File EMBOSS.spec of Package EMBOSS
#
# spec file for package EMBOSS
#
# Copyright (c) 2016 SUSE LINUX GmbH, Nuernberg, Germany.
#
# All modifications and additions to the file contributed by third parties
# remain the property of their copyright owners, unless otherwise agreed
# upon. The license for this file, and modifications and additions to the
# file, is the same license as for the pristine package itself (unless the
# license for the pristine package is not an Open Source License, in which
# case the license is the MIT License). An "Open Source License" is a
# license that conforms to the Open Source Definition (Version 1.9)
# published by the Open Source Initiative.
# Please submit bugfixes or comments via http://bugs.opensuse.org/
#
# 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.
# Find out what patch-1-24.gz actually does and if it's still necessary on 6.6.0
#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: 6.6.0
Release: 0
Summary: The European Molecular Biology Open Software Suite
License: GPL-2.0+ and LGPL-2.1+ and BSD-3-Clause
Group: Productivity/Scientific/Other
# Files under jemboss/, ajax/ensembl/ are LGPLv2+
# Files under ajax/pcre/ are BSD
# Files under ajax/zlib/ are zlib/libpng
Url: http://www.emboss.org/
Source0: ftp://emboss.open-bio.org/pub/%{name}/%{name}-%{version}.tar.gz
Source1: %{name}-rpmlintrc
# Upstream patch
#Patch0: patch-1-24.gz
Patch1: EMBOSS-6.6.0-system-pcre.patch
Patch2: EMBOSS-6.6.0-system-expat.patch
Patch3: EMBOSS-6.6.0-system-zlib.patch
Patch4: EMBOSS-6.6.0-implicit_declarations.patch
Patch5: EMBOSS-6.6.0-disable_end_update.patch
BuildRoot: %{_tmppath}/%{name}-%{version}-build
BuildRequires: autoconf >= 2.64
BuildRequires: automake
BuildRequires: libtool
BuildRequires: fdupes
BuildRequires: gcc-c++
BuildRequires: gd-devel
BuildRequires: libexpat-devel
BuildRequires: libharu-devel
BuildRequires: libmysqlclient-devel
BuildRequires: glibc-devel
BuildRequires: pam-devel
BuildRequires: pcre-devel
BuildRequires: postgresql-devel
BuildRequires: unzip
BuildRequires: xorg-x11-libX11-devel
BuildRequires: zlib-devel
%if 0%{?suse_version} <= 1120
BuildRequires: libpng-devel
%else
BuildRequires: libfreetype6
BuildRequires: libpng16-compat-devel
%endif
%if %{with jemboss}
BuildRequires: ant
BuildRequires: classpathx-mail
BuildRequires: desktop-file-utils
BuildRequires: gnu-jaf
BuildRequires: java-1_6_0-openjdk-devel
BuildRequires: jpackage-utils
BuildRequires: regexp
BuildRequires: xerces-j2
%endif
%if %{with sunjava}
Requires: jdk = 2000:1.6.0_17-fcs
%endif
%description
EMBOSS is a 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/Other
Requires: %{name}-libs = %{version}-%{release}
Requires: gd-devel
Requires: glibc-devel
Requires: libexpat-devel
Requires: libharu-devel
%if 0%{?suse_version} <= 1120
Requires: libpng-devel
%else
Requires: libpng16-compat-devel
%endif
Requires: pam-devel
Requires: pcre-devel
Requires: zlib-devel
%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/Libraries
%description libs
The %{name}-libs package includes the dynamic libraries necessary for %{name}.
%package docs
Summary: Documentation for %{name}
Group: Documentation/Other
%description docs
The %{name}-docs package includes the documentation for %{name}.
%package test
Summary: Test files for %{name}
Group: Productivity/Scientific/Other
%description test
The %{name}-test package includes the test files for %{name} development.
%if %{with jemboss}
%package -n jemboss
Summary: Java interface to %{name}
Group: Applications/Engineering
Requires: %{name} = %{version}-%{release}
Requires: gnu-jaf
Requires: java >= 1:1.6.0
Requires: javamail
Requires: jpackage-utils
Requires: regexp
Requires: xerces-j2
%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
%patch2 -p1
%patch3 -p1
%patch4 -p1
%patch5 -p1
#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
%endif
%build
autoreconf -fi
%if %{with sunjava}
export PATH=$PATH:%{_java}/bin/
%endif
# Remove bundled expat, pcre and zlib to make sure that system versions are used
rm -rf ajax/{expat,pcre,zlib}
%configure \
--disable-static \
--with-x \
--with-auth \
--with-thread \
--includedir=%{_includedir}/EMBOSS \
--enable-systemlibs \
%ifarch ppc64 sparc64 x86_64
--enable-64 \
%endif
%if %{with jemboss}
--with-java=/usr/lib/jvm/java/include \
--with-javaos=/usr/lib/jvm/java/include/linux
%endif
%if %{with sunjava}
--with-java=%{_java}/include
--with-javaos=%{_java}/include/linux
%endif
make %{?_smp_mflags}
%install
%if %{with sunjava}
export PATH=$PATH:%{_java}/bin/
%endif
make install DESTDIR=%{buildroot}
install -m 755 -d %{buildroot}/%{_sysconfdir}/profile.d
cat << __EOF__ >> %{buildroot}/%{_sysconfdir}/profile.d/emboss.sh
export PLPLOT_LIB=%{emhome}
export EMBOSS_ACDROOT=%{emhome}/acd
export EMBOSS_DOCROOT=%{_datadir}/doc/packages/EMBOSS
export EMBOSS_DATABASE_DIR=%{emhome}/data
export EMBOSS_DATA=%{emhome}/data
__EOF__
cat << __EOF__ >> %{buildroot}/%{_sysconfdir}/profile.d/emboss.csh
setenv PLPLOT_LIB %{emhome}
setenv EMBOSS_ACDROOT %{emhome}/acd
setenv EMBOSS_DOCROOT %{_datadir}/doc/packages/EMBOSS
setenv EMBOSS_DATABASE_DIR %{emhome}/data
setenv EMBOSS_DATA %{emhome}/data
__EOF__
#this file has zero length, so kill it
rm %{buildroot}%{_datadir}/EMBOSS/test/data/dna.aln
%if %{with jemboss}
#fix executable permissions
pushd %{buildroot}%{_datadir}/EMBOSS/jemboss/utils
chmod +x install-jemboss-server.sh keys.sh makeFileManagerJNLP.sh makeJar.csh \
makeJNLP.sh
popd
pushd %{buildroot}%{_datadir}/EMBOSS/jemboss/api
chmod +x getClasses.pl makeDocs.csh
popd
%endif
#rename conflicting binaries
mv %{buildroot}%{_bindir}/chaos %{buildroot}%{_bindir}/em_chaos
#move doc to /usr/share/doc/packages/EMBOSS
mkdir -p %{buildroot}%{_datadir}/doc/packages/EMBOSS
mv %{buildroot}%{_datadir}/EMBOSS/doc/manuals %{buildroot}%{_datadir}/doc/packages/EMBOSS
mv %{buildroot}%{_datadir}/EMBOSS/doc/programs %{buildroot}%{_datadir}/doc/packages/EMBOSS
mv %{buildroot}%{_datadir}/EMBOSS/doc/tutorials %{buildroot}%{_datadir}/doc/packages/EMBOSS
rm -rf %{buildroot}%{_datadir}/EMBOSS/doc
ln -s ../doc/packages/EMBOSS %{buildroot}%{_datadir}/EMBOSS/doc
mv AUTHORS ChangeLog FAQ INSTALL NEWS README THANKS LICENSE COPYING %{buildroot}%{_datadir}/doc/packages/EMBOSS
%fdupes %{buildroot}
%post libs -p /sbin/ldconfig
%postun libs -p /sbin/ldconfig
%files
%defattr(-,root,root,-)
%{_bindir}/*
%exclude %{_bindir}/runJemboss.csh
%exclude %{_bindir}/jembossctl
%{_datadir}/EMBOSS
%exclude %{_datadir}/EMBOSS/jemboss
%exclude %{_datadir}/EMBOSS/test
%exclude %{_datadir}/EMBOSS/doc
%config %{_sysconfdir}/profile.d/*
%files devel
%defattr(-,root,root,-)
%{_libdir}/*.so
%{_libdir}/*.la
%{_includedir}/EMBOSS
%files libs
%defattr(-,root,root,-)
%{_libdir}/*.so.*
%files docs
%defattr(-,root,root,-)
%{_datadir}/doc/packages/EMBOSS
%{_datadir}/EMBOSS/doc
%files test
%defattr(-,root,root,-)
%{_datadir}/EMBOSS/test
%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
