diff tool_dependencies.xml @ 0:8723292f7d97 draft default tip

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Wed Aug 05 12:07:02 2015 -0400
@@ -0,0 +1,52 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="perl" version="5.18.1">
+        <repository changeset_revision="f19b96171787" name="package_perl_5_18" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="snvphyl" version="1.2">
+        <install version="1.0">
+            <actions>
+                <action type="setup_perl_environment">
+                    <repository changeset_revision="f19b96171787" name="package_perl_5_18" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
+                        <package name="perl" version="5.18.1" />
+                    </repository>
+                    <package>Parallel::ForkManager</package>
+                    <package>https://cpan.metacpan.org/authors/id/S/SA/SANKO/Readonly-2.00.tar.gz</package>
+                    <package>https://cpan.metacpan.org/authors/id/C/CJ/CJFIELDS/BioPerl-1.6.901.tar.gz</package>
+                    <package>https://cpan.metacpan.org/authors/id/A/AJ/AJPAGE/Bio-Pipeline-Comparison-1.123050.tar.gz</package>
+		    <package>https://cpan.metacpan.org/authors/id/R/RE/REHSACK/List-MoreUtils-0.410.tar.gz</package>
+		    <package>https://cpan.metacpan.org/authors/id/T/TO/TOBYINK/Exporter-Tiny-0.042.tar.gz</package>
+		    <package>https://cpan.metacpan.org/authors/id/M/MA/MAKAMAKA/JSON-2.90.tar.gz</package>
+		    <package>https://cpan.metacpan.org/authors/id/O/OV/OVID/Test-JSON-0.11.tar.gz</package>
+		    <package>https://cpan.metacpan.org/authors/id/M/MI/MIKO/String-Util-1.24.tar.gz</package>
+		    <package>https://cpan.metacpan.org/authors/id/R/RE/REHSACK/Hash-Merge-0.200.tar.gz</package>
+                </action>
+
+                <action type="change_directory">../</action>
+                <action type="shell_command">git clone http://irida.corefacility.ca/gitlab/analysis-pipelines/snvphyl-tools.git</action>
+                <action type="change_directory">snvphyl-tools</action>
+                <action type="shell_command">git checkout f2396b267002ccc5696d9fecb583e000dc26fe75</action>
+                <action type="change_directory">bcfplugins/bcftools-1.2</action>
+                <action type="shell_command">make</action>
+                <action type="change_directory">../..</action>
+                <action type="move_directory_files">
+                    <source_directory>.</source_directory>
+                    <destination_directory>$INSTALL_DIR/snvphyl</destination_directory>
+                </action>
+
+                <action type="set_environment">
+                    <environment_variable action="set_to" name="VCF2PSEUDO">$INSTALL_DIR/snvphyl</environment_variable>
+                    <environment_variable action="append_to" name="LD_LIBRARY_PATH">$INSTALL_DIR/snvphyl/bcfplugins/bcftools-1.2/htslib-1.2.1</environment_variable>
+                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/snvphyl/bcfplugins/bcftools-1.2</environment_variable>
+                    <environment_variable action="prepend_to" name="PERL5LIB">$INSTALL_DIR/lib/perl5</environment_variable>
+                    <environment_variable action="set_to" name="BCFTOOLS_PLUGINS">$INSTALL_DIR/snvphyl/bcfplugins/bcftools-1.2/plugins</environment_variable>
+                </action>
+
+            </actions>
+        </install>
+        <readme>
+        </readme>
+    </package>
+
+
+</tool_dependency>