rpms/EMBOSS/devel EMBOSS-6.1.0-rebuild.patch, NONE, 1.1 jemboss.desktop, NONE, 1.1 .cvsignore, 1.2, 1.3 EMBOSS.spec, 1.1, 1.2 README.fixes, 1.1, 1.2 sources, 1.2, 1.3
belegdol
belegdol at fedoraproject.org
Tue Dec 15 18:49:01 UTC 2009
Author: belegdol
Update of /cvs/pkgs/rpms/EMBOSS/devel
In directory cvs1.fedora.phx.redhat.com:/tmp/cvs-serv13542
Modified Files:
.cvsignore EMBOSS.spec README.fixes sources
Added Files:
EMBOSS-6.1.0-rebuild.patch jemboss.desktop
Log Message:
* Sun Dec 13 2009 Julian Sikorski <belegdol at 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
EMBOSS-6.1.0-rebuild.patch:
Makefile.am | 5 +++++
Makefile.in | 31 +++++++++++++++++--------------
2 files changed, 22 insertions(+), 14 deletions(-)
--- NEW FILE EMBOSS-6.1.0-rebuild.patch ---
--- jemboss/lib/Makefile.am.rebuild 2009-06-30 10:33:58.000000000 +0200
+++ jemboss/lib/Makefile.am 2009-10-21 07:56:01.000000000 +0200
@@ -1,5 +1,10 @@
SUBDIRS = axis
+all-local:
+if EHAVEANT
+ ant -f ../build.xml package -Demboss.data=../emboss/data -Dname=client -Djar.dir=lib -Dnotformemboss=yes;
+endif
+
# The install-exec-hook is for the case where a client.jar has
# been created by the 'ant' packaging for a standalone Jemboss.
# In that case it needs to be copied to the install dir.
--- jemboss/lib/Makefile.in.rebuild 2009-07-15 01:16:01.000000000 +0200
+++ jemboss/lib/Makefile.in 2009-10-21 07:56:46.000000000 +0200
@@ -507,7 +507,7 @@
done
check-am: all-am
check: check-recursive
-all-am: Makefile $(DATA)
+all-am: Makefile $(DATA) all-local
installdirs: installdirs-recursive
installdirs-am:
for dir in "$(DESTDIR)$(pkgdatadir)"; do \
@@ -609,21 +609,24 @@
install-am install-exec-am install-strip tags-recursive
.PHONY: $(RECURSIVE_CLEAN_TARGETS) $(RECURSIVE_TARGETS) CTAGS GTAGS \
- all all-am check check-am clean clean-generic clean-libtool \
- ctags ctags-recursive distclean distclean-generic \
- distclean-libtool distclean-tags distdir dvi dvi-am html \
- html-am info info-am install install-am install-data \
- install-data-am install-dvi install-dvi-am install-exec \
- install-exec-am install-exec-hook install-html install-html-am \
- install-info install-info-am install-man install-pdf \
- install-pdf-am install-pkgdataDATA install-ps install-ps-am \
- install-strip installcheck installcheck-am installdirs \
- installdirs-am maintainer-clean maintainer-clean-generic \
- mostlyclean mostlyclean-generic mostlyclean-libtool pdf pdf-am \
- ps ps-am tags tags-recursive uninstall uninstall-am \
- uninstall-pkgdataDATA
+ all all-am all-local check check-am clean clean-generic \
+ clean-libtool ctags ctags-recursive distclean \
+ distclean-generic distclean-libtool distclean-tags distdir dvi \
+ dvi-am html html-am info info-am install install-am \
+ install-data install-data-am install-dvi install-dvi-am \
+ install-exec install-exec-am install-exec-hook install-html \
+ install-html-am install-info install-info-am install-man \
+ install-pdf install-pdf-am install-pkgdataDATA install-ps \
+ install-ps-am install-strip installcheck installcheck-am \
+ installdirs installdirs-am maintainer-clean \
+ maintainer-clean-generic mostlyclean mostlyclean-generic \
+ mostlyclean-libtool pdf pdf-am ps ps-am tags tags-recursive \
+ uninstall uninstall-am uninstall-pkgdataDATA
+all-local:
+ at EHAVEANT_TRUE@ ant -f ../build.xml package -Demboss.data=../emboss/data -Dname=client -Djar.dir=lib -Dnotformemboss=yes;
+
# The install-exec-hook is for the case where a client.jar has
# been created by the 'ant' packaging for a standalone Jemboss.
# In that case it needs to be copied to the install dir.
--- NEW FILE jemboss.desktop ---
[Desktop Entry]
Version=1.0
Terminal=false
Icon=jemboss
Exec=runJemboss.csh
Name=Jemboss
GenericName=GUI for EMBOSS
Comment=Graphical user interface for the European Molecular Biology Open Software Suite.
Type=Application
Categories=Biology;Science;Education;
Index: .cvsignore
===================================================================
RCS file: /cvs/pkgs/rpms/EMBOSS/devel/.cvsignore,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -p -r1.2 -r1.3
--- .cvsignore 17 Oct 2009 22:47:55 -0000 1.2
+++ .cvsignore 15 Dec 2009 18:49:00 -0000 1.3
@@ -1,2 +1,2 @@
EMBOSS-6.1.0.tar.gz
-patch-1-2.gz
+patch-1-3.gz
Index: EMBOSS.spec
===================================================================
RCS file: /cvs/pkgs/rpms/EMBOSS/devel/EMBOSS.spec,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -p -r1.1 -r1.2
--- EMBOSS.spec 17 Oct 2009 22:47:55 -0000 1.1
+++ EMBOSS.spec 15 Dec 2009 18:49:01 -0000 1.2
@@ -5,7 +5,7 @@
Name: EMBOSS
Version: 6.1.0
-Release: 5%{?dist}
+Release: 6%{?dist}
Summary: The European Molecular Biology Open Software Suite
Group: Applications/Engineering
@@ -13,22 +13,28 @@ License: GPLv2+
URL: http://emboss.sf.net/
Source0: ftp://emboss.open-bio.org/pub/EMBOSS/%{name}-%{version}.tar.gz
Source1: README.fixes
+Source2: jemboss.desktop
#Upstream patch
-Patch0: ftp://emboss.open-bio.org/pub/EMBOSS/fixes/patches/patch-1-2.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
-#Add missing destdir. Sent upstream.
+#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: ant
+BuildRequires: desktop-file-utils
BuildRequires: gd-devel
-#BuildRequires: java-devel
+BuildRequires: java-devel >= 1:1.6.0
+BuildRequires: jpackage-utils
BuildRequires: pam-devel
BuildRequires: pcre-devel
-#BuildRequires: axis classpathx-jaf jakarta-commons-discovery
-#BuildRequires: jakarta-commons-logging log4j wsdl4j
+BuildRequires: axis jaf javamail jakarta-commons-discovery jakarta-commons-logging
+BuildRequires: log4j regexp servlet xerces-j2 wsdl4j
%description
EMBOSS is a new, free Open Source software analysis package specially
@@ -64,21 +70,23 @@ The %{name}-libs package includes the dy
necessary for %{name}.
-#%package java
-#Summary: Java interface to %{name}
-#Group: Applications/Engineering
-#Requires: %{name} = %{version}-%{release}
-#Requires: axis classpathx-jaf jakarta-commons-discovery
-#Requires: jakarta-commons-logging log4j wsdl4j
-
-#%description java
-#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/
%prep
@@ -87,6 +95,7 @@ necessary for %{name}.
%patch1 -p1 -b .pcre
%patch2 -p0 -b .fedora
%patch3 -p0 -b .destdir
+%patch4 -p0 -b .jemboss-rebuild
#install the patch readme
install -pm 644 %{SOURCE1} README.fixes
@@ -94,30 +103,29 @@ install -pm 644 %{SOURCE1} README.fixes
#these files were executable for some reason
chmod 644 emboss/prettyplot.c emboss/polydot.c emboss/supermatcher.c
+#use newer log4j version
+sed -i "s at 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
-#pushd jemboss/lib
-#rm activation.jar;
-#ln -s %{_javadir}/activation.jar activation.jar;
-#pushd axis
-#for i in axis-ant axis jaxrpc saaj;
-#do
-# rm $i.jar;
-# ln -s %{_javadir}/axis/$i.jar $i.jar;
-#done
-#for i in commons-discovery commons-logging wsdl4j;
-#do
-# rm $i.jar;
-# ln -s %{_javadir}/$i.jar $i.jar;
-#done
-#rm log4j-1.2.8.jar
-#ln -s %{_javadir}/log4j.jar log4j-1.2.8.jar
-#popd
-#popd
+rm jemboss/lib/{activation,client,jakarta-regexp-1.2,mail,xerces}.jar
+build-jar-repository -s -p jemboss/lib activation regexp javamail xerces-j2
+mv jemboss/lib/regexp.jar jemboss/lib/jakarta-regexp-1.2.jar
+mv jemboss/lib/javamail.jar jemboss/lib/mail.jar
+mv jemboss/lib/xerces-j2.jar jemboss/lib/xerces.jar
+rm jemboss/lib/axis/*.jar
+build-jar-repository -s -p jemboss/lib/axis axis/axis-ant axis/axis axis/jaxrpc axis/saaj commons-discovery commons-logging log4j-1.2.14 servlet wsdl4j
+for i in axis axis-ant jaxrpc saaj;
+do
+mv jemboss/lib/axis/axis_$i.jar jemboss/lib/axis/$i.jar;
+done
%build
%configure \
- --without-java \
--disable-static \
--with-x \
--with-auth \
@@ -126,6 +134,9 @@ chmod 644 emboss/prettyplot.c emboss/pol
%ifarch ppc64 sparc64 x86_64
--enable-64 \
%endif
+ --with-java=/usr/lib/jvm/java/include \
+ --with-javaos=/usr/lib/jvm/java/include/linux \
+
%{__make} %{?_smp_mflags}
@@ -169,6 +180,11 @@ popd
#rename conflicting binaries
mv $RPM_BUILD_ROOT%{_bindir}/chaos $RPM_BUILD_ROOT%{_bindir}/em_chaos
+#install the desktop file
+desktop-file-install \
+--dir=${RPM_BUILD_ROOT}%{_datadir}/applications \
+%{SOURCE2}
+
%clean
rm -rf $RPM_BUILD_ROOT
@@ -201,15 +217,28 @@ rm -rf $RPM_BUILD_ROOT
%{_libdir}/*.so.*
-#%files java
-#%defattr(-,root,root,-)
-#%doc jemboss/README jemboss/resources jemboss/api
-#%{_bindir}/runJemboss.csh
-#%{_bindir}/jembossctl
-#%{_datadir}/EMBOSS/jemboss
+%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
%changelog
+* Sun Dec 13 2009 Julian Sikorski <belegdol at 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 at fedoraproject.org> - 6.1.0-5
- Added comments explaining the purpose of each patch
Index: README.fixes
===================================================================
RCS file: /cvs/pkgs/rpms/EMBOSS/devel/README.fixes,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -p -r1.1 -r1.2
--- README.fixes 17 Oct 2009 22:47:55 -0000 1.1
+++ README.fixes 15 Dec 2009 18:49:01 -0000 1.2
@@ -30,3 +30,79 @@ Fix 2. EMBOSS-6.1.0/ajax/ajmem.h
This fixes a bug in processing SwissProt complex descriptions.
Fix definition of AJRESIZE0 macro.
Fix processing of first match in a profile alignment (prophet).
+
+Fix 3. EMBOSS-6.1.0/ajax/ajfeat.c
+ EMBOSS-6.1.0/ajax/ajfeat.h
+ EMBOSS-6.1.0/ajax/ajgraph.c
+ EMBOSS-6.1.0/ajax/ajmath.c
+ EMBOSS-6.1.0/ajax/ajseq.c
+ EMBOSS-6.1.0/ajax/ajseqread.c
+ EMBOSS-6.1.0/ajax/ajseqwrite.c
+ EMBOSS-6.1.0/nucleus/embmisc.c
+ EMBOSS-6.1.0/nucleus/embmisc.h
+ EMBOSS-6.1.0/nucleus/embpat.c
+ EMBOSS-6.1.0/emboss/coderet.c
+ EMBOSS-6.1.0/emboss/extractfeat.c
+ EMBOSS-6.1.0/emboss/notseq.c
+ EMBOSS-6.1.0/emboss/prettyplot.c
+ EMBOSS-6.1.0/emboss/seqmatchall.c
+ EMBOSS-6.1.0/emboss/showfeat.c
+ EMBOSS-6.1.0/emboss/showpep.c
+ EMBOSS-6.1.0/emboss/showseq.c
+ EMBOSS-6.1.0/emboss/twofeat.c
+ EMBOSS-6.1.0/jemboss/utils/install-jemboss-server.sh
+ EMBOSS-6.1.0/jemboss/org/emboss/jemboss/server/AppendToLogFileThread.java
+ EMBOSS-6.1.0/jemboss/org/emboss/jemboss/server/JembossAuthServer.java
+
+02-Dec-2009: Fixes problems with extractfeat. The fix includes cleaner
+ definitions of functions used to match feature tags and
+ feature types which result in minor updates to 6 other
+ applications.
+
+ Extractfeat in previous versions used its own text parser
+ to extract feature data from only a limited set of
+ formats. In release 6.1.0 it was replaced by the standard
+ EMBOSS feature table. With no options set, extractfeat
+ rejected all features (type '*' was needed to extract
+ features). Extractfeat default settings now extract all
+ features from an entry.
+
+ Features on the reverse strand were incorrectly processed
+ (an effect caused by some of the old extractfeat code
+ remaining). Reverse strand features are now correctly
+ parsed, including both "join(complement())" and
+ "complement(join())" syntax in EMBL/GenBank/DDBJ feature
+ tables.
+
+ Fixes an issue in GenBank parsing where the ORIGIN line is absent.
+
+ Fixes scaling errors in prettyplot, especially in mEMBOSS
+ when plotting to a window on screen (the default
+ output). The plplot library does not report the true
+ width and height for several devices. The assumptions in
+ prettyplot depend on reasonable size estimates. Release
+ 6.2.0 will have further corrections to plplot device
+ scaling.
+
+ Fixes the counting of non-coding features in coderet.
+
+ Fixes a seqmatchall error for short sequences with perfect matches
+
+ When reverse-complementing sequences, also reverses
+ the quality scores.
+
+ Allows '-' in format names in the USA syntax, to allow
+ fastq-sanger fastq-illumina and fastq-solexa format names
+ to be used.
+
+ When reading protein sequences, a sequence with only a
+ stop is now recognized as empty (zero length) after
+ processing ambiguity codes and stops.
+
+ Fixes a problem writing features in PIR format when the
+ feature table is empty, for example a report file with no hits.
+
+ Fixes a dependency on 'ant' to install a Jemboss server.
+
+ Fixes a problem in logging Jemboss info/error messages.
+
Index: sources
===================================================================
RCS file: /cvs/pkgs/rpms/EMBOSS/devel/sources,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -p -r1.2 -r1.3
--- sources 17 Oct 2009 22:47:55 -0000 1.2
+++ sources 15 Dec 2009 18:49:01 -0000 1.3
@@ -1,2 +1,2 @@
6c5163c571bc0be94d64420ce0d71824 EMBOSS-6.1.0.tar.gz
-faec6ddd399ef243f4d6ffbcc878b009 patch-1-2.gz
+4a5f96d849409fdecf39e92380e5381e patch-1-3.gz
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