Mercurial > repos > iuc > package_tpp_4_7_0
changeset 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
| author | iuc |
|---|---|
| date | Fri, 17 Jul 2015 14:18:10 -0400 |
| parents | 6aff23e46906 |
| children | |
| files | tool_dependencies.xml |
| diffstat | 1 files changed, 17 insertions(+), 17 deletions(-) [+] |
line wrap: on
line diff
--- a/tool_dependencies.xml Tue May 19 15:03:23 2015 -0400 +++ b/tool_dependencies.xml Fri Jul 17 14:18:10 2015 -0400 @@ -1,22 +1,22 @@ <?xml version="1.0"?> <tool_dependency> <package name="libgd" version="2.1.0"> - <repository changeset_revision="3ec0c9e073da" name="package_libgd_2_1" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> + <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="114b6af405fa" name="package_perl_5_18" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> + <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="f744bc704064" name="package_bzlib_1_0" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> + <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="3c03e7c7f7bb" name="package_boost_1_55" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> + <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" /> @@ -25,7 +25,7 @@ <install version="1.0"> <actions> <action type="setup_perl_environment"> - <repository changeset_revision="114b6af405fa" name="package_perl_5_18" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu"> + <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"> @@ -44,16 +44,16 @@ <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="3ec0c9e073da" name="package_libgd_2_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu"> + <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="f744bc704064" name="package_bzlib_1_0" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu"> + <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="3c03e7c7f7bb" name="package_boost_1_55" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu"> + <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"> @@ -93,14 +93,14 @@ <!-- 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 -e 's/# www.boost.org/ifeq "$(strip $(BOOST_LIBDIR))" ""/' Makefile.incl</action> - <action type="shell_command">sed -i -e 's/# Proteowizrd/endif/' Makefile.incl</action> + <action type="shell_command">sed -i.bak -e 's/# www.boost.org/ifeq "$(strip $(BOOST_LIBDIR))" ""/' Makefile.incl</action> + <action type="shell_command">sed -i.bak -e 's/# Proteowizrd/endif/' Makefile.incl</action> <!-- replace build-in expat library with the more recent toolshed one --> - <action type="shell_command">sed -i -e 's/# Build expat library/ifeq "$(strip $(EXPAT_LIB))" ""/' Makefile.incl</action> - <action type="shell_command">sed -i -e 's/# Build HDF5/endif\n# Build HDF5/' Makefile.incl</action> + <action type="shell_command">sed -i.bak -e 's/# Build expat library/ifeq "$(strip $(EXPAT_LIB))" ""/' Makefile.incl</action> + <action type="shell_command">sed -i.bak -e 's/# Build HDF5/endif\n# Build HDF5/' Makefile.incl</action> - <action type="shell_command">sed -i -e 's/# HTMLDOC/ifeq "$(strip $(HTMLDOC_BIN))" "not-needed"/' Makefile.incl</action> - <action type="shell_command">sed -i -e 's/# put common.*/endif/' Makefile.incl</action> + <action type="shell_command">sed -i.bak -e 's/# HTMLDOC/ifeq "$(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 > /home/bag/makefile.incl.txt</action> @@ -110,9 +110,9 @@ 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 -e 's/qw(.*) /(&) /' ../perl/tpp_models.pl</action>--> - <action type="shell_command">sed -i -e 's/qw(.*) /(&) /' ../CGI/show_nspbin.pl</action> - <action type="shell_command">sed -i -e 's/qw(.*) /(&) /' ../perl/exporTPP.pl</action> + <!--<action type="shell_command">sed -i.bak -e 's/qw(.*) /(&) /' ../perl/tpp_models.pl</action>--> + <action type="shell_command">sed -i.bak -e 's/qw(.*) /(&) /' ../CGI/show_nspbin.pl</action> + <action type="shell_command">sed -i.bak -e 's/qw(.*) /(&) /' ../perl/exporTPP.pl</action> <action type="shell_command">echo '' > ../perl/tpp_models.pl</action> <action type="shell_command">make</action>