From c07d48ff8e012d81be846fa0f47cbd775fce4e8e Mon Sep 17 00:00:00 2001 From: belegdol Date: Feb 24 2010 20:29:24 +0000 Subject: - 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 --- diff --git a/.cvsignore b/.cvsignore index 3c56458..80472ff 100644 --- a/.cvsignore +++ b/.cvsignore @@ -1,2 +1 @@ -EMBOSS-6.1.0.tar.gz -patch-1-3.gz +EMBOSS-6.2.0.tar.gz diff --git a/EMBOSS-6.1.0-destdir.patch b/EMBOSS-6.1.0-destdir.patch deleted file mode 100644 index 38b3377..0000000 --- a/EMBOSS-6.1.0-destdir.patch +++ /dev/null @@ -1,22 +0,0 @@ ---- jemboss/Makefile.am.destdir 2009-06-15 13:08:19.000000000 +0200 -+++ jemboss/Makefile.am 2009-07-29 12:52:37.000000000 +0200 -@@ -64,7 +64,7 @@ - echo "(cd $(prefix)/share/$(PACKAGE)/jemboss; java org/emboss/jemboss/Jemboss &)" >> $(DESTDIR)$(bindir)/runJemboss.csh; \ - chmod 755 $(DESTDIR)$(bindir)/runJemboss.csh; \ - (cd $(DESTDIR)$(prefix)/share/$(PACKAGE)/jemboss/resources; sed "s|user.auth=true|user.auth=false|" jemboss.properties | sed "s|jemboss.server=true|jemboss.server=false|" | sed "s|/packages/emboss/STABLE|$(prefix)|" > jemboss.properties.new; mv -f jemboss.properties.new jemboss.properties; cd -); \ -- sed "s|JEMBOSS_HOME=.|JEMBOSS_HOME=$(DESTDIR)$(prefix)/share/$(PACKAGE)/jemboss/|" runJemboss.sh > $(DESTDIR)$(prefix)/share/$(PACKAGE)/jemboss/runJemboss.sh; \ -+ sed "s|JEMBOSS_HOME=.|JEMBOSS_HOME=$(prefix)/share/$(PACKAGE)/jemboss/|" runJemboss.sh > $(DESTDIR)$(prefix)/share/$(PACKAGE)/jemboss/runJemboss.sh; \ - chmod 755 $(DESTDIR)$(prefix)/share/$(PACKAGE)/jemboss/runJemboss.sh; - - pkgdata_DATA = LICENSE readme.html README ---- jemboss/Makefile.in.destdir 2009-07-15 01:16:00.000000000 +0200 -+++ jemboss/Makefile.in 2009-07-29 12:52:39.000000000 +0200 -@@ -682,7 +682,7 @@ - echo "(cd $(prefix)/share/$(PACKAGE)/jemboss; java org/emboss/jemboss/Jemboss &)" >> $(DESTDIR)$(bindir)/runJemboss.csh; \ - chmod 755 $(DESTDIR)$(bindir)/runJemboss.csh; \ - (cd $(DESTDIR)$(prefix)/share/$(PACKAGE)/jemboss/resources; sed "s|user.auth=true|user.auth=false|" jemboss.properties | sed "s|jemboss.server=true|jemboss.server=false|" | sed "s|/packages/emboss/STABLE|$(prefix)|" > jemboss.properties.new; mv -f jemboss.properties.new jemboss.properties; cd -); \ -- sed "s|JEMBOSS_HOME=.|JEMBOSS_HOME=$(DESTDIR)$(prefix)/share/$(PACKAGE)/jemboss/|" runJemboss.sh > $(DESTDIR)$(prefix)/share/$(PACKAGE)/jemboss/runJemboss.sh; \ -+ sed "s|JEMBOSS_HOME=.|JEMBOSS_HOME=$(prefix)/share/$(PACKAGE)/jemboss/|" runJemboss.sh > $(DESTDIR)$(prefix)/share/$(PACKAGE)/jemboss/runJemboss.sh; \ - chmod 755 $(DESTDIR)$(prefix)/share/$(PACKAGE)/jemboss/runJemboss.sh; - - # tar to pick up the other directories diff --git a/EMBOSS-6.1.0-rebuild.patch b/EMBOSS-6.1.0-rebuild.patch deleted file mode 100644 index 4cacc9f..0000000 --- a/EMBOSS-6.1.0-rebuild.patch +++ /dev/null @@ -1,62 +0,0 @@ ---- 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 e23d3a0..ae2c668 100644 --- a/EMBOSS.spec +++ b/EMBOSS.spec @@ -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/Libraries The %{name}-libs package includes the dynamic libraries necessary for %{name}. - -#%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/ +%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. + +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@log4j-1.2.8@log4j-1.2.14@" \ jemboss/lib/axis/Makefile.am \ @@ -111,7 +130,7 @@ sed -i "s@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 - 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 - 6.1.0-6 - Added the upstream 1-3 patch - Fixed bogus Patch3 description diff --git a/README.fixes b/README.fixes deleted file mode 100644 index fef95d4..0000000 --- a/README.fixes +++ /dev/null @@ -1,108 +0,0 @@ -The files in this directory are bugfix replacements for files in -the EMBOSS-6.1.0 distribution. Just drop the replacement files in -the location shown and redo the 'make install.' - -Fix 1. EMBOSS-6.1.0/ajax/ajfeat.c - EMBOSS-6.1.0/ajax/ajseqread.c - EMBOSS-6.1.0/ajax/ajseqwrite.c - EMBOSS-6.1.0/jemboss/org/emboss/jemboss/gui/Browser.java - EMBOSS-6.1.0/jemboss/org/emboss/jemboss/gui/BuildProgramMenu.java - EMBOSS-6.1.0/jemboss/org/emboss/jemboss/gui/form/BuildJembossForm.java - EMBOSS-6.1.0/jemboss/org/emboss/jemboss/gui/sequenceChooser/InputSequenceAttributes.java - EMBOSS-6.1.0/jemboss/org/emboss/jemboss/soap/GetVersion.java - EMBOSS-6.1.0/jemboss/org/emboss/jemboss/soap/ShowDB.java - EMBOSS-6.1.0/jemboss/utils/install-jemboss-server.sh - EMBOSS-6.1.0/jemboss/lib/client.jar - -29 Jul 2009: Fix feature specification problems in Jemboss. - Use version number to point to documentation URLs - Remove standalone option from server script. - Correct FASTQ input searching for '@' to start next sequence - Standardize FASTQ sequence formats with other OpenBio projects - Correct issues in igstrict, genpept and refseqp formats - -Fix 2. EMBOSS-6.1.0/ajax/ajmem.h - EMBOSS-6.1.0/ajax/ajstr.c - EMBOSS-6.1.0/ajax/ajstr.h - EMBOSS-6.1.0/nucleus/embaln.c - -24-Aug-2009: Fix string extension so that pointers in lists remain valid. - 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/sources b/sources index 8fb2dec..a9e48c6 100644 --- a/sources +++ b/sources @@ -1,2 +1 @@ -6c5163c571bc0be94d64420ce0d71824 EMBOSS-6.1.0.tar.gz -4a5f96d849409fdecf39e92380e5381e patch-1-3.gz +2e2937dd0493814ca0f64981f4c79319 EMBOSS-6.2.0.tar.gz