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comparison tool_dependencies.xml @ 18:6f144bd786a8 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_perl_5_18 commit ef528e0f943065b3d7c5ea1cd58476e26f14c5c9-dirty
author iuc
date Wed, 30 Dec 2015 12:40:49 -0500
parents d5193a5f6203
children 66db6ede3e0e
comparison
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17:d5193a5f6203 18:6f144bd786a8
1 <?xml version="1.0"?>
2 <tool_dependency> 1 <tool_dependency>
3 <package name="gnu_coreutils" version="8.22">
4 <repository changeset_revision="1016a386a647" name="package_gnu_coreutils_8_22" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
5 </package>
6 <package name="perl" version="5.18.1"> 2 <package name="perl" version="5.18.1">
7 <install version="1.0"> 3 <install version="1.0">
8 <actions> 4 <actions>
5
9 <!-- install perl --> 6 <!-- install perl -->
10 <action type="download_by_url">http://www.cpan.org/src/5.0/perl-5.18.1.tar.gz</action> 7 <action type="download_by_url">http://www.cpan.org/src/5.0/perl-5.18.1.tar.gz</action>
11 <!-- get coreutils in path, to avoid using system's mktemp, which might have differing syntax -->
12 <action type="set_environment_for_install">
13 <repository changeset_revision="1016a386a647" name="package_gnu_coreutils_8_22" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
14 <package name="gnu_coreutils" version="8.22" />
15 </repository>
16 </action>
17 <action type="shell_command">./Configure -des -Dprefix=$INSTALL_DIR -Dstartperl='#!/usr/bin/env perl'</action> 8 <action type="shell_command">./Configure -des -Dprefix=$INSTALL_DIR -Dstartperl='#!/usr/bin/env perl'</action>
18 <action type="make_install" /> 9 <action type="make_install" />
19 <action type="change_directory">..</action> 10 <action type="change_directory">..</action>
20 <action type="download_file">http://www.cpan.org/authors/id/A/AP/APEIRON/local-lib-1.008009.tar.gz</action> 11 <action type="download_file">http://www.cpan.org/authors/id/A/AP/APEIRON/local-lib-1.008009.tar.gz</action>
21 <action type="shell_command">tar xfvz local-lib-1.008009.tar.gz</action> 12 <action type="shell_command">tar xfvz local-lib-1.008009.tar.gz</action>
22 <action type="change_directory">local-lib-1.008009</action> 13 <action type="change_directory">local-lib-1.008009</action>
23 <!-- TODO: Here we need to use the new installed perl binary --> 14 <!-- TODO: Here we need to use the new installed perl binary -->
24 <!-- Test whether $TMP_WORK_DIR exists (introduced in galaxy release 15.07). 15 <action type="shell_command">export PATH=$INSTALL_DIR/bin/:$PATH; perl Makefile.PL --bootstrap=$INSTALL_DIR/local-lib/ --no-manpages</action>
25 If not, fall back to using mktemp. Should be set to HOME=$TEMP_WORK_DIR in the future. -->
26 <action type="shell_command">if [ -d "$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>
27 <action type="shell_command">make install</action> 16 <action type="shell_command">make install</action>
28 <action type="shell_command">export PATH=$INSTALL_DIR/bin/:$PATH; eval $(perl -I$INSTALL_DIR/local-lib/lib/perl5 -Mlocal::lib=$INSTALL_DIR/local-lib)</action> 17 <action type="shell_command">export PATH=$INSTALL_DIR/bin/:$PATH; eval $(perl -I$INSTALL_DIR/local-lib/perl5 -Mlocal::lib=$INSTALL_DIR/local-lib)</action>
29 <action type="change_directory">..</action> 18 <action type="change_directory">..</action>
30 <!-- install cpanminus into our new perl environment --> 19 <!-- install cpanminus into our new perl environment -->
31 <action type="download_file">https://raw.github.com/miyagawa/cpanminus/c0c88f71118ecec334d62ba280e883933e7a6d39/cpanm</action> 20 <action type="download_file">https://raw.github.com/miyagawa/cpanminus/c0c88f71118ecec334d62ba280e883933e7a6d39/cpanm</action>
32 <!-- prepending means that the new install perl binary will be used after the pipe --> 21 <!-- prepanding means that the new install perl binary will be used after the pipe -->
33 <action type="shell_command">if [ -d "$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/:$PATH ; cat cpanm | perl - App::cpanminus</action> 22 <action type="shell_command">export PERL5LIB=$INSTALL_DIR/lib/perl5/:$PERL5LIB ; export PATH=$INSTALL_DIR/bin/:$PATH ; cat cpanm | perl - App::cpanminus</action>
34 <action type="shell_command">LC_ALL=C sed -i.bak -e 's|#!$INSTALL_DIR/bin/|#!/usr/bin/env |' $INSTALL_DIR/bin/*</action> 23 <action type="shell_command">sed -i -e 's|#!$INSTALL_DIR/bin/|#!/usr/bin/env |' $INSTALL_DIR/bin/*</action>
24
35 <action type="set_environment"> 25 <action type="set_environment">
36 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable> 26 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
37 <environment_variable action="prepend_to" name="PERL5LIB">$INSTALL_DIR/lib/perl5</environment_variable> 27 <environment_variable name="PERL5LIB" action="prepend_to">$INSTALL_DIR/lib/perl5</environment_variable>
38 <environment_variable action="set_to" name="PERL_ROOT_DIR">$INSTALL_DIR</environment_variable> 28 <environment_variable name="PERL_ROOT_DIR" action="set_to">$INSTALL_DIR</environment_variable>
39 <environment_variable action="set_to" name="PERL_LOCALLIB_DIR">$INSTALL_DIR/local-lib</environment_variable> 29 <environment_variable name="PERL_LOCALLIB_DIR" action="set_to">$INSTALL_DIR/local-lib</environment_variable>
40 </action> 30 </action>
41 </actions> 31 </actions>
42 </install> 32 </install>
43 <readme> 33 <readme>
44 Perl 5 is a highly capable, feature-rich programming language with over 25 years of development. 34 Perl 5 is a highly capable, feature-rich programming language with over 25 years of development.