| -rw-r--r-- | configure.ac | 62 | ||||
| -rw-r--r-- | doc/build-cobalt.txt | 24 | ||||
| -rw-r--r-- | src/Makefile.am | 6 | ||||
| -rw-r--r-- | src/assign/assign_blast_scores.c | 27 | ||||
| -rw-r--r-- | src/assign/assign_blast_scores.h | 12 | ||||
| -rw-r--r-- | src/updator.c | 20 |
6 files changed, 127 insertions, 24 deletions
diff --git a/configure.ac b/configure.ac index 59c5f36..f1ecdf9 100644 --- a/configure.ac +++ b/configure.ac @@ -7,20 +7,16 @@ AC_CONFIG_FILES([ src/Makefile ]) -################ -# MODULE: HDF5 # -################ +# Headers Checks -AC_SEARCH_LIBS([H5Fcreate],[hdf5],[], -[AC_MSG_ERROR(The HDF5 libraries are needed to build the system.)], -[-lirc -lmpi -lz -lsz]) +AC_CHECK_HEADERS([hdf5.h],[], +[AC_MSG_ERROR("The HDF5 headers are needed to build the system.")]) -AC_SEARCH_LIBS([H5TBmake_table],[hdf5_hl],[], -[AC_MSG_ERROR(The HDF5 libraries are needed to build the system.)], -[-lirc -lhdf5 -lmpi -lz -lsz]) +AC_CHECK_HEADERS([petscconf.h],[], +[AC_MSG_ERROR("The PETSc headers are needed to build the system.")]) -AC_CHECK_HEADERS([hdf5.h],[], -[AC_MSG_ERROR(The HDF5 headers are needed to build the system.)]) +AC_CHECK_HEADERS([petscmat.h],[], +[AC_MSG_ERROR("The PETSc headers are needed to build the system.")]) ######################## # MODULE: NCBI Toolkit # @@ -28,18 +24,52 @@ AC_CHECK_HEADERS([hdf5.h],[], # Check for the NCBI ToolBox libraries. AC_SEARCH_LIBS([log10],[m],[], -[AC_MSG_ERROR(The C Math Library is needed to build the system.)]) +[AC_MSG_ERROR("The C Math Library is needed to build the system.")]) AC_SEARCH_LIBS([NlmThreadsAvailable],[ncbi],[], -[AC_MSG_ERROR(The NCBI ToolBox is needed to build the system. Information on this API can be found on-line at http://www.ncbi.nlm.nih.gov/IEB/ToolBox/index.cgi. Debian users can add the package libncbi6-dev to fulfill this dependency.)]) +[AC_MSG_ERROR("The NCBI ToolBox is needed to build the system. Information on this API can be found on-line at http://www.ncbi.nlm.nih.gov/IEB/ToolBox/index.cgi. Debian users can add the package libncbi6-dev to fulfill this dependency.")]) AC_SEARCH_LIBS([SeqAlignNew],[ncbiobj],[], -[AC_MSG_ERROR(The NCBI ToolBox is needed to build the system. Information on this API can be found on-line at http://www.ncbi.nlm.nih.gov/IEB/ToolBox/index.cgi. Debian users can add the package libncbi6-dev to fulfill this dependency.)]) +[AC_MSG_ERROR("The NCBI ToolBox is needed to build the system. Information on this API can be found on-line at http://www.ncbi.nlm.nih.gov/IEB/ToolBox/index.cgi. Debian users can add the package libncbi6-dev to fulfill this dependency.")]) AC_SEARCH_LIBS([Blast_RedoOneMatch],[blastcompadj],[], -[AC_MSG_ERROR(The NCBI ToolBox is needed to build the system. Information on this API can be found on-line at http://www.ncbi.nlm.nih.gov/IEB/ToolBox/index.cgi. Debian users can add the package libncbi6-dev to fulfill this dependency.)]) +[AC_MSG_ERROR("The NCBI ToolBox is needed to build the system. Information on this API can be found on-line at http://www.ncbi.nlm.nih.gov/IEB/ToolBox/index.cgi. Debian users can add the package libncbi6-dev to fulfill this dependency.")]) AC_SEARCH_LIBS([BioseqBlastEngine],[ncbitool],[], -[AC_MSG_ERROR(The NCBI ToolBox is needed to build the system. Information on this API can be found on-line at http://www.ncbi.nlm.nih.gov/IEB/ToolBox/index.cgi. Debian users can add the package libncbi6-dev to fulfill this dependency.)]) +[AC_MSG_ERROR("The NCBI ToolBox is needed to build the system. Information on this API can be found on-line at http://www.ncbi.nlm.nih.gov/IEB/ToolBox/index.cgi. Debian users can add the package libncbi6-dev to fulfill this dependency.")]) + +################ +# MODULE: HDF5 # +################ + +AC_SEARCH_LIBS([__intel_rtc_uninit_use],[irc]) +AC_SEARCH_LIBS([MPI_File_open],[mpi]) +AC_SEARCH_LIBS([compress2],[z]) +AC_SEARCH_LIBS([SZ_BufftoBuffCompress],[sz]) + +AC_SEARCH_LIBS([H5Fcreate],[hdf5],[], +[AC_MSG_ERROR("The HDF5 libraries are needed to build the system.")]) + +AC_SEARCH_LIBS([H5TBmake_table],[hdf5_hl],[], +[AC_MSG_ERROR("The HDF5 libraries are needed to build the system.")]) + +################# +# MODULE: PETSc # +################# + +# The AC_SEARCH_LIBS other-libraries list is not particularly useful. +# Autoconf determines if the other-libraries are necessary however in +# the cases where they are indeed necessary they are not actually +# added to the library list. + +# These are the dependencies. Random functions are selected from +# these libraries from the list of otherwise undefined references at +# link time. +AC_SEARCH_LIBS([PetscInitialize],[petsc]) +AC_SEARCH_LIBS([VecNorm],[petscvec]) + +# MatCreateSeqAIJ is acutally used in the code for this project. +AC_SEARCH_LIBS([MatCreateSeqAIJ],[petscmat],[], +[AC_MSG_ERROR("The Portable Extensible Tookit for Scientific Computation PETSc is needed to build the system.")]) AC_OUTPUT |
