annotate tool_dependencies.xml @ 1:2b778f0f7a0e draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_tpp_4_7_0 commit 025696892784ba9fd07404ce4d21f3dca4ac1a1e-dirty

<?xml version="1.0"?>
<tool_dependency>
    <package name="libgd" version="2.1.0">
        <repository changeset_revision="9ff7903354f2" name="package_libgd_2_1" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
    </package>
    <package name="perl" version="5.18.1">
        <repository changeset_revision="fd34b72b501b" 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="bzlib" version="1.0.6">
        <repository changeset_revision="c494aad769a8" name="package_bzlib_1_0" 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="boost" version="1.55.0">
        <repository changeset_revision="f0da948c5302" name="package_boost_1_55" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
    </package>
    <package name="e2fsprogs" version="1.42.9">
        <repository changeset_revision="7bdf636806dd" name="package_e2fsprogs_1_42_9" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
    </package>
    <package name="trans_proteomic_pipeline" version="4.7.0">
        <install version="1.0">
            <actions>
                <action type="setup_perl_environment">
                    <repository changeset_revision="fd34b72b501b" name="package_perl_5_18" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
                        <package name="perl" version="5.18.1" />
                    </repository>
                    <repository changeset_revision="0b8d0fa6cea6" name="package_expat_2_1" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu">
                        <package name="expat" version="2.1.0" />
                    </repository>
                    <!-- allow downloading and installing an Perl package from cpan.org-->

                    <package>http://search.cpan.org/CPAN/authors/id/T/TO/TODDR/XML-Parser-2.41.tar.gz</package>
                    <!-- Also possible but not reproducible, due to the fact that always the latest version is installed.
                        <package>XML::Parser</package>
                    -->
                   <package>http://search.cpan.org/CPAN/authors/id/L/LD/LDS/CGI.pm-3.43.tar.gz</package>
                   <!--<package>http://search.cpan.org/CPAN/authors/id/S/SK/SKIMO/FCGI-0.67.tar.gz</package>-->
                </action>
                <action type="change_directory">..</action>
                <action type="download_file">http://downloads.sourceforge.net/project/sashimi/Trans-Proteomic%20Pipeline%20%28TPP%29/TPP%20v4.7%20%28polar%20vortex%29%20rev%200/TPP_4.7.0-src.tgz</action>
                <!-- populate the environment variables from the dependend repos -->
                <action type="set_environment_for_install">
                    <repository changeset_revision="9ff7903354f2" 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="c494aad769a8" 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="f0da948c5302" name="package_boost_1_55" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
                        <package name="boost" version="1.55.0" />
                    </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="7bdf636806dd" name="package_e2fsprogs_1_42_9" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
                        <package name="e2fsprogs" version="1.42.9" />
                    </repository>
                </action>
                <action type="shell_command">tar xfz TPP_4.7.0-src.tgz</action>

                <action type="change_directory">./TPP-4.7.0/trans_proteomic_pipeline/src/</action>
                <action type="make_directory">../build/</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 'OBJ_ARCH=../build' &gt;&gt; Makefile.config.incl</action>

                <!-- define some BOOST variables to link against the toolshed boost version -->
                <action type="shell_command">echo "BOOST_DIR=$BOOST_ROOT_DIR" &gt;&gt; Makefile.config.incl</action>
                <action type="shell_command">echo "BOOST_LIBDIR=$BOOST_ROOT_DIR/lib/" &gt;&gt; Makefile.config.incl</action>
                <action type="shell_command">echo 'BOOST_LIB_EXT=so' &gt;&gt; Makefile.config.incl</action>
                <action type="shell_command">echo 'BOOST_INCL=-isystem $(BOOST_DIR) -isystem $(BOOST_DIR)/.. -I$(SRC_ROOT).' &gt;&gt; Makefile.config.incl</action>
                <action type="shell_command">echo 'BOOST_LIBS=$(BOOST_LIBDIR)*' &gt;&gt; Makefile.config.incl</action>
                <action type="shell_command">echo 'HTMLDOC_BIN=' &gt;&gt; Makefile.config.incl</action>

                <action type="shell_command">echo 'LINK=shared' &gt;&gt; Makefile.config.incl</action>
                <action type="shell_command">echo 'LIBEXT=a' &gt;&gt; Makefile.config.incl</action>
                <!--action type="shell_command">echo "BZ2_LIB=$BZLIB_LIB_DIR/libbz2.a" &gt;&gt; Makefile.config.incl</action-->

                <action type="shell_command">echo "EXPAT_LIB=$EXPAT_ROOT_DIR/lib/libexpat.a" &gt;&gt; Makefile.config.incl</action>
                <action type="shell_command">echo "EXPAT_INCL=$EXPAT_ROOT_DIR/include/" &gt;&gt; Makefile.config.incl</action>

                <action type="shell_command">cat Makefile.config.incl &gt; /home/bag/blablabla.txt</action>


                <!-- do not use the build-in boost version
                    Boost version 1.54 is known to have a build bug and can't be used on some systems without a patch.
                -->
                <action type="shell_command">sed -i.bak -e 's/# www.boost.org/ifeq "$(strip $(BOOST_LIBDIR))" ""/' Makefile.incl</action>
                <action type="shell_command">sed -i.bak -e 's/# Proteowizrd/endif/' Makefile.incl</action>
                <!-- replace build-in expat library with the more recent toolshed one -->
                <action type="shell_command">sed -i.bak -e 's/# Build expat library/ifeq "$(strip $(EXPAT_LIB))" ""/' Makefile.incl</action>
                <action type="shell_command">sed -i.bak -e 's/# Build HDF5/endif\n# Build HDF5/' Makefile.incl</action>

                <action type="shell_command">sed -i.bak -e 's/# HTMLDOC/ifeq "$(strip $(HTMLDOC_BIN))" "not-needed"/' Makefile.incl</action>
                <action type="shell_command">sed -i.bak -e 's/# put common.*/endif/' Makefile.incl</action>

                <action type="shell_command">cat Makefile.incl &gt; /home/bag/makefile.incl.txt</action>



                <!--
                    TPP is fails with a error due to an deprecated use of qw()
                    See the rant @ http://blogs.perl.org/users/rurban/2010/09/qw-in-list-context-deprecated.html
                -->
                <!--<action type="shell_command">sed -i.bak -e 's/qw(.*) /(&amp;) /' ../perl/tpp_models.pl</action>-->
                <action type="shell_command">sed -i.bak -e 's/qw(.*) /(&amp;) /' ../CGI/show_nspbin.pl</action>
                <action type="shell_command">sed -i.bak -e 's/qw(.*) /(&amp;) /' ../perl/exporTPP.pl</action>
                <action type="shell_command">echo '' &gt; ../perl/tpp_models.pl</action>

                <action type="shell_command">make</action>
                <action type="shell_command">make install</action>
                <action type="set_environment">
                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/tpp/bin</environment_variable>
                    <environment_variable action="prepend_to" name="PERL5LIB">$INSTALL_DIR/lib/perl5</environment_variable>
                    <environment_variable action="set_to" name="TPP_ROOT_PATH">$INSTALL_DIR</environment_variable>
                </action>
            </actions>
        </install>
        <readme>
            Installs and complils the trans proteomic pipeline in version 4.7.0.
            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>