rpms/EMBOSS/devel .cvsignore, 1.3, 1.4 EMBOSS.spec, 1.3, 1.4 sources, 1.3, 1.4 EMBOSS-6.1.0-destdir.patch, 1.1, NONE EMBOSS-6.1.0-rebuild.patch, 1.1, NONE README.fixes, 1.2, NONE
belegdol
belegdol at fedoraproject.org
Wed Feb 24 20:29:24 UTC 2010
Author: belegdol
Update of /cvs/pkgs/rpms/EMBOSS/devel
In directory cvs1.fedora.phx.redhat.com:/tmp/cvs-serv17114
Modified Files:
.cvsignore EMBOSS.spec sources
Removed Files:
EMBOSS-6.1.0-destdir.patch EMBOSS-6.1.0-rebuild.patch
README.fixes
Log Message:
* Wed Feb 24 2010 Julian Sikorski <belegdol at 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
Index: .cvsignore
===================================================================
RCS file: /cvs/pkgs/rpms/EMBOSS/devel/.cvsignore,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -p -r1.3 -r1.4
--- .cvsignore 15 Dec 2009 18:49:00 -0000 1.3
+++ .cvsignore 24 Feb 2010 20:29:23 -0000 1.4
@@ -1,2 +1 @@
-EMBOSS-6.1.0.tar.gz
-patch-1-3.gz
+EMBOSS-6.2.0.tar.gz
Index: EMBOSS.spec
===================================================================
RCS file: /cvs/pkgs/rpms/EMBOSS/devel/EMBOSS.spec,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -p -r1.3 -r1.4
--- EMBOSS.spec 15 Dec 2009 19:11:30 -0000 1.3
+++ EMBOSS.spec 24 Feb 2010 20:29:24 -0000 1.4
@@ -1,40 +1,57 @@
# TODO:
# fix jemboss and enable it
+#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: 6.1.0
-Release: 6%{?dist}
+Version: 6.2.0
+Release: 1%{?dist}
Summary: The European Molecular Biology Open Software Suite
Group: Applications/Engineering
-License: GPLv2+
+#Files under jemboss/, ajax/ensembl/ are LGPLv2+
+#Files under ajax/pcre/ are BSD
+#Files under ajax/zlib/ are zlib/libpng
+License: GPLv2+ and LGPLv2+ and BSD and zlib/libpng
URL: http://emboss.sf.net/
Source0: ftp://emboss.open-bio.org/pub/EMBOSS/%{name}-%{version}.tar.gz
-Source1: README.fixes
+#Source1: README.fixes
+%if %{with jemboss}
Source2: jemboss.desktop
+%endif
#Upstream patch
-Patch0: ftp://emboss.open-bio.org/pub/EMBOSS/fixes/patches/patch-1-3.gz
+#Patch0: ftp://emboss.open-bio.org/pub/EMBOSS/fixes/patches/patch-1-3.gz
#Use system-wide pcre. Sent upstream.
Patch1: %{name}-system-pcre.patch
#Fedora-specific. Not sent upstream.
Patch2: %{name}-fedora.patch
-#Remove extra destdir. Sent upstream.
-Patch3: %{name}-6.1.0-destdir.patch
-#Patch ensuring jemboss rebuild backported from CVS
-Patch4: %{name}-6.1.0-rebuild.patch
BuildRoot: %{_tmppath}/%{name}-%{version}-%{release}-root-%(%{__id_u} -n)
+BuildRequires: gd-devel
+BuildRequires: pam-devel
+BuildRequires: pcre-devel
+%if %{with jemboss}
BuildRequires: ant
BuildRequires: desktop-file-utils
-BuildRequires: gd-devel
BuildRequires: java-devel >= 1:1.6.0
BuildRequires: jpackage-utils
-BuildRequires: pam-devel
-BuildRequires: pcre-devel
-BuildRequires: axis jaf javamail jakarta-commons-discovery jakarta-commons-logging
+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
@@ -69,40 +86,42 @@ Group: System Environment/Libra
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.
-#%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/
+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 .pcre
+#%patch0 -p1
%patch2 -p0 -b .fedora
-%patch3 -p0 -b .destdir
-%patch4 -p0 -b .jemboss-rebuild
+
+#Remove expat, pcre and zlib just to be sure that system versions are used
+#rm -rf ajax/{expat,pcre,zlib}
#install the patch readme
-install -pm 644 %{SOURCE1} README.fixes
+#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 at log4j-1.2.8@log4j-1.2.14@" \
jemboss/lib/axis/Makefile.am \
@@ -111,7 +130,7 @@ sed -i "s at log4j-1.2.8@log4j-1.2.14@" \
jemboss/utils/makeJNLP.sh
#use system java libraries
-rm jemboss/lib/{activation,client,jakarta-regexp-1.2,mail,xerces}.jar
+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
@@ -122,9 +141,14 @@ 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=$PATH:%{_java}/bin/
+%endif
+
%configure \
--disable-static \
--with-x \
@@ -134,14 +158,24 @@ done
%ifarch ppc64 sparc64 x86_64
--enable-64 \
%endif
+%if %{with jemboss}
--with-java=/usr/lib/jvm/java/include \
- --with-javaos=/usr/lib/jvm/java/include/linux \
+ --with-javaos=/usr/lib/jvm/java/include/linux
+%endif
+%if %{with sunjava}
+ --with-java=%{_java}/include
+ --with-javaos=%{_java}/include/linux
+%endif
%{__make} %{?_smp_mflags}
%install
+%if %{with sunjava}
+export PATH=$PATH:%{_java}/bin/
+%endif
+
rm -rf $RPM_BUILD_ROOT
%{__make} install DESTDIR=$RPM_BUILD_ROOT
@@ -180,10 +214,12 @@ 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}
+desktop-file-install \
+--dir=${RPM_BUILD_ROOT}%{_datadir}/applications \
+%{SOURCE2}
+%endif
%clean
@@ -198,7 +234,7 @@ rm -rf $RPM_BUILD_ROOT
%files
%defattr(-,root,root,-)
-%doc AUTHORS ChangeLog COPYING FAQ INSTALL LICENSE NEWS README README.fixes THANKS
+%doc AUTHORS ChangeLog COPYING FAQ INSTALL LICENSE NEWS README THANKS
%{_bindir}/*
%exclude %{_bindir}/runJemboss.csh
%exclude %{_bindir}/jembossctl
@@ -218,16 +254,25 @@ rm -rf $RPM_BUILD_ROOT
%{_libdir}/*.so.*
-#%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
+%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 Feb 24 2010 Julian Sikorski <belegdol at 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 at fedoraproject.org> - 6.1.0-6
- Added the upstream 1-3 patch
- Fixed bogus Patch3 description
Index: sources
===================================================================
RCS file: /cvs/pkgs/rpms/EMBOSS/devel/sources,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -p -r1.3 -r1.4
--- sources 15 Dec 2009 18:49:01 -0000 1.3
+++ sources 24 Feb 2010 20:29:24 -0000 1.4
@@ -1,2 +1 @@
-6c5163c571bc0be94d64420ce0d71824 EMBOSS-6.1.0.tar.gz
-4a5f96d849409fdecf39e92380e5381e patch-1-3.gz
+2e2937dd0493814ca0f64981f4c79319 EMBOSS-6.2.0.tar.gz
--- EMBOSS-6.1.0-destdir.patch DELETED ---
--- EMBOSS-6.1.0-rebuild.patch DELETED ---
--- README.fixes DELETED ---
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