Mercurial > repos > iuc > package_perl_5_18
diff 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
| author | iuc |
|---|---|
| date | Fri, 25 Sep 2015 09:17:12 -0400 |
| parents | fd34b72b501b |
| children | d905bb415eca |
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--- a/tool_dependencies.xml Fri Jul 17 10:44:28 2015 -0400 +++ b/tool_dependencies.xml Fri Sep 25 09:17:12 2015 -0400 @@ -1,10 +1,19 @@ +<?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=$INSTALL_DIR -Dstartperl='#!/usr/bin/env perl'</action> <action type="make_install" /> <action type="change_directory">..</action> @@ -12,21 +21,22 @@ <action type="shell_command">tar xfvz local-lib-1.008009.tar.gz</action> <action type="change_directory">local-lib-1.008009</action> <!-- TODO: Here we need to use the new installed perl binary --> - <action type="shell_command">export PATH=$INSTALL_DIR/bin/:$PATH; perl Makefile.PL --bootstrap=$INSTALL_DIR/local-lib/ --no-manpages</action> + <!-- 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/perl5 -Mlocal::lib=$INSTALL_DIR/local-lib)</action> + <action type="shell_command">export PATH=$INSTALL_DIR/bin/:$PATH; eval $(perl -I$INSTALL_DIR/local-lib/lib/perl5 -Mlocal::lib=$INSTALL_DIR/local-lib)</action> <action type="change_directory">..</action> <!-- install cpanminus into our new perl environment --> <action type="download_file">https://raw.github.com/miyagawa/cpanminus/c0c88f71118ecec334d62ba280e883933e7a6d39/cpanm</action> - <!-- prepanding means that the new install perl binary will be used after the pipe --> - <action type="shell_command">export PERL5LIB=$INSTALL_DIR/lib/perl5/:$PERL5LIB ; export PATH=$INSTALL_DIR/bin/:$PATH ; cat cpanm | perl - App::cpanminus</action> - <action type="shell_command">sed -i.bak -e 's|#!$INSTALL_DIR/bin/|#!/usr/bin/env |' $INSTALL_DIR/bin/*</action> - + <!-- prepending means that the new install perl binary will be used after the pipe --> + <action type="shell_command">if [ -d "$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 |' $INSTALL_DIR/bin/*</action> <action type="set_environment"> - <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> - <environment_variable name="PERL5LIB" action="prepend_to">$INSTALL_DIR/lib/perl5</environment_variable> - <environment_variable name="PERL_ROOT_DIR" action="set_to">$INSTALL_DIR</environment_variable> - <environment_variable name="PERL_LOCALLIB_DIR" action="set_to">$INSTALL_DIR/local-lib</environment_variable> + <environment_variable action="prepend_to" name="PATH">$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>