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File EMBOSS.spec of Package EMBOSS
# # spec file for package EMBOSS # # Copyright (c) 2013 SUSE LINUX Products 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. #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: %{name}-%{version}.tar.gz BuildRoot: %{_tmppath}/%{name}-%{version}-build BuildRequires: autoconf BuildRequires: automake BuildRequires: libtool BuildRequires: fdupes BuildRequires: gcc-c++ BuildRequires: gd-devel BuildRequires: libexpat-devel BuildRequires: libharu-devel BuildRequires: mariadb BuildRequires: libmariadb-devel BuildRequires: glibc-devel BuildRequires: pam-devel BuildRequires: pcre-devel BuildRequires: libpq5 BuildRequires: postgresql-devel BuildRequires: postgresql-server BuildRequires: postgresql-server-devel BuildRequires: unzip BuildRequires: xorg-x11-libX11-devel BuildRequires: zlib-devel BuildRequires: libfreetype6 BuildRequires: libpng12-devel %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} %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 #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 # Remove check if EMBOSS version is latest on make install sed -i '/install-exec-hook/d' Makefile.am sed -i '/embossupdate/d' Makefile.am %build autoreconf -fi %if %{with sunjava} export PATH=$PATH:%{_java}/bin/ %endif %configure LIBS=-lexpat \ --disable-static \ --with-x \ --with-auth \ --with-thread \ --includedir=%{_includedir}/EMBOSS \ --enable-systemlibs \ %ifarch ppc64 sparc64 x86_64 --enable-64 \ %endif %if %{with jemboss} --with-java=/usr/lib/jvm/java/include \ --with-javaos=/usr/lib/jvm/java/include/linux %endif %if %{with sunjava} --with-java=%{_java}/include \ --with-javaos=%{_java}/include/linux %endif %{__make} %{?_smp_mflags} %install %if %{with sunjava} export PATH=$PATH:%{_java}/bin/ %endif rm -rf %{buildroot} %{__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} %clean %post libs -p /sbin/ldconfig %postun libs -p /sbin/ldconfig %files %defattr(-,root,root,-) %{_bindir}/* %exclude %{_bindir}/runJemboss.sh %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.sh %{_bindir}/jembossctl %{_datadir}/applications/jemboss.desktop %{_datadir}/EMBOSS/jemboss %endif %changelog
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