Update of /cvsroot/fink/dists/10.2/unstable/main/finkinfo/sci
In directory sc8-pr-cvs1:/tmp/cvs-serv12752
Added Files:
emboss-2.7.1-2.info emboss-2.7.1-2.patch
Removed Files:
emboss-2.7.1-1.info emboss-2.7.1-1.patch
Log Message:
New revision now links to gd2. Tracker #753682
--- NEW FILE: emboss-2.7.1-2.info ---
Package: emboss
Version: 2.7.1
Revision: 2
Maintainer: Koen van der Drift <[EMAIL PROTECTED]>
Depends: x11, libpng3-shlibs, libjpeg-shlibs, gd2-shlibs, tcltk-shlibs
BuildDepends: libpng3, libjpeg, gd2, tcltk-dev, dlcompat-dev
Source: mirror:custom:EMBOSS-%v.tar.gz
CustomMirror: <<
Primary: ftp://ftp.uk.embnet.org/pub/EMBOSS/
Secondary: ftp://ftp.uk.embnet.org/pub/EMBOSS/old/
<<
Source-MD5: 7d86aa7101070513b640b265698e8e38
Patch: %f.patch
NoSetLDFLAGS: true
SetLIBS: -L%p/lib
ConfigureParams:
--with-java=/System/Library/Frameworks/JavaVM.framework/Versions/1.3.1/Home
--with-javaos=/System/Library/Frameworks/JavaVM.framework/Versions/1.3.1/Home/include
#ConfigureParams: --with-java=/Library/Java/Home
--with-javaos=/Library/Java/Home/include Installscript: <<
make install DESTDIR=%d
<<
RunTimeVars: PLPLOT_LIB: %p/share/EMBOSS/
DocFiles: AUTHORS ChangeLog COMPAT COPYING FAQ KNOWN_BUGS LICENSE NEWS ONEWS README
THANKS
Description: Molecular Biology Open Software Suite
DescDetail: <<
EMBOSS is a 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.
<<
DescUsage: <<
See the README file for other environment variables you may need to configure.
PLPLOT_LIB is already set by fink in /sw/etc/profile.d/.
script. See http://www.uk.embnet.org/Software/EMBOSS/Jemboss/readme.html
for information on using the Jemboss GUI for EMBOSS.
Install emboss-kaptain for a GUI that works with X-Windows.
<<
DescPackaging: <<
The package uses shared libraries, but does not install the headers.
Thus I have not made a splitoff for the libraries since they are not
useful. This may be changed in future versions per the developers.
<<
Homepage: http://www.hgmp.mrc.ac.uk/Software/EMBOSS/
License: GPL
--- NEW FILE: emboss-2.7.1-2.patch ---
diff -Naur emboss-2.7.1/jemboss/Makefile.in emboss-2.7.1 patched/jemboss/Makefile.in
--- emboss-2.7.1/jemboss/Makefile.in Tue Jun 3 08:40:04 2003
+++ emboss-2.7.1 patched/jemboss/Makefile.in Thu Jun 12 18:22:49 2003
@@ -497,12 +497,12 @@
fi
install-exec-hook:
- rm -f $(bindir)/runJemboss.csh; \
- echo "#!/bin/csh" >> $(bindir)/runJemboss.csh; \
- echo "setenv LD_LIBRARY_PATH $(libdir)" >> $(bindir)/runJemboss.csh; \
- echo "setenv CLASSPATH
$(prefix)/share/$(PACKAGE)/jemboss/lib/JembossAlignment.jar:$(prefix)/share/$(PACKAGE)/jemboss/lib/xerces.jar:$(prefix)/share/$(PACKAGE)/jemboss/lib/mail.jar:$(prefix)/share/$(PACKAGE)/jemboss/lib/activation.jar:$(prefix)/share/$(PACKAGE)/jemboss/lib/jakarta-regexp-1.2.jar:$(prefix)/share/$(PACKAGE)/jemboss/lib/jalview.jar:$(prefix)/share/$(PACKAGE)/jemboss/lib/jcert.jar:$(prefix)/share/$(PACKAGE)/jemboss/lib/jnet.jar:$(prefix)/share/$(PACKAGE)/jemboss/lib/jsse.jar:$(prefix)/share/$(PACKAGE)/jemboss/lib/axis/axis-ant.jar:$(prefix)/share/$(PACKAGE)/jemboss/lib/axis/axis.jar:$(prefix)/share/$(PACKAGE)/jemboss/lib/axis/commons-discovery.jar:$(prefix)/share/$(PACKAGE)/jemboss/lib/axis/commons-logging.jar:$(prefix)/share/$(PACKAGE)/jemboss/lib/axis/jaxrpc.jar:$(prefix)/share/$(PACKAGE)/jemboss/lib/axis/log4j-1.2.4.jar:$(prefix)/share/$(PACKAGE)/jemboss/lib/axis/saaj.jar:$(prefix)/share/$(PACKAGE)/jemboss/lib/axis/wsdl4j.jar:$(prefix)/share/$(PACKAGE)/jemboss/lib/axis/servlet.jar:$(prefix)/share/$(PACKAGE)/jemboss"
>> $(bindir)/runJemboss.csh; \
- echo "(cd $(prefix)/share/$(PACKAGE)/jemboss; java org/emboss/jemboss/Jemboss
&)" >> $(bindir)/runJemboss.csh; \
- chmod 755 $(bindir)/runJemboss.csh;
+ rm -f $(DESTDIR)$(bindir)/runJemboss.csh; \
+ echo "#!/bin/csh" >> $(DESTDIR)$(bindir)/runJemboss.csh; \
+ echo "setenv LD_LIBRARY_PATH $(libdir)" >> $(DESTDIR)$(bindir)/runJemboss.csh;
\
+ echo "setenv CLASSPATH
$(prefix)/share/$(PACKAGE)/jemboss/lib/JembossAlignment.jar:$(prefix)/share/$(PACKAGE)/jemboss/lib/xerces.jar:$(prefix)/share/$(PACKAGE)/jemboss/lib/mail.jar:$(prefix)/share/$(PACKAGE)/jemboss/lib/activation.jar:$(prefix)/share/$(PACKAGE)/jemboss/lib/jakarta-regexp-1.2.jar:$(prefix)/share/$(PACKAGE)/jemboss/lib/jalview.jar:$(prefix)/share/$(PACKAGE)/jemboss/lib/jcert.jar:$(prefix)/share/$(PACKAGE)/jemboss/lib/jnet.jar:$(prefix)/share/$(PACKAGE)/jemboss/lib/jsse.jar:$(prefix)/share/$(PACKAGE)/jemboss/lib/axis/axis-ant.jar:$(prefix)/share/$(PACKAGE)/jemboss/lib/axis/axis.jar:$(prefix)/share/$(PACKAGE)/jemboss/lib/axis/commons-discovery.jar:$(prefix)/share/$(PACKAGE)/jemboss/lib/axis/commons-logging.jar:$(prefix)/share/$(PACKAGE)/jemboss/lib/axis/jaxrpc.jar:$(prefix)/share/$(PACKAGE)/jemboss/lib/axis/log4j-1.2.4.jar:$(prefix)/share/$(PACKAGE)/jemboss/lib/axis/saaj.jar:$(prefix)/share/$(PACKAGE)/jemboss/lib/axis/wsdl4j.jar:$(prefix)/share/$(PACKAGE)/jemboss/lib/axis/servlet.jar:$(prefix)/share/$(PACKAGE)/jemboss"
>> $(DESTDIR)$(bindir)/runJemboss.csh; \
+ echo "(cd $(prefix)/share/$(PACKAGE)/jemboss; java org/emboss/jemboss/Jemboss
&)" >> $(DESTDIR)$(bindir)/runJemboss.csh; \
+ chmod 755 $(DESTDIR)$(bindir)/runJemboss.csh;
# tar to pick up the other directories
# then remove any CVS subdirectories
diff -Naur emboss-2.7.1/jemboss/org/emboss/jemboss/Makefile.in emboss-2.7.1
patched/jemboss/org/emboss/jemboss/Makefile.in
--- emboss-2.7.1/jemboss/org/emboss/jemboss/Makefile.in Tue Jun 3 08:40:07 2003
+++ emboss-2.7.1 patched/jemboss/org/emboss/jemboss/Makefile.in Wed Jun 11 21:08:40
2003
@@ -476,9 +476,9 @@
@if test "${JAVA_OK}" != "yes" ; then \
echo "No class files to copy"; \
else \
- $(top_srcdir)/mkinstalldirs
$(prefix)/share/$(PACKAGE)/jemboss/org/emboss/jemboss; \
+ $(top_srcdir)/mkinstalldirs $(DESTDIR)$(pkgdatadir); \
for i in *.class; do \
- ${INSTALL_DATA} $$i $(prefix)/share/$(PACKAGE)/jemboss/org/emboss/jemboss; \
+ ${INSTALL_DATA} $$i $(DESTDIR)$(pkgdatadir); \
done; \
fi
# Tell versions [3.59,3.63) of GNU make to not export all variables.
diff -Naur emboss-2.7.1/jemboss/org/emboss/jemboss/gui/Makefile.in emboss-2.7.1
patched/jemboss/org/emboss/jemboss/gui/Makefile.in
--- emboss-2.7.1/jemboss/org/emboss/jemboss/gui/Makefile.in Tue Jun 3 08:40:07
2003
+++ emboss-2.7.1 patched/jemboss/org/emboss/jemboss/gui/Makefile.in Wed Jun 11
21:12:17 2003
@@ -482,9 +482,9 @@
@if test "${JAVA_OK}" != "yes" ; then \
echo "No class files to copy"; \
else \
- $(top_srcdir)/mkinstalldirs
$(prefix)/share/$(PACKAGE)/jemboss/org/emboss/jemboss/gui; \
+ $(top_srcdir)/mkinstalldirs $(DESTDIR)$(pkgdatadir); \
for i in *.class; do \
- ${INSTALL_DATA} $$i
$(prefix)/share/$(PACKAGE)/jemboss/org/emboss/jemboss/gui; \
+ ${INSTALL_DATA} $$i $(DESTDIR)$(pkgdatadir); \
done; \
fi
# Tell versions [3.59,3.63) of GNU make to not export all variables.
diff -Naur emboss-2.7.1/jemboss/org/emboss/jemboss/gui/filetree/Makefile.in
emboss-2.7.1 patched/jemboss/org/emboss/jemboss/gui/filetree/Makefile.in
--- emboss-2.7.1/jemboss/org/emboss/jemboss/gui/filetree/Makefile.in Tue Jun 3
08:40:07 2003
+++ emboss-2.7.1 patched/jemboss/org/emboss/jemboss/gui/filetree/Makefile.in Wed
Jun 11 21:14:17 2003
@@ -327,9 +327,9 @@
@if test "${JAVA_OK}" != "yes" ; then \
echo "No class files to copy"; \
else \
- $(top_srcdir)/mkinstalldirs
$(prefix)/share/$(PACKAGE)/jemboss/org/emboss/jemboss/gui/filetree; \
+ $(top_srcdir)/mkinstalldirs $(DESTDIR)$(pkgdatadir); \
for i in *.class; do \
- ${INSTALL_DATA} $$i
$(prefix)/share/$(PACKAGE)/jemboss/org/emboss/jemboss/gui/filetree; \
+ ${INSTALL_DATA} $$i $(DESTDIR)$(pkgdatadir); \
done; \
fi
# Tell versions [3.59,3.63) of GNU make to not export all variables.
diff -Naur emboss-2.7.1/jemboss/org/emboss/jemboss/gui/form/Makefile.in emboss-2.7.1
patched/jemboss/org/emboss/jemboss/gui/form/Makefile.in
--- emboss-2.7.1/jemboss/org/emboss/jemboss/gui/form/Makefile.in Tue Jun 3
08:40:07 2003
+++ emboss-2.7.1 patched/jemboss/org/emboss/jemboss/gui/form/Makefile.in Wed
Jun 11 21:13:50 2003
@@ -329,9 +329,9 @@
@if test "${JAVA_OK}" != "yes" ; then \
echo "No class files to copy"; \
else \
- $(top_srcdir)/mkinstalldirs
$(prefix)/share/$(PACKAGE)/jemboss/org/emboss/jemboss/gui/form; \
+ $(top_srcdir)/mkinstalldirs $(DESTDIR)$(pkgdatadir); \
for i in *.class; do \
- ${INSTALL_DATA} $$i
$(prefix)/share/$(PACKAGE)/jemboss/org/emboss/jemboss/gui/form; \
+ ${INSTALL_DATA} $$i $(DESTDIR)$(pkgdatadir); \
done; \
fi
# Tell versions [3.59,3.63) of GNU make to not export all variables.
diff -Naur emboss-2.7.1/jemboss/org/emboss/jemboss/gui/sequenceChooser/Makefile.in
emboss-2.7.1 patched/jemboss/org/emboss/jemboss/gui/sequenceChooser/Makefile.in
--- emboss-2.7.1/jemboss/org/emboss/jemboss/gui/sequenceChooser/Makefile.in Tue
Jun 3 08:40:07 2003
+++ emboss-2.7.1 patched/jemboss/org/emboss/jemboss/gui/sequenceChooser/Makefile.in
Wed Jun 11 21:13:24 2003
@@ -327,9 +327,9 @@
@if test "${JAVA_OK}" != "yes" ; then \
echo "No class files to copy"; \
else \
- $(top_srcdir)/mkinstalldirs
$(prefix)/share/$(PACKAGE)/jemboss/org/emboss/jemboss/gui/sequenceChooser; \
+ $(top_srcdir)/mkinstalldirs $(DESTDIR)$(pkgdatadir); \
for i in *.class; do \
- ${INSTALL_DATA} $$i
$(prefix)/share/$(PACKAGE)/jemboss/org/emboss/jemboss/gui/sequenceChooser; \
+ ${INSTALL_DATA} $$i $(DESTDIR)$(pkgdatadir); \
done; \
fi
# Tell versions [3.59,3.63) of GNU make to not export all variables.
diff -Naur emboss-2.7.1/jemboss/org/emboss/jemboss/gui/startup/Makefile.in
emboss-2.7.1 patched/jemboss/org/emboss/jemboss/gui/startup/Makefile.in
--- emboss-2.7.1/jemboss/org/emboss/jemboss/gui/startup/Makefile.in Tue Jun 3
08:40:08 2003
+++ emboss-2.7.1 patched/jemboss/org/emboss/jemboss/gui/startup/Makefile.in Wed
Jun 11 21:12:54 2003
@@ -324,9 +324,9 @@
@if test "${JAVA_OK}" != "yes" ; then \
echo "No class files to copy"; \
else \
- $(top_srcdir)/mkinstalldirs
$(prefix)/share/$(PACKAGE)/jemboss/org/emboss/jemboss/gui/startup; \
+ $(top_srcdir)/mkinstalldirs $(DESTDIR)$(pkgdatadir); \
for i in *.class; do \
- ${INSTALL_DATA} $$i
$(prefix)/share/$(PACKAGE)/jemboss/org/emboss/jemboss/gui/startup; \
+ ${INSTALL_DATA} $$i $(DESTDIR)$(pkgdatadir); \
done; \
fi
# Tell versions [3.59,3.63) of GNU make to not export all variables.
diff -Naur emboss-2.7.1/jemboss/org/emboss/jemboss/parser/Makefile.in emboss-2.7.1
patched/jemboss/org/emboss/jemboss/parser/Makefile.in
--- emboss-2.7.1/jemboss/org/emboss/jemboss/parser/Makefile.in Tue Jun 3 08:40:08
2003
+++ emboss-2.7.1 patched/jemboss/org/emboss/jemboss/parser/Makefile.in Wed Jun 11
21:10:54 2003
@@ -479,9 +479,9 @@
@if test "${JAVA_OK}" != "yes" ; then \
echo "No class files to copy"; \
else \
- $(top_srcdir)/mkinstalldirs
$(prefix)/share/$(PACKAGE)/jemboss/org/emboss/jemboss/parser; \
+ $(top_srcdir)/mkinstalldirs $(DESTDIR)$(pkgdatadir); \
for i in *.class; do \
- ${INSTALL_DATA} $$i
$(prefix)/share/$(PACKAGE)/jemboss/org/emboss/jemboss/parser; \
+ ${INSTALL_DATA} $$i $(DESTDIR)$(pkgdatadir); \
done; \
fi
# Tell versions [3.59,3.63) of GNU make to not export all variables.
diff -Naur emboss-2.7.1/jemboss/org/emboss/jemboss/parser/acd/Makefile.in emboss-2.7.1
patched/jemboss/org/emboss/jemboss/parser/acd/Makefile.in
--- emboss-2.7.1/jemboss/org/emboss/jemboss/parser/acd/Makefile.in Tue Jun 3
08:40:08 2003
+++ emboss-2.7.1 patched/jemboss/org/emboss/jemboss/parser/acd/Makefile.in Wed
Jun 11 21:11:49 2003
@@ -324,9 +324,9 @@
@if test "${JAVA_OK}" != "yes" ; then \
echo "No class files to copy"; \
else \
- $(top_srcdir)/mkinstalldirs
$(prefix)/share/$(PACKAGE)/jemboss/org/emboss/jemboss/parser/acd; \
+ $(top_srcdir)/mkinstalldirs $(DESTDIR)$(pkgdatadir); \
for i in *.class; do \
- ${INSTALL_DATA} $$i
$(prefix)/share/$(PACKAGE)/jemboss/org/emboss/jemboss/parser/acd; \
+ ${INSTALL_DATA} $$i $(DESTDIR)$(pkgdatadir); \
done; \
fi
# Tell versions [3.59,3.63) of GNU make to not export all variables.
diff -Naur emboss-2.7.1/jemboss/org/emboss/jemboss/programs/Makefile.in emboss-2.7.1
patched/jemboss/org/emboss/jemboss/programs/Makefile.in
--- emboss-2.7.1/jemboss/org/emboss/jemboss/programs/Makefile.in Tue Jun 3
08:40:08 2003
+++ emboss-2.7.1 patched/jemboss/org/emboss/jemboss/programs/Makefile.in Wed
Jun 11 21:10:23 2003
@@ -327,9 +327,9 @@
@if test "${JAVA_OK}" != "yes" ; then \
echo "No class files to copy"; \
else \
- $(top_srcdir)/mkinstalldirs
$(prefix)/share/$(PACKAGE)/jemboss/org/emboss/jemboss/programs; \
+ $(top_srcdir)/mkinstalldirs $(DESTDIR)$(pkgdatadir); \
for i in *.class; do \
- ${INSTALL_DATA} $$i
$(prefix)/share/$(PACKAGE)/jemboss/org/emboss/jemboss/programs; \
+ ${INSTALL_DATA} $$i $(DESTDIR)$(pkgdatadir); \
done; \
fi
# Tell versions [3.59,3.63) of GNU make to not export all variables.
diff -Naur emboss-2.7.1/jemboss/org/emboss/jemboss/server/Makefile.in emboss-2.7.1
patched/jemboss/org/emboss/jemboss/server/Makefile.in
--- emboss-2.7.1/jemboss/org/emboss/jemboss/server/Makefile.in Tue Jun 3 08:40:08
2003
+++ emboss-2.7.1 patched/jemboss/org/emboss/jemboss/server/Makefile.in Wed Jun 11
21:09:49 2003
@@ -327,9 +327,9 @@
@if test "${JAVA_OK}" != "yes" ; then \
echo "No class files to copy"; \
else \
- $(top_srcdir)/mkinstalldirs
$(prefix)/share/$(PACKAGE)/jemboss/org/emboss/jemboss/server; \
+ $(top_srcdir)/mkinstalldirs $(DESTDIR)$(pkgdatadir); \
if test -f JembossServer.class ; then \
- ${INSTALL_DATA} *.class
$(prefix)/share/$(PACKAGE)/jemboss/org/emboss/jemboss/server; \
+ ${INSTALL_DATA} *.class $(DESTDIR)$(pkgdatadir); \
fi \
fi
# Tell versions [3.59,3.63) of GNU make to not export all variables.
diff -Naur emboss-2.7.1/jemboss/org/emboss/jemboss/soap/Makefile.in emboss-2.7.1
patched/jemboss/org/emboss/jemboss/soap/Makefile.in
--- emboss-2.7.1/jemboss/org/emboss/jemboss/soap/Makefile.in Tue Jun 3 08:40:08
2003
+++ emboss-2.7.1 patched/jemboss/org/emboss/jemboss/soap/Makefile.in Wed Jun 11
21:09:15 2003
@@ -331,9 +331,9 @@
@if test "${JAVA_OK}" != "yes" ; then \
echo "No class files to copy"; \
else \
- $(top_srcdir)/mkinstalldirs
$(prefix)/share/$(PACKAGE)/jemboss/org/emboss/jemboss/soap; \
+ $(top_srcdir)/mkinstalldirs $(DESTDIR)$(pkgdatadir); \
for i in *.class; do \
- ${INSTALL_DATA} $$i
$(prefix)/share/$(PACKAGE)/jemboss/org/emboss/jemboss/soap; \
+ ${INSTALL_DATA} $$i $(DESTDIR)$(pkgdatadir); \
done; \
fi
# Tell versions [3.59,3.63) of GNU make to not export all variables.
diff -Naur emboss-2.7.1/jemboss/resources/Makefile.in emboss-2.7.1
patched/jemboss/resources/Makefile.in
--- emboss-2.7.1/jemboss/resources/Makefile.in Tue Jun 3 08:40:08 2003
+++ emboss-2.7.1 patched/jemboss/resources/Makefile.in Wed Jun 11 23:03:49 2003
@@ -323,14 +323,14 @@
install-exec-hook:
@if test "${JAVA_OK}" = "yes" ; then \
- (if test -d $(prefix)/share/$(PACKAGE)/jemboss/resources; then \
+ (if test -d $(DESTDIR)$(pkgdatadir); then \
echo "resources exists"; \
else \
- mkdir $(prefix)/share/$(PACKAGE)/jemboss/resources; \
+ mkdir $(DESTDIR)$(pkgdatadir); \
fi); \
- rm -f $(prefix)/share/$(PACKAGE)/jemboss/resources/acdstore.jar; \
+ rm -f $(DESTDIR)$(pkgdatadir)/acdstore.jar; \
cd $(EMBOSS_TOP)/emboss/acd; \
- jar cvf $(prefix)/share/$(PACKAGE)/jemboss/resources/acdstore.jar
*.acd; \
+ jar cvf $(DESTDIR)$(pkgdatadir)/acdstore.jar *.acd; \
fi
# Tell versions [3.59,3.63) of GNU make to not export all variables.
# Otherwise a system limit (for SysV at least) may be exceeded.
--- emboss-2.7.1-1.info DELETED ---
--- emboss-2.7.1-1.patch DELETED ---
-------------------------------------------------------
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