| Previous changeset 2:b36c9ee883e9 (2015-05-23) Next changeset 4:f27d2f8761ae (2016-02-16) |
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Commit message:
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modified:
tool_dependencies.xml |
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| diff -r b36c9ee883e9 -r 0538fd672119 tool_dependencies.xml --- a/tool_dependencies.xml Sat May 23 16:52:20 2015 -0400 +++ b/tool_dependencies.xml Thu Jul 16 05:43:42 2015 -0400 |
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| @@ -15,7 +15,22 @@ <environment_variable action="set_to" name="ATLAS_LAPACK_LIB_DIR">$INSTALL_DIR/lib/atlas</environment_variable> <environment_variable action="set_to" name="ATLAS_ROOT_PATH">$INSTALL_DIR</environment_variable> <environment_variable action="prepend_to" name="LD_LIBRARY_PATH">$INSTALL_DIR/lib</environment_variable> + <environment_variable action="prepend_to" name="LD_LIBRARY_PATH">$INSTALL_DIR/lib/atlas</environment_variable> </action> + <action type="shell_command"><![CDATA[ + command -v gfortran || return 0 + BUNDLED_LGF_CANON=$INSTALL_DIR/lib/libgfortran.so.3.0.0 && + BUNDLED_LGF_VERS=`objdump -p $BUNDLED_LGF_CANON | grep GFORTRAN_1 | sed -r 's/.*GFORTRAN_1\.([0-9])+/\1/' | sort -n | tail -1` && + echo 'program test; end program test' > test.f90 && + gfortran -o test test.f90 && + LGF=`ldd test | grep libgfortran | awk '{print $3}'` && + LGF_CANON=`readlink -f $LGF` && + LGF_VERS=`objdump -p $LGF_CANON | grep GFORTRAN_1 | sed -r 's/.*GFORTRAN_1\.([0-9])+/\1/' | sort -n | tail -1` && + if [ $LGF_VERS -gt $BUNDLED_LGF_VERS ]; then + cp -p $BUNDLED_LGF_CANON ${BUNDLED_LGF_CANON}.bundled && + cp -p $LGF_CANON $BUNDLED_LGF_CANON + fi + ]]></action> </actions> <actions architecture="x86_64" os="darwin"> <!-- NOOP: On OS X we will use Apple's vecLib --> @@ -28,17 +43,17 @@ <action type="download_file">https://depot.galaxyproject.org/patch/atlas/cpu-throttling-check.diff</action> <action type="shell_command">tar -jxvf atlas3.10.2.tar.bz2</action> <!-- a 64-bit architecture is assumed for compilation --> - <action type="shell_command"> - cd ATLAS && - mkdir ATLAS/build && - patch -p1 </host/static_full_blas_lapack.diff && - patch -p1 </host/shared_libraries.diff && - patch -p1 </host/cpu-throttling-check.diff && - cd build && - ../configure --prefix="$INSTALL_DIR" -D c -DWALL -b 64 -Fa alg '-fPIC' --with-netlib-lapack-tarfile=../../lapack-3.5.0.tgz -v 2 -t 0 -Si cputhrchk 0 && - make && + <action type="shell_command"><![CDATA[ + cd ATLAS && + mkdir ATLAS/build && + patch -p1 </host/static_full_blas_lapack.diff && + patch -p1 </host/shared_libraries.diff && + patch -p1 </host/cpu-throttling-check.diff && + cd build && + ../configure --prefix="$INSTALL_DIR" -D c -DWALL -b 64 -Fa alg '-fPIC' --with-netlib-lapack-tarfile=../../lapack-3.5.0.tgz -v 2 -t 0 -Si cputhrchk 0 && + make && make install - </action> + ]]></action> <action type="set_environment"> <environment_variable action="set_to" name="ATLAS_LIB_DIR">$INSTALL_DIR/lib</environment_variable> <environment_variable action="set_to" name="ATLAS_INCLUDE_DIR">$INSTALL_DIR/include</environment_variable> |