diff --git a/.cvsignore b/.cvsignore index e69de29..279d48e 100644 --- a/.cvsignore +++ b/.cvsignore @@ -0,0 +1,2 @@ +EMBOSS-6.1.0.tar.gz +patch-1-2.gz diff --git a/EMBOSS-6.1.0-destdir.patch b/EMBOSS-6.1.0-destdir.patch new file mode 100644 index 0000000..38b3377 --- /dev/null +++ b/EMBOSS-6.1.0-destdir.patch @@ -0,0 +1,22 @@ +--- 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-fedora.patch b/EMBOSS-fedora.patch new file mode 100644 index 0000000..857ced4 --- /dev/null +++ b/EMBOSS-fedora.patch @@ -0,0 +1,14 @@ +--- jemboss/resources/jemboss.properties.fedora 2008-05-02 15:27:28.000000000 +0200 ++++ jemboss/resources/jemboss.properties 2009-04-16 20:11:28.000000000 +0200 +@@ -5,8 +5,8 @@ + service.public=JembossAuthServer + service.private=JembossAuthServer + plplot=/packages/emboss/STABLE/share/EMBOSS/ +-embossData=/packages/emboss/STABLE/share/EMBOSS/data/ +-embossBin=/packages/emboss/STABLE/bin/ ++embossData=/usr/share/EMBOSS/data/ ++embossBin=/usr/bin/ + embossPath=/usr/bin:/bin:/packages/clustal/:/packages/primer3/bin:/data/jobqueue/bin/:/usr/ucb/ +-acdDirToParse=/packages/emboss/STABLE/share/EMBOSS/acd/ ++acdDirToParse=/usr/share/EMBOSS/acd/ + embossURL=http://emboss.sourceforge.net/ diff --git a/EMBOSS-system-pcre.patch b/EMBOSS-system-pcre.patch new file mode 100644 index 0000000..9b0fbfa --- /dev/null +++ b/EMBOSS-system-pcre.patch @@ -0,0 +1,192 @@ +diff -up EMBOSS-6.1.0/ajax/ajreg.h.pcre EMBOSS-6.1.0/ajax/ajreg.h +--- EMBOSS-6.1.0/ajax/ajreg.h.pcre 2007-02-09 19:30:59.000000000 +0100 ++++ EMBOSS-6.1.0/ajax/ajreg.h 2009-09-27 03:17:19.000000000 +0200 +@@ -16,8 +16,8 @@ extern "C" + #define ajreg_h + + #include "ajax.h" +-#include "pcre_internal.h" +-#include "pcreposix.h" ++#include ++#include + + #define AJREG_OVECSIZE 30 + +@@ -37,7 +37,7 @@ extern "C" + ******************************************************************************/ + + typedef struct AjSRegexp { +- real_pcre *pcre; ++ struct real_pcre *pcre; + pcre_extra *extra; + int *ovector; + const char* orig; +diff -up EMBOSS-6.1.0/ajax/Makefile.in.pcre EMBOSS-6.1.0/ajax/Makefile.in +--- EMBOSS-6.1.0/ajax/Makefile.in.pcre 2009-07-15 01:15:58.000000000 +0200 ++++ EMBOSS-6.1.0/ajax/Makefile.in 2009-09-27 03:17:19.000000000 +0200 +@@ -81,7 +81,7 @@ am__libajax_la_SOURCES_DIST = ajacd.c aj + ajphylo.c ajrange.c ajreg.c ajreport.c ajseq.c ajseqabi.c \ + ajseqdb.c ajseqread.c ajseqtype.c ajseqwrite.c ajsort.c \ + ajstr.c ajsys.c ajtable.c ajtime.c ajtranslate.c ajtree.c \ +- ajutil.c ajvector.c pcre.c pcre_study.c pcreposix.c ajgraph.c \ ++ ajutil.c ajvector.c \ + ajhist.c + am__objects_1 = ajacd.lo ajalign.lo ajarr.lo ajassert.lo ajbase.lo \ + ajcall.lo ajcod.lo ajdan.lo ajdmx.lo ajdom.lo ajdomain.lo \ +@@ -92,7 +92,7 @@ am__objects_1 = ajacd.lo ajalign.lo ajar + ajreport.lo ajseq.lo ajseqabi.lo ajseqdb.lo ajseqread.lo \ + ajseqtype.lo ajseqwrite.lo ajsort.lo ajstr.lo ajsys.lo \ + ajtable.lo ajtime.lo ajtranslate.lo ajtree.lo ajutil.lo \ +- ajvector.lo pcre.lo pcre_study.lo pcreposix.lo ++ ajvector.lo + am__objects_2 = ajgraph.lo ajhist.lo + @ISCYGWIN_FALSE@am_libajax_la_OBJECTS = $(am__objects_1) + @ISCYGWIN_TRUE@am_libajax_la_OBJECTS = $(am__objects_1) \ +@@ -159,7 +159,6 @@ EXEEXT = @EXEEXT@ + FGREP = @FGREP@ + GREP = @GREP@ + HAVE_MEMMOVE = @HAVE_MEMMOVE@ +-HAVE_STRERROR = @HAVE_STRERROR@ + INSTALL = @INSTALL@ + INSTALL_DATA = @INSTALL_DATA@ + INSTALL_PROGRAM = @INSTALL_PROGRAM@ +@@ -172,7 +171,7 @@ LD = @LD@ + LDFLAGS = @LDFLAGS@ + LIBOBJS = @LIBOBJS@ + #LDFLAGS = -no-undefined +-LIBS = ++LIBS = @LIBS@ + LIBTOOL = @LIBTOOL@ + LIPO = @LIPO@ + LN_S = @LN_S@ +@@ -193,13 +192,6 @@ PACKAGE_STRING = @PACKAGE_STRING@ + PACKAGE_TARNAME = @PACKAGE_TARNAME@ + PACKAGE_VERSION = @PACKAGE_VERSION@ + PATH_SEPARATOR = @PATH_SEPARATOR@ +-PCRE_DATE = @PCRE_DATE@ +-PCRE_LIB_VERSION = @PCRE_LIB_VERSION@ +-PCRE_MAJOR = @PCRE_MAJOR@ +-PCRE_MINOR = @PCRE_MINOR@ +-PCRE_POSIXLIB_VERSION = @PCRE_POSIXLIB_VERSION@ +-PCRE_VERSION = @PCRE_VERSION@ +-POSIX_MALLOC_THRESHOLD = @POSIX_MALLOC_THRESHOLD@ + RANLIB = @RANLIB@ + SED = @SED@ + SET_MAKE = @SET_MAKE@ +@@ -272,8 +264,6 @@ top_srcdir = @top_srcdir@ + @ISAIXIA64_TRUE@@ISSHARED_TRUE@@NEEDAJAX_FALSE@AM_CFLAGS = -Wl,-G -L../plplot/.libs -L.libs -leplplot -lm + @ISAIXIA64_TRUE@@ISSHARED_TRUE@@NEEDAJAX_TRUE@AM_CFLAGS = -Wl,-G -L../plplot/.libs -L.libs -lajax -leplplot -lm + @ISCYGWIN_TRUE@AM_LDFLAGS = -no-undefined -Wl,--add-stdcall-alias -Wl,--export-all-symbols -Wl,--enable-auto-import -L../plplot -leplplot +-PCRELIBVERSION = @PCRE_LIB_VERSION@ +-PCREPOSIXLIBVERSION = @PCRE_POSIXLIB_VERSION@ + INCLUDES = -DAJAX_FIXED_ROOT=$(AJAX_FIXED_ROOT) -DPREFIX=\"$(prefix)\" -I$(top_srcdir)/plplot $(POSIX_MALLOC_THRESHOLD) + AJAXSRC = ajacd.c ajalign.c ajarr.c ajassert.c \ + ajbase.c ajcall.c ajcod.c \ +@@ -288,8 +278,7 @@ ajrange.c ajreg.c ajreport.c \ + ajseq.c ajseqabi.c ajseqdb.c ajseqread.c ajseqtype.c ajseqwrite.c \ + ajsort.c ajstr.c ajsys.c \ + ajtable.c ajtime.c ajtranslate.c ajtree.c \ +-ajutil.c ajvector.c \ +-pcre.c pcre_study.c pcreposix.c ++ajutil.c ajvector.c + + AJAXGSRC = ajgraph.c ajhist.c + include_HEADERS = ajax.h ajarch.h ajdefine.h \ +@@ -303,9 +292,7 @@ ajpat.h ajpdb.h ajpdbio.h ajphylo.h \ + ajrange.h ajreg.h ajreport.h \ + ajseq.h ajseqabi.h ajseqdata.h ajseqdb.h ajseqread.h ajseqtype.h ajseqwrite.h \ + ajsort.h ajstr.h ajsys.h \ +-ajtable.h ajtime.h ajtranslate.h ajtree.h ajutil.h ajvector.h \ +-pcre.h pcre_chartables.c pcre_config.h pcre_get.c pcre_printint.c \ +-pcre_internal.h pcreposix.h ++ajtable.h ajtime.h ajtranslate.h ajtree.h ajutil.h ajvector.h + + @ISCYGWIN_FALSE@libajax_la_SOURCES = $(AJAXSRC) + @ISCYGWIN_TRUE@libajax_la_SOURCES = $(AJAXSRC) $(AJAXGSRC) +@@ -440,9 +427,6 @@ distclean-compile: + @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/ajtree.Plo@am__quote@ + @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/ajutil.Plo@am__quote@ + @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/ajvector.Plo@am__quote@ +-@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/pcre.Plo@am__quote@ +-@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/pcre_study.Plo@am__quote@ +-@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/pcreposix.Plo@am__quote@ + + .c.o: + @am__fastdepCC_TRUE@ $(COMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ $< +diff -up EMBOSS-6.1.0/configure.pcre EMBOSS-6.1.0/configure +--- EMBOSS-6.1.0/configure.pcre 2009-07-15 01:15:56.000000000 +0200 ++++ EMBOSS-6.1.0/configure 2009-09-27 03:21:32.000000000 +0200 +@@ -16724,6 +16724,73 @@ _ACEOF + + fi + ++{ echo "$as_me:$LINENO: checking for pcre_compile in -lpcre" >&5 ++echo $ECHO_N "checking for pcre_compile in -lpcre... $ECHO_C" >&6; } ++if test "${ac_cv_lib_pcre_pcre_compile+set}" = set; then ++ echo $ECHO_N "(cached) $ECHO_C" >&6 ++else ++ ac_check_lib_save_LIBS=$LIBS ++LIBS="-lpcre $LIBS" ++cat >conftest.$ac_ext <<_ACEOF ++/* confdefs.h. */ ++_ACEOF ++cat confdefs.h >>conftest.$ac_ext ++cat >>conftest.$ac_ext <<_ACEOF ++/* end confdefs.h. */ ++ ++/* Override any GCC internal prototype to avoid an error. ++ Use char because int might match the return type of a GCC ++ builtin and then its argument prototype would still apply. */ ++#ifdef __cplusplus ++extern "C" ++#endif ++char pcre_compile (); ++int ++main () ++{ ++return pcre_compile (); ++ ; ++ return 0; ++} ++_ACEOF ++rm -f conftest.$ac_objext conftest$ac_exeext ++if { (ac_try="$ac_link" ++case "(($ac_try" in ++ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; ++ *) ac_try_echo=$ac_try;; ++esac ++eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5 ++ (eval "$ac_link") 2>conftest.er1 ++ ac_status=$? ++ grep -v '^ *+' conftest.er1 >conftest.err ++ rm -f conftest.er1 ++ cat conftest.err >&5 ++ echo "$as_me:$LINENO: \$? = $ac_status" >&5 ++ (exit $ac_status); } && { ++ test -z "$ac_c_werror_flag" || ++ test ! -s conftest.err ++ } && test -s conftest$ac_exeext && ++ $as_test_x conftest$ac_exeext; then ++ ac_cv_lib_pcre_pcre_compile=yes ++else ++ echo "$as_me: failed program was:" >&5 ++sed 's/^/| /' conftest.$ac_ext >&5 ++ ++ ac_cv_lib_pcre_pcre_compile=no ++fi ++ ++rm -f core conftest.err conftest.$ac_objext conftest_ipa8_conftest.oo \ ++ conftest$ac_exeext conftest.$ac_ext ++LIBS=$ac_check_lib_save_LIBS ++fi ++{ echo "$as_me:$LINENO: result: $ac_cv_lib_pcre_pcre_compile" >&5 ++echo "${ECHO_T}$ac_cv_lib_pcre_pcre_compile" >&6; } ++if test "x$ac_cv_lib_pcre_pcre_compile" = x""yes; then ++ LIBS="-lpcre $LIBS" ++else ++ LIBS="$LIBS" ++fi ++ + + if test "`uname`" = "FreeBSD" && ${with_pngdriver} != "no"; then + { $as_echo "$as_me:$LINENO: checking for main in -liconv" >&5 diff --git a/EMBOSS.spec b/EMBOSS.spec new file mode 100644 index 0000000..0a5dee2 --- /dev/null +++ b/EMBOSS.spec @@ -0,0 +1,282 @@ +# TODO: +# fix jemboss and enable it + +%define emhome %{_datadir}/EMBOSS + +Name: EMBOSS +Version: 6.1.0 +Release: 5%{?dist} +Summary: The European Molecular Biology Open Software Suite + +Group: Applications/Engineering +License: GPLv2+ +URL: http://emboss.sf.net/ +Source0: ftp://emboss.open-bio.org/pub/EMBOSS/%{name}-%{version}.tar.gz +Source1: README.fixes +#Upstream patch +Patch0: ftp://emboss.open-bio.org/pub/EMBOSS/fixes/patches/patch-1-2.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. +Patch3: %{name}-6.1.0-destdir.patch +BuildRoot: %{_tmppath}/%{name}-%{version}-%{release}-root-%(%{__id_u} -n) + +BuildRequires: gd-devel +#BuildRequires: java-devel +BuildRequires: pam-devel +BuildRequires: pcre-devel +#BuildRequires: axis classpathx-jaf jakarta-commons-discovery +#BuildRequires: jakarta-commons-logging log4j wsdl4j + +%description +EMBOSS is a new, 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 +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 Environment/Libraries + +%description libs +The %{name}-libs package includes the dynamic libraries +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. + +#Documentation on Jemboss can be found at: +#http://www.hgmp.mrc.ac.uk/Software/EMBOSS/Jemboss/ + + +%prep +%setup -q +%patch0 -p1 +%patch1 -p1 -b .pcre +%patch2 -p0 -b .fedora +%patch3 -p0 -b .destdir + +#install the patch readme +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 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 + + +%build +%configure \ + --without-java \ + --disable-static \ + --with-x \ + --with-auth \ + --with-thread \ + --includedir=%{_includedir}/EMBOSS \ +%ifarch ppc64 sparc64 x86_64 + --enable-64 \ +%endif + +%{__make} %{?_smp_mflags} + + +%install +rm -rf $RPM_BUILD_ROOT + +%{__make} install DESTDIR=$RPM_BUILD_ROOT + +install -m 755 -d $RPM_BUILD_ROOT/%{_sysconfdir}/profile.d +cat << __EOF__ >> $RPM_BUILD_ROOT/%{_sysconfdir}/profile.d/emboss.sh +export PLPLOT_LIB=%{emhome} +export EMBOSS_ACDROOT=%{emhome}/acd +export EMBOSS_DOCROOT=%{emhome}/doc +export EMBOSS_DATABASE_DIR=%{emhome}/data +export EMBOSS_DATA=%{emhome}/data +__EOF__ + +cat << __EOF__ >> $RPM_BUILD_ROOT/%{_sysconfdir}/profile.d/emboss.csh +setenv PLPLOT_LIB %{emhome} +setenv EMBOSS_ACDROOT %{emhome}/acd +setenv EMBOSS_DOCROOT %{emhome}/doc +setenv EMBOSS_DATABASE_DIR %{emhome}/data +setenv EMBOSS_DATA %{emhome}/data +__EOF__ + +rm $RPM_BUILD_ROOT%{_libdir}/*.la + +#this file has zero length, so kill it +rm $RPM_BUILD_ROOT%{_datadir}/EMBOSS/test/data/dna.aln + +#fix executable permissions +pushd $RPM_BUILD_ROOT%{_datadir}/EMBOSS/jemboss/utils +chmod +x install-jemboss-server.sh keys.sh makeFileManagerJNLP.sh makeJar.csh \ + makeJNLP.sh +popd +pushd $RPM_BUILD_ROOT%{_datadir}/EMBOSS/jemboss/api +chmod +x getClasses.pl makeDocs.csh +popd + +#rename conflicting binaries +mv $RPM_BUILD_ROOT%{_bindir}/chaos $RPM_BUILD_ROOT%{_bindir}/em_chaos + + +%clean +rm -rf $RPM_BUILD_ROOT + + +%post libs -p /sbin/ldconfig + + +%postun libs -p /sbin/ldconfig + + +%files +%defattr(-,root,root,-) +%doc AUTHORS ChangeLog COPYING FAQ INSTALL LICENSE NEWS README README.fixes THANKS +%{_bindir}/* +%exclude %{_bindir}/runJemboss.csh +%exclude %{_bindir}/jembossctl +%{_datadir}/EMBOSS +%exclude %{_datadir}/EMBOSS/jemboss +%config %{_sysconfdir}/profile.d/* + + +%files devel +%defattr(-,root,root,-) +%{_libdir}/*.so +%{_includedir}/EMBOSS + +%files libs +%defattr(-,root,root,-) +%{_libdir}/*.so.* + + +#%files java +#%defattr(-,root,root,-) +#%doc jemboss/README jemboss/resources jemboss/api +#%{_bindir}/runJemboss.csh +#%{_bindir}/jembossctl +#%{_datadir}/EMBOSS/jemboss + + +%changelog +* Sat Oct 17 2009 Julian Sikorski - 6.1.0-5 +- Added comments explaining the purpose of each patch + +* Mon Oct 05 2009 Julian Sikorski - 6.1.0-4 +- Renamed conflicting binaries +- Disabled jemboss + +* Tue Sep 29 2009 Julian Sikorski - 6.1.0-3 +- Re-enabled system pcre usage +- Initial attempt at using system-wide .jar files + +* Tue Sep 22 2009 Julian Sikorski - 6.1.0-2 +- Added the upstream 1-2 patch + +* Wed Jul 29 2009 Julian Sikorski - 6.1.0-1 +- Updated to 6.1.0 +- Dropped pcre-devel from BuildRequires for the time being +- Ditto --with-java and --with-javaos +- Patched jemboss/Makefile.am not to include DESTDIR in runJemboss.sh +- Install the header files in EMBOSS subdir +- Added the missing executable bits + +* Fri Jun 12 2009 Julian Sikorski - 6.0.1-3 +- Updated the upstream patch to 1-12 +- Added the patch readme to %%doc + +* Thu Apr 16 2009 Julian Sikorski - 6.0.1-2 +- Own %%{_datadir}/EMBOSS +- Don't use %%{name} macro in %%files +- Updated the upstream patch to 1-7 +- Use dist instead of dist_tag +- Adjusted whitespaces +- Added pcre-devel to BuildRequires +- Fixed spurious executable permissions +- Removed the empty dna.aln file +- Patched jemboss.properties to include the paths this package uses +- Made the -java package require the main one + +* Mon Sep 29 2008 Dominik Mierzejewski 6.0.1-1 +- updated to 6.0.1 +- applied upstream patch 1-1 +- patched to use system pcre + +* Tue Jan 08 2008 Dominik Mierzejewski 5.0.0-1 +- Cleaned up BioRPMs' spec +- Updated to 5.0.0 + +* Thu Mar 17 2005 Bent Terp +- Upped to 2.10.0 + +* Fri Jul 16 2004 Bent Terp +- Had forgotten the emboss_database_dir env var + +* Wed Feb 18 2004 Bent Terp +- Tried to make the building more dynamic. Added Requires and BuildRequires + +* Thu Dec 04 2003 Luc Ducazu +- Build for EMBOSS 2.8.0 +- subpackage jemboss + +* Wed Jun 11 2003 Luc Ducazu +- Build for EMBOSS 2.7.1 + +* Tue Jan 28 2003 Luc Ducazu +- Build for EMBOSS 2.6.0 +- Programs moved to /usr/local/bin +- Adopted many ideas from Guillaume Rousse + +* Wed Nov 27 2002 Luc Ducazu +- Initial build for EMBOSS 2.5.1 diff --git a/README.fixes b/README.fixes new file mode 100644 index 0000000..9dfcfd2 --- /dev/null +++ b/README.fixes @@ -0,0 +1,32 @@ +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). diff --git a/import.log b/import.log new file mode 100644 index 0000000..4a11558 --- /dev/null +++ b/import.log @@ -0,0 +1 @@ +EMBOSS-6_1_0-5_fc11:F-12:EMBOSS-6.1.0-5.fc11.src.rpm:1255819735 diff --git a/sources b/sources index e69de29..055976e 100644 --- a/sources +++ b/sources @@ -0,0 +1,2 @@ +6c5163c571bc0be94d64420ce0d71824 EMBOSS-6.1.0.tar.gz +faec6ddd399ef243f4d6ffbcc878b009 patch-1-2.gz