Mercurial > repos > iuc > package_tpp_4_6_3

changeset 0:aad4e1a162c5

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author iuc
date Thu, 05 Jun 2014 19:27:54 -0400
parents
children 0bce36ee6bf2
files tool_dependencies.xml
diffstat 1 files changed, 75 insertions(+), 0 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Thu Jun 05 19:27:54 2014 -0400
@@ -0,0 +1,75 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="libgd" version="2.1.0">
+        <repository changeset_revision="99a41bc40067" name="package_libgd_2_1" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="libpng" version="1.2.5">
+        <repository changeset_revision="e0719be25969" name="package_libpng_1_2" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="bzlib" version="1.0.6">
+        <repository changeset_revision="a8d7180642fa" name="package_bzlib_1_0" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="perl" version="5.18.1">
+        <repository changeset_revision="34b039b3943b" name="package_perl_5_18" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="expat" version="2.1.0">
+        <repository changeset_revision="0b8d0fa6cea6" name="package_expat_2_1" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="trans_proteomic_pipeline" version="4.6.3">
+        <install version="1.0">
+            <actions>
+                <!-- populate the environment variables from the dependent repos -->
+                <action type="set_environment_for_install">
+                    <repository changeset_revision="99a41bc40067" name="package_libgd_2_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
+                        <package name="libgd" version="2.1.0" />
+                    </repository>
+                    <repository changeset_revision="e0719be25969" name="package_libpng_1_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
+                        <package name="libpng" version="1.2.5" />
+                    </repository>
+                    <repository changeset_revision="a8d7180642fa" name="package_bzlib_1_0" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
+                        <package name="bzlib" version="1.0.6" />
+                    </repository>
+                    <repository changeset_revision="0b8d0fa6cea6" name="package_expat_2_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
+                        <package name="expat" version="2.1.0" />
+                    </repository>
+                    <repository changeset_revision="34b039b3943b" name="package_perl_5_18" owner="iuc" toolshed="https://toolshed.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>
+                <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" CGI --force</action>
+                <action type="download_file">https://dl.dropbox.com/u/226794/TPP-4.6.3.tgz</action>
+                <action type="shell_command">tar -zxf TPP-4.6.3.tgz</action>
+
+                <action type="change_directory">./TPP-4.6.3/trans_proteomic_pipeline/src/</action>
+                <action type="shell_command">echo 'TPP_ROOT=$INSTALL_DIR/tpp/' &gt; Makefile.config.incl</action>
+                <action type="shell_command">echo 'TPP_WEB=/tpp/' &gt;&gt; Makefile.config.incl</action>
+                <action type="shell_command">echo 'CGI_USER_DIR=$INSTALL_DIR/cgi-bin/' &gt;&gt; Makefile.config.incl</action>
+
+                <action type="shell_command">echo "TPP_ROOT=$INSTALL_DIR/\nTPP_WEB=/tpp/\nXSLT_PROC=/usr/bin/xsltproc\nCGI_USERS_DIR=$INSTALL_DIR/cgi-bin/" &gt; "Makefile.config.incl"</action>
+
+
+                <action type="shell_command">sed -i -e 's/qw(.*) /(&amp;) /' ../CGI/show_nspbin.pl</action>
+                <action type="shell_command">sed -i -e 's/qw(.*) /(&amp;) /' ../perl/exporTPP.pl</action>
+                <action type="shell_command">echo '' &gt; ../perl/tpp_models.pl</action>
+
+                <action type="shell_command">eval $(perl -I$PERL_LOCALLIB_DIR/lib/perl5 -Mlocal::lib=$PERL_LOCALLIB_DIR); make; make install</action>
+
+                <action type="set_environment">
+                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
+                    <environment_variable action="set_to" name="TPP_ROOT_PATH">$INSTALL_DIR</environment_variable>
+                </action>
+
+            </actions>
+        </install>
+        <readme>
+            Installs and compiles 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.
+
+            http://tools.proteomecenter.org/
+
+            PATH will be set.
+            TPP_ROOT_PATH will point to the root path of the installation.
+        </readme>
+    </package>
+</tool_dependency>