rpms/EMBOSS/F-11 EMBOSS-6.1.0-rebuild.patch, NONE, 1.1 jemboss.desktop, NONE, 1.1 .cvsignore, 1.2, 1.3 README.fixes, 1.1, 1.2 sources, 1.2, 1.3

Thu Dec 24 08:15:08 UTC 2009

Author: belegdol

Update of /cvs/pkgs/rpms/EMBOSS/F-11
In directory cvs1.fedora.phx.redhat.com:/tmp/cvs-serv17220

Modified Files:
	.cvsignore README.fixes sources 
Added Files:
	EMBOSS-6.1.0-rebuild.patch jemboss.desktop 
Log Message:
* Sat Oct 17 2009 Julian Sikorski <belegdol at fedoraproject.org> - 6.1.0-5
- Added comments explaining the purpose of each patch


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/F-11/.cvsignore,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -p -r1.2 -r1.3
--- .cvsignore	17 Oct 2009 22:50:58 -0000	1.2
+++ .cvsignore	24 Dec 2009 08:15:07 -0000	1.3
@@ -1,2 +1,2 @@
 EMBOSS-6.1.0.tar.gz
-patch-1-2.gz
+patch-1-3.gz


Index: README.fixes
===================================================================
RCS file: /cvs/pkgs/rpms/EMBOSS/F-11/README.fixes,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -p -r1.1 -r1.2
--- README.fixes	17 Oct 2009 22:50:58 -0000	1.1
+++ README.fixes	24 Dec 2009 08:15:08 -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/F-11/sources,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -p -r1.2 -r1.3
--- sources	17 Oct 2009 22:50:58 -0000	1.2
+++ sources	24 Dec 2009 08:15:08 -0000	1.3
@@ -1,2 +1,2 @@
 6c5163c571bc0be94d64420ce0d71824  EMBOSS-6.1.0.tar.gz
-faec6ddd399ef243f4d6ffbcc878b009  patch-1-2.gz
+4a5f96d849409fdecf39e92380e5381e  patch-1-3.gz


