annotate tool_dependencies.xml @ 7:35f117d7396b draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_perl_5_18 commit f89eded5fc193e44837f7a62af46e07f198076a3

1 <?xml version="1.0"?>
2 <tool_dependency>
3     <package name="gnu_coreutils" version="8.25">
4         <repository changeset_revision="a177f177d42f" name="package_gnu_coreutils_8_25" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
5     </package>
6     <package name="perl" version="5.18.1">
7         <install version="1.0">
8             <actions>
9                 <!-- install perl -->
10                 <action sha256sum="655e11a8ffba8853efcdce568a142c232600ed120ac24aaebb4e6efe74e85b2b" type="download_by_url">https://depot.galaxyproject.org/software/perl/perl_5.18_src_all.tar.gz</action>
11                 <action type="shell_command">./Configure -des -Dprefix=$INSTALL_DIR -Dstartperl='#!/usr/bin/env perl'</action>
12                 <action type="make_install" />
13                 <action type="change_directory">..</action>
14                 <action sha256sum="5c69adb47ab828aa3e8b5be89b88cd49c6a0d0dae2e8b3bca17a9ce699190e7b" type="download_file">http://www.cpan.org/authors/id/A/AP/APEIRON/local-lib-1.008009.tar.gz</action>
15                 <action type="shell_command">tar xfvz local-lib-1.008009.tar.gz</action>
16                 <action type="change_directory">local-lib-1.008009</action>
17                 <!-- TODO: Here we need to use the new installed perl binary -->
18                 <!-- Test whether $TMP_WORK_DIR exists (introduced in galaxy release 15.07).
19                 If not, fall back to using mktemp. Should be set to HOME=$TEMP_WORK_DIR in the future. -->
20                 <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=$INSTALL_DIR/local-lib/ --no-manpages</action>
21                 <action type="shell_command">make install</action>
22                 <action type="shell_command">export PATH=$INSTALL_DIR/bin/:$PATH; eval $(perl -I$INSTALL_DIR/local-lib/lib/perl5 -Mlocal::lib=$INSTALL_DIR/local-lib)</action>
23                 <action type="change_directory">..</action>
24                 <!-- install cpanminus into our new perl environment -->
25                 <action sha256sum="0b67f5c721259d4185bacdcbc87b835821246fe8ac7ad980d3b1a18ecdd10ff6" type="download_file">https://raw.github.com/miyagawa/cpanminus/c0c88f71118ecec334d62ba280e883933e7a6d39/cpanm</action>
26                 <!-- prepending means that the new install perl binary will be used after the pipe -->
27                 <action type="shell_command">if [ -d "$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/:$PATH ; cat cpanm | perl - App::cpanminus</action>
28                 <action type="shell_command">LC_ALL=C sed -i.bak -e 's|#!$INSTALL_DIR/bin/|#!/usr/bin/env |' $INSTALL_DIR/bin/*</action>
29                 <action type="set_environment">
30                     <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
31                     <environment_variable action="prepend_to" name="PERL5LIB">$INSTALL_DIR/lib/perl5</environment_variable>
32                     <environment_variable action="set_to" name="PERL_ROOT_DIR">$INSTALL_DIR</environment_variable>
33                     <environment_variable action="set_to" name="PERL_LOCALLIB_DIR">$INSTALL_DIR/local-lib</environment_variable>
34                 </action>
35             </actions>
36         </install>
37         <readme>
38             Perl 5 is a highly capable, feature-rich programming language with over 25 years of development.
39             https://www.perl.org/
40 
41             This repository contains local-lib and cpanm in addition.
42             It is recommended to use something like "cpanm --local-lib=$PERL_ROOT_DIR XML::Parser" to install additional perl modules.
43         </readme>
44     </package>
45 </tool_dependency>