# TODO:
# fix jemboss and enable it
# This would involve packaging jalview (specifically, the Applet)
# The jalview code has a LOT of bundled pre-built jars.
#jemboss is disabled by default due to the fact it bundles a few .jar files which are not built from source.
%bcond_with jemboss
#use --with sunjava if sun's jre is used
%bcond_with sunjava
%if %{with sunjava}
%define _java /usr/java/default
%endif
%define emhome %{_datadir}/EMBOSS
Name: EMBOSS
Version: 6.3.1
Release: 4%{?dist}
Summary: The European Molecular Biology Open Software Suite
Group: Applications/Engineering
# Files under jemboss/, ajax/ensembl/ are LGPLv2+
#
# There are some other files which are included in the source tarball
# but not used, specifically:
# Files under ajax/pcre/ are BSD
# Files under ajax/zlib/ are zlib/libpng
# Because they are not used (they're deleted in %%prep),
# we do not include them in the license tag.
License: GPLv2+ and LGPLv2+
URL: http://emboss.sf.net/
Source0: ftp://emboss.open-bio.org/pub/EMBOSS/%{name}-%{version}.tar.gz
Source1: ftp://emboss.open-bio.org/pub/EMBOSS/fixes/README.fixes
%if %{with jemboss}
Source2: jemboss.desktop
%endif
# Upstream patch
Patch0: ftp://emboss.open-bio.org/pub/EMBOSS/fixes/patches/patch-1-4.gz
# Use system-wide pcre. Sent upstream.
Patch1: EMBOSS-6.3.1-system-pcre.patch
# Use system-wide plplot
Patch3: EMBOSS-6.3.1-system-plplot.patch
# Use system-wide expat
Patch4: EMBOSS-6.3.1-system-expat.patch
#Fedora-specific. Not sent upstream.
Patch5: %{name}-fedora.patch
Patch6: EMBOSS-6.3.1-prevent-autotooling.patch
Patch7: EMBOSS-6.3.1-system-hack.patch
# Sent upstream on 2010-10-27
Patch8: EMBOSS-6.3.1-fix-doc-finding.patch
BuildRoot: %{_tmppath}/%{name}-%{version}-%{release}-root-%(%{__id_u} -n)
BuildRequires: gd-devel
BuildRequires: pam-devel
BuildRequires: pcre-devel
BuildRequires: zlib-devel
BuildRequires: plplot-devel
BuildRequires: expat-devel
BuildRequires: libharu-devel
%if %{with jemboss}
BuildRequires: ant
BuildRequires: desktop-file-utils
BuildRequires: java-devel >= 1:1.6.0
BuildRequires: jpackage-utils
BuildRequires: axis classpathx-mail jaf jakarta-commons-discovery jakarta-commons-logging
BuildRequires: log4j regexp servlet xerces-j2 wsdl4j
%endif
%if %{with sunjava}
Requires: jdk = 2000:1.6.0_17-fcs
%endif
%description
EMBOSS is a new, free Open Source software analysis package specially
developed for the needs of the molecular biology (e.g. EMBnet) user community.
The software automatically copes with data in a variety of formats and even
allows transparent retrieval of sequence data from the web. Also, as extensive
libraries are provided with the package, it is a platform to allow other
scientists to develop and release software in true open source spirit.
EMBOSS also integrates a range of currently available packages and tools for
sequence analysis into a seamless whole.
Reference for EMBOSS: Rice,P. Longden,I. and Bleasby,A.
"EMBOSS: The European Molecular Biology Open Software Suite"
Trends in Genetics June 2000, vol 16, No 6. pp.276-277
%package devel
Summary: Development tools for programs which will use the %{name} library
Group: Development/Libraries
Requires: %{name}-libs = %{version}-%{release}
%description devel
The %{name}-devel package includes the header files and static libraries
necessary for developing programs which will use the %{name} library.
%package libs
Summary: Shared libraries for %{name}
Group: System Environment/Libraries
%description libs
The %{name}-libs package includes the dynamic libraries
necessary for %{name}.
%if %{with jemboss}
%package -n jemboss
Summary: Java interface to %{name}
Group: Applications/Engineering
Requires: %{name} = %{version}-%{release}
Requires: java >= 1:1.6.0
Requires: jpackage-utils
Requires: axis jaf javamail jakarta-commons-discovery jakarta-commons-logging
Requires: log4j regexp servlet xerces-j2 wsdl4j
%description -n jemboss
Jemboss is a Java interface to EMBOSS, developed at
the HGMP-RC and in close collaboration with the EMBOSS
development team. It is distributed as part of the EMBOSS
software.
Documentation on Jemboss can be found at:
http://www.hgmp.mrc.ac.uk/Software/EMBOSS/Jemboss/
%endif
%prep
%setup -q
%patch0 -p1
%patch1 -p1 -b .system-pcre
%patch3 -p1 -b .system-plplot
%patch4 -p1 -b .system-expat
%patch5 -p0 -b .fedora
%patch6 -p1 -b .autobarf
%patch7 -p1 -b .system
%patch8 -p1 -b .fix-doc-finding
# Remove bundled plplot, expat, pcre and zlib to make sure that system versions are used
rm -rf plplot/
rm -rf ajax/{expat,pcre,zlib}
#install the patch readme
#install -pm 644 %{SOURCE1} README.fixes
#these files were executable for some reason
chmod 644 emboss/prettyplot.c emboss/polydot.c emboss/supermatcher.c
%if %{with jemboss}
#use newer log4j version
sed -i "s@log4j-1.2.8@log4j-1.2.14@" \
jemboss/lib/axis/Makefile.am \
jemboss/lib/axis/Makefile.in \
jemboss/utils/makeFileManagerJNLP.sh \
jemboss/utils/makeJNLP.sh
#use system java libraries
rm jemboss/lib/{activation,jakarta-regexp-1.2,jemboss,mail,xerces}.jar
build-jar-repository -s -p jemboss/lib activation regexp javamail xerces-j2
mv jemboss/lib/regexp.jar jemboss/lib/jakarta-regexp-1.2.jar
mv jemboss/lib/javamail.jar jemboss/lib/mail.jar
mv jemboss/lib/xerces-j2.jar jemboss/lib/xerces.jar
rm jemboss/lib/axis/*.jar
build-jar-repository -s -p jemboss/lib/axis axis/axis-ant axis/axis axis/jaxrpc axis/saaj commons-discovery commons-logging log4j-1.2.14 servlet wsdl4j
for i in axis axis-ant jaxrpc saaj;
do
mv jemboss/lib/axis/axis_$i.jar jemboss/lib/axis/$i.jar;
done
%endif
%build
%if %{with sunjava}
export PATH=$PATH:%{_java}/bin/
%endif
%configure \
--disable-static \
--with-x \
--with-auth \
--with-thread \
--includedir=%{_includedir}/EMBOSS \
--enable-systemlibs \
%ifarch ppc64 sparc64 x86_64
--enable-64 \
%endif
%if %{with jemboss}
--with-java=/usr/lib/jvm/java/include \
--with-javaos=/usr/lib/jvm/java/include/linux
%endif
%if %{with sunjava}
--with-java=%{_java}/include
--with-javaos=%{_java}/include/linux
%endif
%{__make} %{?_smp_mflags}
%install
%if %{with sunjava}
export PATH=$PATH:%{_java}/bin/
%endif
rm -rf $RPM_BUILD_ROOT
%{__make} install DESTDIR=$RPM_BUILD_ROOT
install -m 755 -d $RPM_BUILD_ROOT/%{_sysconfdir}/profile.d
cat << __EOF__ >> $RPM_BUILD_ROOT/%{_sysconfdir}/profile.d/emboss.sh
export PLPLOT_LIB=%{emhome}
export EMBOSS_ACDROOT=%{emhome}/acd
export EMBOSS_DOCROOT=%{emhome}/doc
export EMBOSS_DATABASE_DIR=%{emhome}/data
export EMBOSS_DATA=%{emhome}/data
__EOF__
cat << __EOF__ >> $RPM_BUILD_ROOT/%{_sysconfdir}/profile.d/emboss.csh
setenv PLPLOT_LIB %{emhome}
setenv EMBOSS_ACDROOT %{emhome}/acd
setenv EMBOSS_DOCROOT %{emhome}/doc
setenv EMBOSS_DATABASE_DIR %{emhome}/data
setenv EMBOSS_DATA %{emhome}/data
__EOF__
rm $RPM_BUILD_ROOT%{_libdir}/*.la
#this file has zero length, so kill it
rm $RPM_BUILD_ROOT%{_datadir}/EMBOSS/test/data/dna.aln
#fix executable permissions
pushd $RPM_BUILD_ROOT%{_datadir}/EMBOSS/jemboss/utils
chmod +x install-jemboss-server.sh keys.sh makeFileManagerJNLP.sh makeJar.csh \
makeJNLP.sh
popd
# pushd $RPM_BUILD_ROOT%{_datadir}/EMBOSS/jemboss/api
# chmod +x getClasses.pl makeDocs.csh
# popd
#rename conflicting binaries
mv $RPM_BUILD_ROOT%{_bindir}/chaos $RPM_BUILD_ROOT%{_bindir}/em_chaos
%if %{with jemboss}
#install the desktop file
desktop-file-install \
--dir=${RPM_BUILD_ROOT}%{_datadir}/applications \
%{SOURCE2}
%endif
%clean
rm -rf $RPM_BUILD_ROOT
%post libs -p /sbin/ldconfig
%postun libs -p /sbin/ldconfig
%files
%defattr(-,root,root,-)
%doc AUTHORS ChangeLog FAQ INSTALL NEWS README THANKS
%{_bindir}/*
%exclude %{_bindir}/runJemboss.csh
%exclude %{_bindir}/jembossctl
%{_datadir}/EMBOSS
%exclude %{_datadir}/EMBOSS/jemboss
%config %{_sysconfdir}/profile.d/*
%files devel
%defattr(-,root,root,-)
%{_libdir}/*.so
%{_includedir}/EMBOSS
%files libs
%defattr(-,root,root,-)
%doc COPYING LICENSE
%{_libdir}/*.so.*
%if 0%{?with_jemboss} || 0%{?with_sunjava}
%files -n jemboss
%defattr(-,root,root,-)
%doc jemboss/README jemboss/resources jemboss/api
%{_bindir}/runJemboss.csh
%{_bindir}/jembossctl
%{_datadir}/applications/jemboss.desktop
%{_datadir}/EMBOSS/jemboss
%endif
%changelog
* Wed Oct 27 2010 Tom "spot" Callaway <tcallawa@redhat.com> - 6.3.1-4
- fix doc finding (bz 647140)
* Mon Oct 11 2010 Orion Poplawski <orion@cora.nwra.com> - 6.3.1-3
- Rebuild for plplot 5.9.7
* Tue Aug 10 2010 Julian Sikorski <belegdol@fedoraproject.org> - 6.3.1-2
- Updated the upstream patch to 1-4
* Mon Aug 02 2010 Tom "spot" Callaway <tcallawa@redhat.com> - 6.3.1-1
- update to 6.3.1
* Wed Jul 07 2010 Tom "spot" Callaway <tcallawa@redhat.com> - 6.2.0-4
- include license information in EMBOSS-libs package, instead of EMBOSS
since EMBOSS-libs always gets pulled in when EMBOSS is installed
* Wed Apr 07 2010 Julian Sikorski <belegdol@fedoraproject.org> - 6.2.0-3
- Added upstream 1-18 patch
* Wed Apr 7 2010 Tom "spot" Callaway <tcallawa@redhat.com> - 6.2.0-2
- fix pcre patch, use system pcre
- add patch to use system zlib
- add patch to use system plplot
- add patch to use system expat
* Wed Feb 24 2010 Julian Sikorski <belegdol@fedoraproject.org> - 6.2.0-1
- Updated to 6.2.0
- jemboss can be built using --with jemboss
- Disabled the pcre patch
- Made the licensing information more detailed
- --with sunjava allows building against Sun's JVM
* Sun Dec 13 2009 Julian Sikorski <belegdol@fedoraproject.org> - 6.1.0-6
- Added the upstream 1-3 patch
- Fixed bogus Patch3 description
- Jemboss is still disabled, but some improvements have been made
- Backported patch enabling jemboss rebuild from CVS
- Added ant and jpackage-utils to BuildRequires
- Made java-devel dependency versioned
- Switched to build-jar-repository to fill the dependencies
- Replaced versioned log4j calls with latest version
- Renamed EMBOSS-java to jemboss
- Added a desktop entry for jemboss from Debian
* Sat Oct 17 2009 Julian Sikorski <belegdol@fedoraproject.org> - 6.1.0-5
- Added comments explaining the purpose of each patch
* Mon Oct 05 2009 Julian Sikorski <belegdol@fedoraproject.org> - 6.1.0-4
- Renamed conflicting binaries
- Disabled jemboss
* Tue Sep 29 2009 Julian Sikorski <belegdol@fedoraproject.org> - 6.1.0-3
- Re-enabled system pcre usage
- Initial attempt at using system-wide .jar files
* Tue Sep 22 2009 Julian Sikorski <belegdol@fedoraproject.org> - 6.1.0-2
- Added the upstream 1-2 patch
* Wed Jul 29 2009 Julian Sikorski <belegdol@fedoraproject.org> - 6.1.0-1
- Updated to 6.1.0
- Dropped pcre-devel from BuildRequires for the time being
- Ditto --with-java and --with-javaos
- Patched jemboss/Makefile.am not to include DESTDIR in runJemboss.sh
- Install the header files in EMBOSS subdir
- Added the missing executable bits
* Fri Jun 12 2009 Julian Sikorski <belegdol@fedoraproject.org> - 6.0.1-3
- Updated the upstream patch to 1-12
- Added the patch readme to %%doc
* Thu Apr 16 2009 Julian Sikorski <belegdol@fedoraproject.org> - 6.0.1-2
- Own %%{_datadir}/EMBOSS
- Don't use %%{name} macro in %%files
- Updated the upstream patch to 1-7
- Use dist instead of dist_tag
- Adjusted whitespaces
- Added pcre-devel to BuildRequires
- Fixed spurious executable permissions
- Removed the empty dna.aln file
- Patched jemboss.properties to include the paths this package uses
- Made the -java package require the main one
* Mon Sep 29 2008 Dominik Mierzejewski <rpm@greysector.net> 6.0.1-1
- updated to 6.0.1
- applied upstream patch 1-1
- patched to use system pcre
* Tue Jan 08 2008 Dominik Mierzejewski <rpm@greysector.net> 5.0.0-1
- Cleaned up BioRPMs' spec
- Updated to 5.0.0
* Thu Mar 17 2005 Bent Terp <Bent.Terp@biosci.ki.se>
- Upped to 2.10.0
* Fri Jul 16 2004 Bent Terp <Bent.Terp@biosci.ki.se>
- Had forgotten the emboss_database_dir env var
* Wed Feb 18 2004 Bent Terp <Bent.Terp@biosci.ki.se>
- Tried to make the building more dynamic. Added Requires and BuildRequires
* Thu Dec 04 2003 Luc Ducazu <luc@biolinux.org>
- Build for EMBOSS 2.8.0
- subpackage jemboss
* Wed Jun 11 2003 Luc Ducazu <luc@biolinux.org>
- Build for EMBOSS 2.7.1
* Tue Jan 28 2003 Luc Ducazu <luc@biolinux.org>
- Build for EMBOSS 2.6.0
- Programs moved to /usr/local/bin
- Adopted many ideas from Guillaume Rousse <g.rousse@linux-mandrake.com>
* Wed Nov 27 2002 Luc Ducazu <luc@biolinux.org>
- Initial build for EMBOSS 2.5.1