annotate tool_dependencies.xml @ 1:0bce36ee6bf2

Edit tpp_gui.pl to change from CGI deprecated endform to end_form

<?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>

                <!-- Change deprecated CGI endform to end_form -->
                <action type="shell_command">sed -i.orig 's/endform/end_form/' TPP-4.6.3/trans_proteomic_pipeline/CGI/tpp_gui/tpp_gui.pl</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>