# 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.

# NOTE: If EMBOSS updates, please ensure that Patch9 is properly redone to match.

# Notably, emboss/acd/epscan.acd should stay in sync with pscan.acd.

#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}

%global _java /usr/java/default

%endif

%global emhome %{_datadir}/EMBOSS

Name:           EMBOSS

Version:        6.6.0

Release:        16%{?dist}

Summary:        The European Molecular Biology Open Software Suite

# 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.

# There are some included ontologies, thanks to Debian for tracking down all

# the licenses:

# emboss/data/OBO/gene_ontology*.obo : CC-BY-3.0

# emboss/data/OBO/evidence_code.obo : GPLv3+

# emboss/data/OBO/pathway.obo : CC-BY-3.0

# emboss/data/OBO/ro.obo : CC-BY-3.0

# emboss/data/OBO/so.obo : Public Domain

License:        GPLv2+ and LGPLv2+ and CC-BY and GPLv3+ and Public Domain

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

# Use system-wide pcre. Sent upstream. Updated patch created on 2011-11-23.

Patch1:         EMBOSS-6.6.0-system-pcre.patch

# Use system-wide plplot

# Patch3:        EMBOSS-6.3.1-system-plplot.patch

# Use system-wide expat. Updated patch created on 2011-11-23.

Patch4:         EMBOSS-6.6.0-system-expat.patch

# Use system-wide zlib. Updated patch created on 2011-11-23.

Patch5:         EMBOSS-6.6.0-system-zlib.patch

# Fedora-specific. Not sent upstream.

Patch7:         %{name}-fedora.patch

# Fix conflict with pscan (Fedora package, unrelated to EMBOSS)

# https://bugzilla.redhat.com/show_bug.cgi?id=797804

# Emailed upstream on the issue on 2012-02-27

Patch9:		EMBOSS-6.6.0-fix-conflict-with-pscan.patch

# No, we don't need to run a non-existent binary to check across the network

# for updates. *sigh*

Patch10:	EMBOSS-6.6.0-no-update.patch

BuildRequires:  gd-devel

BuildRequires:  pam-devel

BuildRequires:  pcre-devel

BuildRequires:  zlib-devel

# BuildRequires:  plplot-devel

BuildRequires:  expat-devel

BuildRequires:  libharu-devel

BuildRequires:  libpq-devel

BuildRequires:  mariadb-connector-c-devel openssl-devel

BuildRequires:  libtool, autoconf

%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

BuildRequires: make

%if %{with sunjava}

Requires:       jdk = 2000:1.6.0_17-fcs

%endif

# We need this to force updates across minor releases where sonames do not change

Requires:       %{name}-libs = %{version}-%{release}

%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

Requires:       %{name}-libs = %{version}-%{release}

Requires:       libeplplot-devel = %{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}

%description libs

The %{name}-libs package includes the dynamic libraries

necessary for %{name}.

%if %{with jemboss}

%package -n jemboss

Summary:        Java interface to %{name}

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

%package -n libeplplot

Summary:        A modified version of plplot used by EMBOSS

%description -n libeplplot

A modified version of plplot used by EMBOSS.

%package -n libeplplot-devel

Summary:        Development files for eplplot

Requires:       libeplplot = %{version}-%{release}

%description -n libeplplot-devel

The libeplplot-devel package includes the header files and libraries

necessary for developing programs which will use the eplplot library.

%prep

%setup -q

%patch1 -p1 -b .system-pcre

%patch4 -p1 -b .system-expat

%patch5 -p1 -b .system-zlib

%patch7 -p0 -b .fedora

%patch9 -p1 -b .fixconflict

%patch10 -p1 -b .noupdate

# Remove bundled expat, pcre and zlib files to make sure that system versions are used

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

autoreconf -i

%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 because of generic names

mv $RPM_BUILD_ROOT%{_bindir}/chaos $RPM_BUILD_ROOT%{_bindir}/em_chaos

mv $RPM_BUILD_ROOT%{_bindir}/remap $RPM_BUILD_ROOT%{_bindir}/em_remap

mv $RPM_BUILD_ROOT%{_bindir}/wordcount $RPM_BUILD_ROOT%{_bindir}/em_wordcount

%if %{with jemboss}

#install the desktop file

desktop-file-install                                    \

--dir=${RPM_BUILD_ROOT}%{_datadir}/applications         \

%{SOURCE2}

%else

# Nuke the binaries so they don't make debuginfo

rm -rf ${RPM_BUILD_ROOT}%{_bindir}/runJemboss.csh

rm -rf ${RPM_BUILD_ROOT}%{_bindir}/jembossctl

rm -rf ${RPM_BUILD_ROOT}%{_datadir}/EMBOSS/jemboss

%endif

%ldconfig_scriptlets libs

%ldconfig_scriptlets -n libeplplot

%files

%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

%{_libdir}/*.so

%{_includedir}/EMBOSS

%exclude %{_includedir}/EMBOSS/eplplot/

%files libs

%license COPYING LICENSE

%{_libdir}/*.so.*

%exclude %{_libdir}/libeplplot*

%if 0%{?with_jemboss} || 0%{?with_sunjava}

%files -n jemboss

%doc jemboss/README jemboss/resources jemboss/api

%{_bindir}/runJemboss.csh

%{_bindir}/jembossctl

%{_datadir}/applications/jemboss.desktop

%{_datadir}/EMBOSS/jemboss

%endif

%files -n libeplplot

%{_libdir}/libeplplot*.so.*

%files -n libeplplot-devel

%{_includedir}/EMBOSS/eplplot/

%changelog

* Mon Jul 27 2020 Fedora Release Engineering <releng@fedoraproject.org> - 6.6.0-16

- Rebuilt for https://fedoraproject.org/wiki/Fedora_33_Mass_Rebuild

* Tue Jan 28 2020 Fedora Release Engineering <releng@fedoraproject.org> - 6.6.0-15

- Rebuilt for https://fedoraproject.org/wiki/Fedora_32_Mass_Rebuild

* Wed Jul 24 2019 Fedora Release Engineering <releng@fedoraproject.org> - 6.6.0-14

- Rebuilt for https://fedoraproject.org/wiki/Fedora_31_Mass_Rebuild

* Thu Jan 31 2019 Fedora Release Engineering <releng@fedoraproject.org> - 6.6.0-13

- Rebuilt for https://fedoraproject.org/wiki/Fedora_30_Mass_Rebuild

* Thu Jul 12 2018 Fedora Release Engineering <releng@fedoraproject.org> - 6.6.0-12

- Rebuilt for https://fedoraproject.org/wiki/Fedora_29_Mass_Rebuild

* Mon May 14 2018 Tom Callaway <spot@fedoraproject.org> - 6.6.0-11

- rename "wordcount" to "em_wordcount" to resolve conflict with texlive

* Wed Feb 07 2018 Fedora Release Engineering <releng@fedoraproject.org> - 6.6.0-10

- Rebuilt for https://fedoraproject.org/wiki/Fedora_28_Mass_Rebuild

* Sat Oct 28 2017 Tom Callaway <spot@fedoraproject.org> - 6.6.0-9

- fix mariadb issues (bz1493684)

* Wed Jul 26 2017 Fedora Release Engineering <releng@fedoraproject.org> - 6.6.0-8

- Rebuilt for https://fedoraproject.org/wiki/Fedora_27_Mass_Rebuild

* Thu Jul 13 2017 Tom Callaway <spot@fedoraproject.org> - 6.6.0-7

- rebuild against new mariadb

* Thu Jun 15 2017 Tom Callaway <spot@fedoraproject.org> - 6.6.0-6

- rebuild against new libharu (2.3.0)

* Tue May 16 2017 Tom Callaway <spot@fedoraproject.org> - 6.6.0-5

- rename "remap" to "em_remap" (bz1450190)

* Fri Feb 10 2017 Fedora Release Engineering <releng@fedoraproject.org> - 6.6.0-4

- Rebuilt for https://fedoraproject.org/wiki/Fedora_26_Mass_Rebuild

* Wed Feb 03 2016 Fedora Release Engineering <releng@fedoraproject.org> - 6.6.0-3

- Rebuilt for https://fedoraproject.org/wiki/Fedora_24_Mass_Rebuild

* Tue Jan 19 2016 Tom Callaway <spot@fedoraproject.org> - 6.6.0-2

- spec file cleanup

* Fri Oct 30 2015 Tom Callaway <spot@fedoraproject.org> - 6.6.0-1

- update to 6.6.0

* Tue Jun 16 2015 Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 6.4.0-14

- Rebuilt for https://fedoraproject.org/wiki/Fedora_23_Mass_Rebuild

* Fri Aug 15 2014 Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 6.4.0-13

- Rebuilt for https://fedoraproject.org/wiki/Fedora_21_22_Mass_Rebuild

* Fri Jun 06 2014 Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 6.4.0-12

- Rebuilt for https://fedoraproject.org/wiki/Fedora_21_Mass_Rebuild

* Tue Sep  3 2013 Tom Callaway <spot@fedoraproject.org> - 6.4.0-11

- add ontology license tags, thanks to Debian

* Fri Aug 02 2013 Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 6.4.0-10

- Rebuilt for https://fedoraproject.org/wiki/Fedora_20_Mass_Rebuild

* Tue Jun 11 2013 Remi Collet <rcollet@redhat.com> - 6.4.0-9

- rebuild for new GD 2.1.0

* Wed Feb 13 2013 Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 6.4.0-8

- Rebuilt for https://fedoraproject.org/wiki/Fedora_19_Mass_Rebuild

* Tue Jul 31 2012 Tom Callaway <spot@fedoraproject.org> - 6.4.0-7

- rebuild for new libharu

* Wed Jul 18 2012 Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 6.4.0-6

- Rebuilt for https://fedoraproject.org/wiki/Fedora_18_Mass_Rebuild

* Mon Feb 27 2012 Tom Callaway <spot@fedoraproject.org> - 6.4.0-5

- resolve conflict with pscan

* Fri Feb 10 2012 Petr Pisar <ppisar@redhat.com> - 6.4.0-4

- Rebuild against PCRE 8.30

* Thu Jan 12 2012 Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 6.4.0-3

- Rebuilt for https://fedoraproject.org/wiki/Fedora_17_Mass_Rebuild

* Sat Jan 07 2012 Julian Sikorski <belegdol@fedoraproject.org> - 6.4.0-2

- Rebuilt for gcc-4.7

- Dropped obsolete Group, Buildroot, %%clean and %%defattr

* Wed Nov 23 2011 Julian Sikorski <belegdol@fedoraproject.org> - 6.4.0-1

- Updated to 6.4.0

- Dropped included new-fix-doc-finding and fix-amd64-check patches

- Updated system libs patches

- tabs → spaces to satisfy rpmlint

* Wed Mar 23 2011 Dan Horák <dan@danny.cz> - 6.3.1-11

- rebuilt for mysql 5.5.10 (soname bump in libmysqlclient)

* Tue Mar 22 2011 Julian Sikorski <belegdol@fedoraproject.org> - 6.3.1-10

- Rebuilt for mysql-5.5.10

* Mon Feb 07 2011 Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 6.3.1-9

- Rebuilt for https://fedoraproject.org/wiki/Fedora_15_Mass_Rebuild

* Fri Dec 10 2010 Tom "spot" Callaway <tcallawa@redhat.com> - 6.3.1-8

- split libeplplot into its own package

* Tue Nov  9 2010 Tom "spot" Callaway <tcallawa@redhat.com> - 6.3.1-7

- use bundled plplot (EMBOSS depends on fork)

- add BR for postgresql-devel and mysql-devel

- use autotools to generate updated configure/Makefiles

- fix amd64 check to be finer grained, eliminate koji false positive

* Thu Nov  4 2010 Tom "spot" Callaway <tcallawa@redhat.com> - 6.3.1-6

- more intricate fix doc finding patch for 6.3.1

* Thu Nov  4 2010 Tom "spot" Callaway <tcallawa@redhat.com> - 6.3.1-5

- add forced requires to ensure proper (and matched) updates

- cleaner fix doc finding patch

* 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