Mercurial > repos > bgruening > prinseq

diff tool_dependencies.xml @ 0:9790cfb46d03 draft default tip

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author bgruening
date Mon, 07 Oct 2013 15:34:32 -0400
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Mon Oct 07 15:34:32 2013 -0400
@@ -0,0 +1,30 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <set_environment version="1.0">
+        <environment_variable name="PRINSEQ_SCRIPT_PATH" action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable>
+    </set_environment>
+    <package name="prinseq_perl_dependencies" version="0.20.3">
+        <install version="1.0">
+            <actions>
+                <action type="download_by_url">http://downloads.sourceforge.net/project/bowtie-bio/bowtie2/2.1.0/bowtie2-2.1.0-source.zip</action>
+                <action type="shell_command">perl Makefile.PL PREFIX=$INSTALL_DIR</action>
+                <action type="shell_command">make</action>
+                <action type="shell_command">make install</action>
+
+                <action type="download_by_url">http://search.cpan.org/CPAN/authors/id/M/MA/MAKAMAKA/JSON-2.59.tar.gz</action>
+                <action type="shell_command">perl Makefile.PL PREFIX=$INSTALL_DIR</action>
+                <action type="shell_command">make</action>
+                <action type="shell_command">make install</action>
+
+                <action type="set_environment">
+                    <environment_variable name="PERL5LIB" action="prepend_to">$INSTALL_DIR/lib/perl5/site_perl</environment_variable>
+                </action>
+            </actions>
+        </install>
+        <readme>
+        </readme>
+    </package>
+</tool_dependency>
+
+<!--fisher_exact-->
+