annotate tool_dependencies.xml @ 4:8b3509930a44 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_perl_5_18 commit 14be1b424bf939451dd8c4706b14a7cac6941165

<?xml version="1.0"?>
<tool_dependency>
    <package name="gnu_coreutils" version="8.22">
        <repository changeset_revision="ac64dfe4b1fb" name="package_gnu_coreutils_8_22" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
    </package>
    <package name="perl" version="5.18.1">
        <install version="1.0">
            <actions>
                <!-- install perl -->
                <action type="download_by_url">http://www.cpan.org/src/5.0/perl-5.18.1.tar.gz</action>
                <!-- get coreutils in path, to avoid using system's mktemp, which might have differing syntax -->
                <action type="set_environment_for_install">
                    <repository changeset_revision="ac64dfe4b1fb" name="package_gnu_coreutils_8_22" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
                        <package name="gnu_coreutils" version="8.22" />
                    </repository>
                </action>
                <action type="shell_command">./Configure -des -Dprefix=$INSTALL_DIR -Dstartperl='#!/usr/bin/env perl'</action>
                <action type="make_install" />
                <action type="change_directory">..</action>
                <action type="download_file">http://www.cpan.org/authors/id/A/AP/APEIRON/local-lib-1.008009.tar.gz</action>
                <action type="shell_command">tar xfvz local-lib-1.008009.tar.gz</action>
                <action type="change_directory">local-lib-1.008009</action>
                <!-- TODO: Here we need to use the new installed perl binary -->
                <!-- Test whether $TMP_WORK_DIR exists (introduced in galaxy release 15.07).
                If not, fall back to using mktemp. Should be set to HOME=$TEMP_WORK_DIR in the future. -->
                <action type="shell_command">if [ -d "$TMP_WORK_DIR" ] ; then export HOME=$TMP_WORK_DIR ; else export HOME=`mktemp -d` ; fi ; export PATH=$INSTALL_DIR/bin/:$PATH; perl Makefile.PL --bootstrap=$INSTALL_DIR/local-lib/ --no-manpages</action>
                <action type="shell_command">make install</action>
                <action type="shell_command">export PATH=$INSTALL_DIR/bin/:$PATH; eval $(perl -I$INSTALL_DIR/local-lib/lib/perl5 -Mlocal::lib=$INSTALL_DIR/local-lib)</action>
                <action type="change_directory">..</action>
                <!-- install cpanminus into our new perl environment -->
                <action type="download_file">https://raw.github.com/miyagawa/cpanminus/c0c88f71118ecec334d62ba280e883933e7a6d39/cpanm</action>
                <!-- prepending means that the new install perl binary will be used after the pipe -->
                <action type="shell_command">if [ -d "$TMP_WORK_DIR" ] ; then export HOME=$TMP_WORK_DIR ; else export HOME=`mktemp -d` ; fi ; unset PERL_MB_OPT PERL_MM_OPT ; export PERL5LIB=$INSTALL_DIR/lib/perl5/:$PERL5LIB ; export PATH=$INSTALL_DIR/bin/:$PATH ; cat cpanm | perl - App::cpanminus</action>
                <action type="shell_command">LC_ALL=C sed -i.bak -e 's|#!$INSTALL_DIR/bin/|#!/usr/bin/env |' $INSTALL_DIR/bin/*</action>
                <action type="set_environment">
                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
                    <environment_variable action="prepend_to" name="PERL5LIB">$INSTALL_DIR/lib/perl5</environment_variable>
                    <environment_variable action="set_to" name="PERL_ROOT_DIR">$INSTALL_DIR</environment_variable>
                    <environment_variable action="set_to" name="PERL_LOCALLIB_DIR">$INSTALL_DIR/local-lib</environment_variable>
                </action>
            </actions>
        </install>
        <readme>
            Perl 5 is a highly capable, feature-rich programming language with over 25 years of development.
            http://www.perl.org/

            This repository contains local-lib and cpanm in addition.
            It is recommended to use something like "cpanm --local-lib=$PERL_ROOT_DIR XML::Parser" to install additional perl modules.
        </readme>
    </package>
</tool_dependency>