Mercurial > repos > bgruening > package_tpp_4_7_0
changeset 2:f35b0eeda699 draft
Uploaded
| author | bgruening |
|---|---|
| date | Mon, 17 Mar 2014 15:45:43 -0400 |
| parents | 8fb6f74d7db6 |
| children | 27fd9cb35186 |
| files | tool_dependencies.xml |
| diffstat | 1 files changed, 16 insertions(+), 3 deletions(-) [+] |
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--- a/tool_dependencies.xml Sun Mar 16 16:27:11 2014 -0400 +++ b/tool_dependencies.xml Mon Mar 17 15:45:43 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="c8aecd67e0f5" name="package_bzlib_1_0" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" /> + <repository changeset_revision="e89ba6f88ab2" 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" /> @@ -47,7 +47,7 @@ <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="c8aecd67e0f5" name="package_bzlib_1_0" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu"> + <repository changeset_revision="e89ba6f88ab2" 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"> @@ -60,9 +60,11 @@ <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> @@ -70,6 +72,8 @@ <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=$(BOOST_LIBDIR)*' >> Makefile.config.incl</action> + <action type="shell_command">echo 'HTMLDOC_BIN=' >> Makefile.config.incl</action> + <action type="shell_command">echo 'LINK=shared' >> Makefile.config.incl</action> <action type="shell_command">echo 'LIBEXT=so' >> Makefile.config.incl</action> @@ -78,7 +82,9 @@ <action type="shell_command">echo "EXPAT_LIB=$EXPAT_ROOT_DIR/lib/libexpat.a" >> Makefile.config.incl</action> <action type="shell_command">echo "EXPAT_INCL=$EXPAT_ROOT_DIR/include/" >> Makefile.config.incl</action> - <action type="shell_command">sed -i -e 's/# Proteowizrd/endif/' Makefile.incl</action> + <action type="shell_command">cat Makefile.config.incl > /home/bag/blablabla.txt</action> + + <!-- do not use the build-in boost version Boost version 1.54 is known to have a build bug and can't be used on some systems without a patch. --> @@ -88,6 +94,13 @@ <action type="shell_command">sed -i -e 's/# Build expat library/ifeq "$(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