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Commit message:
Uploaded |
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modified:
tool_dependencies.xml |
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| diff -r bad79cc1a7b1 -r 4091cf3b81e5 tool_dependencies.xml --- a/tool_dependencies.xml Sat May 24 18:38:31 2014 -0400 +++ b/tool_dependencies.xml Mon May 26 05:11:04 2014 -0400 |
| b |
| @@ -31,17 +31,31 @@ </action> <action type="shell_command"> - # The python build system doesn't check CPATH / C(PLUS)_INCLUDE_PATH which is set by the depended-upon - # tool definitions for these sources, but it does check CPPFLAGS / LDFLAGS - export CPPFLAGS="$CPPFLAGS -I$SQLITE_ROOT_DIR/lib -I$GDBM_ROOT_PATH/lib -I$OPENSSL_ROOT_DIR/lib" - export LDFLAGS="$LDFLAGS -L$SQLITE_ROOT_DIR/include -L$GDBM_ROOT_PATH/include -L$OPENSSL_ROOT_DIR/include" - # Clear variables that may be used in Galaxy's extenal python 2 environment - unset PYTHONPATH - unset PYTHONHOME - ./configure --prefix=$INSTALL_DIR --with-ensurepip --enable-loadable-sqlite-extensions \ - && make \ - && make install - </action> + # The python build system doesn't check CPATH / C(PLUS)_INCLUDE_PATH which is set by the depended-upon + # tool definitions for these sources, but it does check CPPFLAGS / LDFLAGS + # Currently not whitespace-safe, but galaxy itself isn't whitespace-safe either so it doesn't matter (yet) + oldifs="$IFS" + IFS=: + for p in $CPLUS_INCLUDE_PATH + do + CPPFLAGS="$CPPFLAGS -I$p" + done + for p in $LD_LIBRARY_PATH + do + LDFLAGS="$LDFLAGS -L$p/lib" + done + IFS="$oldifs" + export CPPFLAGS + export LDFLAGS + + # Clear variables that may be used in Galaxy's extenal python 2 environment + unset PYTHONPATH + unset PYTHONHOME + + ./configure --prefix="$INSTALL_DIR" --with-ensurepip --enable-loadable-sqlite-extensions \ + && make \ + && make install + </action> <action type="set_environment"> <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable> |