changeset 2:826234dd2977

Test perl expat

--- a/tool_dependencies.xml	Wed Oct 23 23:48:11 2013 -0400
+++ b/tool_dependencies.xml	Tue Nov 05 18:26:33 2013 -0500
@@ -1,29 +1,42 @@
 <?xml version="1.0"?>
 <tool_dependency>
-        <package name="trans_proteomic_pipeline" version="4.6.1">
-            <install version="1.0">
-                <actions>
-                    <action type="download_by_url">https://dl.dropboxusercontent.com/u/226794/galaxy/tpp_4.6.1.tar.gz</action>
-                    <action language="cheetah" type="template_command">
-                        sh install.sh $env.INSTALL_DIR
-                    </action>
-                    <action type="set_environment">
-                        <environment_variable action="set_to" name="TPP_PERL_DIR">$INSTALL_DIR/perl5</environment_variable>
-                        <environment_variable action="set_to" name="PROTK_TPP_ROOT">$INSTALL_DIR</environment_variable>
-                    </action>
-                </actions>
-            </install>
-            <readme>
-                This part of the installer is extremely minimal. It just downloads and runs a shell script that does the install.
-                The installer will attempt to do the following;
+    <package name="libgd" version="2.1.0">
+        <repository changeset_revision="dcbab64c0429" name="package_libgd_2_1" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="perl" version="5.18.1">
+        <repository changeset_revision="ab58b9f990c5" name="package_perl_5_18" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="expat" version="2.1.0">
+        <repository changeset_revision="8fc96166cddd" name="package_expat_2_1" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="trans_proteomic_pipeline" version="4.6.1">
+        <install version="1.0">
+            <actions>
+                <!-- populate the environment variables from the dependend repos -->
+                <action type="set_environment_for_install">
+                    <repository changeset_revision="dcbab64c0429" name="package_libgd_2_1" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu">
+                        <package name="libgd" version="2.1.0" />
+                    </repository>
+                    <repository changeset_revision="8fc96166cddd" name="package_expat_2_1" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu">
+                        <package name="expat" version="2.1.0" />
+                    </repository>
+                    <repository changeset_revision="ab58b9f990c5" name="package_perl_5_18" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu">
+                        <package name="perl" version="5.18.1" />
+                    </repository>
+                </action>
+                <action type="shell_command">eval $(perl -I$PERL_LOCALLIB_DIR/lib/perl5 -Mlocal::lib=$PERL_LOCALLIB_DIR); cpanm --local-lib=$PERL_LOCALLIB_DIR --configure-args="EXPATLIBPATH=$EXPAT_ROOT_DIR/lib EXPATINCPATH=$EXPAT_ROOT_DIR/include" XML::Parser</action>
+            </actions>
+        </install>
+        <readme>
+            Installs and complils the trans proteomic pipeline in version 4.6.3.
+            The Trans-Proteomic Pipeline (TPP) is a collection of integrated tools for MS/MS proteomics, developed at the SPC.
 
-                1. Download and install perl-locallib and cpanminus
-                2. Install perl packages required by the TPP into a self contained perl local lib
-                3. Download the source code of the TPP and compile it.
+            http://tools.proteomecenter.org/
+
+            Dependencies: e2fslibs-dev (e2fsprogs-devel)
 
-                Installation has been tested on an Ubuntu Precise 64 box with the following system packages installed
-                curl build-essential mercurial libperl-dev liblocal-lib-perl cpanminus libxml2-dev expat libexpat1-dev libbz2-dev
-
-            </readme>
-        </package>
+            PATH will be set.
+            TPP_ROOT_PATH will point to the root path of the installation.
+        </readme>
+    </package>
 </tool_dependency>