From c721f49a717dfca9466355c4b2f87b2a8b329d6b Mon Sep 17 00:00:00 2001 From: belegdol Date: Dec 24 2009 08:01:31 +0000 Subject: - 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 --- diff --git a/.cvsignore b/.cvsignore index 279d48e..3c56458 100644 --- a/.cvsignore +++ b/.cvsignore @@ -1,2 +1,2 @@ EMBOSS-6.1.0.tar.gz -patch-1-2.gz +patch-1-3.gz diff --git a/EMBOSS-6.1.0-rebuild.patch b/EMBOSS-6.1.0-rebuild.patch new file mode 100644 index 0000000..4cacc9f --- /dev/null +++ b/EMBOSS-6.1.0-rebuild.patch @@ -0,0 +1,62 @@ +--- 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: ++@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. diff --git a/EMBOSS.spec b/EMBOSS.spec index 0a5dee2..e23d3a0 100644 --- a/EMBOSS.spec +++ b/EMBOSS.spec @@ -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 @@ -64,14 +70,16 @@ The %{name}-libs package includes the dynamic libraries necessary for %{name}. -#%package java +#%package -n jemboss #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 +#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 java +#%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 @@ -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@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/polydot.c emboss/supermatcher.c %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 @@ -196,20 +212,34 @@ rm -rf $RPM_BUILD_ROOT %{_libdir}/*.so %{_includedir}/EMBOSS + %files libs %defattr(-,root,root,-) %{_libdir}/*.so.* -#%files java +#%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 - 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 - 6.1.0-5 - Added comments explaining the purpose of each patch diff --git a/README.fixes b/README.fixes index 9dfcfd2..fef95d4 100644 --- a/README.fixes +++ b/README.fixes @@ -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. + diff --git a/jemboss.desktop b/jemboss.desktop new file mode 100644 index 0000000..702ba16 --- /dev/null +++ b/jemboss.desktop @@ -0,0 +1,10 @@ +[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; diff --git a/sources b/sources index 055976e..8fb2dec 100644 --- a/sources +++ b/sources @@ -1,2 +1,2 @@ 6c5163c571bc0be94d64420ce0d71824 EMBOSS-6.1.0.tar.gz -faec6ddd399ef243f4d6ffbcc878b009 patch-1-2.gz +4a5f96d849409fdecf39e92380e5381e patch-1-3.gz