Mercurial > repos > bgruening > package_tpp_4_7_0
changeset 1:8fb6f74d7db6 draft
Uploaded
| author | bgruening |
|---|---|
| date | Sun, 16 Mar 2014 16:27:11 -0400 |
| parents | b568a3db8e2c |
| children | f35b0eeda699 |
| files | tool_dependencies.xml |
| diffstat | 1 files changed, 37 insertions(+), 23 deletions(-) [+] |
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--- a/tool_dependencies.xml Sat Mar 15 06:25:04 2014 -0400 +++ b/tool_dependencies.xml Sun Mar 16 16:27:11 2014 -0400 @@ -10,7 +10,7 @@ <repository changeset_revision="8fc96166cddd" name="package_expat_2_1" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" /> </package> <package name="bzlib" version="1.0.6"> - <repository changeset_revision="d5188682d08e" name="package_bzlib_1_0" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" /> + <repository changeset_revision="c8aecd67e0f5" name="package_bzlib_1_0" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" /> </package> <package name="libpng" version="1.2.5"> <repository changeset_revision="821c27341c0e" name="package_libpng_1_2" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" /> @@ -35,6 +35,7 @@ <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> @@ -46,46 +47,61 @@ <repository changeset_revision="821c27341c0e" name="package_libpng_1_2" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu"> <package name="libpng" version="1.2.5" /> </repository> - <repository changeset_revision="d5188682d08e" name="package_bzlib_1_0" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu"> + <repository changeset_revision="c8aecd67e0f5" name="package_bzlib_1_0" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu"> <package name="bzlib" version="1.0.6" /> </repository> <repository changeset_revision="1d696f0a53b9" name="package_boost_1_53" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu"> <package name="boost" version="1.53.0" /> </repository> + <repository changeset_revision="8fc96166cddd" name="package_expat_2_1" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu"> + <package name="expat" version="2.1.0" /> + </repository> </action> - <action type="shell_command">tar xfz TPP-4.7.0.tgz</action> - <!-- doanload patched version of htmldoc to prevent a TPP crashed during compilation --> - <!--<action type="download_file">https://github.com/bgruening/download_store/raw/master/htmldoc/htmldoc_1.8.27-8ubuntu1.debian.tar.gz</action> - <action type="shell_command">rm ./TPP-4.6.3/trans_proteomic_pipeline/extern/htmldoc.tgz</action> - <action type="shell_command">mv htmldoc_1.8.27-8ubuntu1.debian.tar.gz ./TPP-4.6.3/trans_proteomic_pipeline/extern/htmldoc.tgz</action> - --> - <!-- - <action type="move_file" rename_to="htmldoc.tgz"> - <source>htmldoc-1.8.27-8.debian.patched.tar.gz</source> - <destination>./TPP-4.6.3/trans_proteomic_pipeline/extern/</destination> - </action> - --> - <action type="change_directory">./TPP-4.6.3/trans_proteomic_pipeline/src/</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="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 'BOOST_INCL=-I$BOOST_ROOT_DIR' >> Makefile.config.incl</action> - <action type="shell_command">echo 'BOOST_LIBDIR=$BOOST_ROOT_DIR/lib/' >> Makefile.config.incl</action> - <action type="shell_command">echo 'BOOST_LIBSPEC=-gcc43-mt' >> 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=$(BOOST_LIBDIR)*' >> Makefile.config.incl</action> + <action type="shell_command">echo 'LINK=shared' >> Makefile.config.incl</action> <action type="shell_command">echo 'LIBEXT=so' >> Makefile.config.incl</action> + <action type="shell_command">echo "BZ2_LIB=$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">sed -i -e 's/# Proteowizrd/endif/' Makefile.incl</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 $(EXPAT_LIB))" ""/' Makefile.incl</action> + <action type="shell_command">sed -i -e 's/# Build HDF5/endif\n# Build HDF5/' Makefile.incl</action> <!-- TPP is fails with a error due to an deprecated use of qw() See the rant @ http://blogs.perl.org/users/rurban/2010/09/qw-in-list-context-deprecated.html - + --> <action type="shell_command">sed -i -e 's/qw(.*) /(&) /' ../perl/tpp_models.pl</action> <action type="shell_command">sed -i -e 's/qw(.*) /(&) /' ../CGI/show_nspbin.pl</action> <action type="shell_command">sed -i -e 's/qw(.*) /(&) /' ../perl/exporTPP.pl</action> - --> - <action type="shell_command">export PERL5LIB=$INSTALL_DIR/lib/perl5/:$PERL5LIB && export PATH=$PERL_ROOT_DIR/bin/:$PATH && export PERL5LIB=$PERL_ROOT_DIR/lib/perl5:$PERL5LIB && make</action> + <action type="shell_command"> + export PERL5LIB=$INSTALL_DIR/lib/perl5/:$PERL5LIB && + export PATH=$PERL_ROOT_DIR/bin/:$PATH && + export PERL5LIB=$PERL_ROOT_DIR/lib/perl5:$PERL5LIB && + make + </action> <action type="shell_command">make install</action> <action type="set_environment"> <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/tpp/bin</environment_variable> @@ -100,8 +116,6 @@ http://tools.proteomecenter.org/ - Dependencies: e2fslibs-dev (e2fsprogs-devel) - PATH will be set. TPP_ROOT_PATH will point to the root path of the installation. </readme>