment_variable>
+                    </action>
                 </actions>
-                <action type="set_environment">
-                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR</environment_variable>
-                    <environment_variable name="FASTQC_JAR_PATH" action="set_to">$INSTALL_DIR</environment_variable>
-                </action>
             </actions_group>
         </install>
     </package>