Name: hmmer
Summary: Sequence analysis using profile hidden Markov Models
Version: 2.3.2
Release: 2
Source: hmmer-2.3.2.tar.gz
Group: Applications/Engineering
Copyright: GPL
Buildroot: /var/tmp/%{name}-buildroot
Provides:	hmmer = 2.3.2
Conflicts:	hmmer-pvm

%description
HMMER is an implementation of profile HMM methods for sensitive
database searches using multiple sequence alignments as
queries. You give HMMER a multiple sequence alignment as
input; it builds a statistical model called a "hidden Markov model"
which you can then use as a query into a sequence database to find
(and/or align) additional homologues of the sequence family.


# RPM foo magic
%define _missing_doc_files_terminate_build    0
%define _unpackaged_files_terminate_build 0
%define debug_package %{nil}

%prep
%setup -q

%build
%ifarch x86_64
CFLAGS="-O3 -static -m64 -msse2  " ./configure --enable-threads --enable-lfs
%endif
%ifarch athlon
CFLAGS="-O3 -static -march=athlon-xp -mmmx -m3dnow " ./configure --enable-threads --enable-lfs
%endif
%ifarch i686
CFLAGS="-O3 -static  -march=pentium3  " ./configure --enable-threads --enable-lfs
%endif
%ifarch p4
CFLAGS="-O3 -static  -march=pentium4  -mfpmath=sse " ./configure --enable-threads --enable-lfs
%endif
%ifarch i386
CFLAGS="-O3 -static -march=pentium " ./configure --enable-threads --enable-lfs
%endif
make

%install
rm -rf $RPM_BUILD_ROOT
mkdir -p $RPM_BUILD_ROOT/%{_bindir}
mkdir -p $RPM_BUILD_ROOT/%{_mandir}/man1
install -s -m 755 src/hmmalign $RPM_BUILD_ROOT/%{_bindir}/hmmalign
install -s -m 755 src/hmmbuild $RPM_BUILD_ROOT/%{_bindir}/hmmbuild
install -s -m 755 src/hmmcalibrate $RPM_BUILD_ROOT/%{_bindir}/hmmcalibrate
install -s -m 755 src/hmmcalibrate $RPM_BUILD_ROOT/%{_bindir}/hmmcalibrate-pvm
install -s -m 755 src/hmmconvert $RPM_BUILD_ROOT/%{_bindir}/hmmconvert
install -s -m 755 src/hmmemit $RPM_BUILD_ROOT/%{_bindir}/hmmemit
install -s -m 755 src/hmmfetch $RPM_BUILD_ROOT/%{_bindir}/hmmfetch
install -s -m 755 src/hmmindex $RPM_BUILD_ROOT/%{_bindir}/hmmindex
install -s -m 755 src/hmmpfam $RPM_BUILD_ROOT/%{_bindir}/hmmpfam
install -s -m 755 src/hmmpfam $RPM_BUILD_ROOT/%{_bindir}/hmmpfam-pvm
install -s -m 755 src/hmmsearch $RPM_BUILD_ROOT/%{_bindir}/hmmsearch
install -s -m 755 src/hmmsearch $RPM_BUILD_ROOT/%{_bindir}/hmmsearch-pvm

install -m 644 documentation/man/hmmalign.man $RPM_BUILD_ROOT/%{_mandir}/man1/hmmalign.1
install -m 644 documentation/man/hmmbuild.man $RPM_BUILD_ROOT/%{_mandir}/man1/hmmbuild.1
install -m 644 documentation/man/hmmcalibrate.man $RPM_BUILD_ROOT/%{_mandir}/man1/hmmcalibrate.1
install -m 644 documentation/man/hmmconvert.man $RPM_BUILD_ROOT/%{_mandir}/man1/hmmconvert.1
install -m 644 documentation/man/hmmemit.man $RPM_BUILD_ROOT/%{_mandir}/man1/hmmemit.1
install -m 644 documentation/man/hmmer.man $RPM_BUILD_ROOT/%{_mandir}/man1/hmmer.1
install -m 644 documentation/man/hmmfetch.man $RPM_BUILD_ROOT/%{_mandir}/man1/hmmfetch.1
install -m 644 documentation/man/hmmindex.man $RPM_BUILD_ROOT/%{_mandir}/man1/hmmindex.1
install -m 644 documentation/man/hmmpfam.man $RPM_BUILD_ROOT/%{_mandir}/man1/hmmpfam.1
install -m 644 documentation/man/hmmsearch.man $RPM_BUILD_ROOT/%{_mandir}/man1/hmmsearch.1

%clean
rm -rf $RPM_BUILD_ROOT

%files
%defattr(-,root,root)
%doc INSTALL NOTES 00README COPYRIGHT LICENSE Userguide.pdf
/%{_bindir}/hmmalign
/%{_bindir}/hmmbuild
/%{_bindir}/hmmcalibrate
/%{_bindir}/hmmcalibrate-pvm
/%{_bindir}/hmmconvert
/%{_bindir}/hmmemit
/%{_bindir}/hmmfetch
/%{_bindir}/hmmindex
/%{_bindir}/hmmpfam
/%{_bindir}/hmmpfam-pvm
/%{_bindir}/hmmsearch
/%{_bindir}/hmmsearch-pvm
/%{_mandir}/man1/hmmalign.1.gz
/%{_mandir}/man1/hmmbuild.1.gz
/%{_mandir}/man1/hmmcalibrate.1.gz
/%{_mandir}/man1/hmmconvert.1.gz
/%{_mandir}/man1/hmmemit.1.gz
/%{_mandir}/man1/hmmer.1.gz
/%{_mandir}/man1/hmmfetch.1.gz
/%{_mandir}/man1/hmmindex.1.gz
/%{_mandir}/man1/hmmpfam.1.gz
/%{_mandir}/man1/hmmsearch.1.gz

%changelog
* Wed Jun 02 2004 Joe Landman <landman@scalableinformatics.com>
- specfile fixes
* Tue May 24 2004 Joe Landman <landman@scalableinformatics.com>
- 2.3.2 with Opteron build tweaks, and specfile fixes

%packager Joe Landman <landman@scalableinformatics.com>
%vendor Scalable Informatics <http://scalableinformatics.com>