Mercurial > repos > iuc > package_tpp_4_7_0
changeset 0:6aff23e46906 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_tpp_4_7_0 commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
| author | iuc |
|---|---|
| date | Tue, 19 May 2015 15:03:23 -0400 |
| parents | |
| children | 2b778f0f7a0e |
| files | tool_dependencies.xml |
| diffstat | 1 files changed, 137 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Tue May 19 15:03:23 2015 -0400 @@ -0,0 +1,137 @@ +<?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" /> + </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" /> + </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" /> + </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" /> + </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" /> + </package> + <package name="trans_proteomic_pipeline" version="4.7.0"> + <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"> + <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"> + <package name="expat" version="2.1.0" /> + </repository> + <!-- allow downloading and installing an Perl package from cpan.org--> + + <package>http://search.cpan.org/CPAN/authors/id/T/TO/TODDR/XML-Parser-2.41.tar.gz</package> + <!-- Also possible but not reproducible, due to the fact that always the latest version is installed. + <package>XML::Parser</package> + --> + <package>http://search.cpan.org/CPAN/authors/id/L/LD/LDS/CGI.pm-3.43.tar.gz</package> + <!--<package>http://search.cpan.org/CPAN/authors/id/S/SK/SKIMO/FCGI-0.67.tar.gz</package>--> + </action> + <action type="change_directory">..</action> + <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"> + <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"> + <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"> + <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"> + <package name="expat" version="2.1.0" /> + </repository> + <repository changeset_revision="7bdf636806dd" name="package_e2fsprogs_1_42_9" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu"> + <package name="e2fsprogs" version="1.42.9" /> + </repository> + </action> + <action type="shell_command">tar xfz TPP_4.7.0-src.tgz</action> + + <action type="change_directory">./TPP-4.7.0/trans_proteomic_pipeline/src/</action> + <action type="make_directory">../build/</action> + <action type="shell_command">echo 'TPP_ROOT=$INSTALL_DIR/tpp/' > Makefile.config.incl</action> + <action type="shell_command">echo 'TPP_WEB=/tpp/' >> Makefile.config.incl</action> + <action type="shell_command">echo 'CGI_USER_DIR=$INSTALL_DIR/cgi-bin/' >> Makefile.config.incl</action> + <action type="shell_command">echo 'OBJ_ARCH=../build' >> Makefile.config.incl</action> + + <!-- define some BOOST variables to link against the toolshed boost version --> + <action type="shell_command">echo "BOOST_DIR=$BOOST_ROOT_DIR" >> Makefile.config.incl</action> + <action type="shell_command">echo "BOOST_LIBDIR=$BOOST_ROOT_DIR/lib/" >> Makefile.config.incl</action> + <action type="shell_command">echo 'BOOST_LIB_EXT=so' >> Makefile.config.incl</action> + <action type="shell_command">echo 'BOOST_INCL=-isystem $(BOOST_DIR) -isystem $(BOOST_DIR)/.. -I$(SRC_ROOT).' >> Makefile.config.incl</action> + <action type="shell_command">echo 'BOOST_LIBS=$(BOOST_LIBDIR)*' >> Makefile.config.incl</action> + <action type="shell_command">echo 'HTMLDOC_BIN=' >> Makefile.config.incl</action> + + <action type="shell_command">echo 'LINK=shared' >> Makefile.config.incl</action> + <action type="shell_command">echo 'LIBEXT=a' >> Makefile.config.incl</action> + <!--action type="shell_command">echo "BZ2_LIB=$BZLIB_LIB_DIR/libbz2.a" >> Makefile.config.incl</action--> + + <action type="shell_command">echo "EXPAT_LIB=$EXPAT_ROOT_DIR/lib/libexpat.a" >> Makefile.config.incl</action> + <action type="shell_command">echo "EXPAT_INCL=$EXPAT_ROOT_DIR/include/" >> Makefile.config.incl</action> + + <action type="shell_command">cat Makefile.config.incl > /home/bag/blablabla.txt</action> + + + <!-- 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 $(BOOST_LIBDIR))" ""/' Makefile.incl</action> + <action type="shell_command">sed -i -e 's/# Proteowizrd/endif/' Makefile.incl</action> + <!-- replace build-in expat library with the more recent toolshed one --> + <action type="shell_command">sed -i -e 's/# Build expat library/ifeq "$(strip $(EXPAT_LIB))" ""/' Makefile.incl</action> + <action type="shell_command">sed -i -e 's/# Build HDF5/endif\n# Build HDF5/' Makefile.incl</action> + + <action type="shell_command">sed -i -e 's/# HTMLDOC/ifeq "$(strip $(HTMLDOC_BIN))" "not-needed"/' Makefile.incl</action> + <action type="shell_command">sed -i -e 's/# put common.*/endif/' Makefile.incl</action> + + <action type="shell_command">cat Makefile.incl > /home/bag/makefile.incl.txt</action> + + + + <!-- + TPP is fails with a error due to an deprecated use of qw() + See the rant @ http://blogs.perl.org/users/rurban/2010/09/qw-in-list-context-deprecated.html + --> + <!--<action type="shell_command">sed -i -e 's/qw(.*) /(&) /' ../perl/tpp_models.pl</action>--> + <action type="shell_command">sed -i -e 's/qw(.*) /(&) /' ../CGI/show_nspbin.pl</action> + <action type="shell_command">sed -i -e 's/qw(.*) /(&) /' ../perl/exporTPP.pl</action> + <action type="shell_command">echo '' > ../perl/tpp_models.pl</action> + + <action type="shell_command">make</action> + <action type="shell_command">make install</action> + <action type="set_environment"> + <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/tpp/bin</environment_variable> + <environment_variable action="prepend_to" name="PERL5LIB">$INSTALL_DIR/lib/perl5</environment_variable> + <environment_variable action="set_to" name="TPP_ROOT_PATH">$INSTALL_DIR</environment_variable> + </action> + </actions> + </install> + <readme> + Installs and complils the trans proteomic pipeline in version 4.7.0. + The Trans-Proteomic Pipeline (TPP) is a collection of integrated tools for MS/MS proteomics, developed at the SPC. + + http://tools.proteomecenter.org/ + + PATH will be set. + TPP_ROOT_PATH will point to the root path of the installation. + </readme> + </package> +</tool_dependency>