Update of /cvsroot/fink/packages/dists/unstable/main/finkinfo/sci
In directory usw-pr-cvs1:/tmp/cvs-serv23503
Added Files:
emboss-2.4.1-1.info emboss-2.4.1-1.patch
Log Message:
New package
--- NEW FILE: emboss-2.4.1-1.info ---
Package: emboss
Version: 2.4.1
Revision: 1
Maintainer: Ben Hines <[EMAIL PROTECTED]>
Depends: x11, libpng-shlibs, libjpeg-shlibs, gd-shlibs, tcltk
BuildDepends: libpng, libjpeg, gd
Source: ftp://ftp.uk.embnet.org/pub/EMBOSS/EMBOSS-%v.tar.gz
Source-MD5: f8e8f053362346d45b696ad6d0ec4aad
Patch: %f.patch
ConfigureParams: --with-java=/Library/Java/Home
--with-javaos=/Library/Java/Home/include
Installscript: <<
make install DESTDIR=%d
mkdir -p %i/etc/profile.d/
echo "setenv PLPLOT_LIB %p/share/EMBOSS/" >%i/etc/profile.d/%n.csh
echo "export PLPLOT_LIB=%p/share/EMBOSS/" >%i/etc/profile.d/%n.sh
chmod 755 %i/etc/profile.d/%n.*
<<
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.
<<
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-2.4.1-1.patch ---
--- emboss-2.4.1/jemboss/Makefile.in Tue May 14 14:07:31 2002
+++ emboss-2.4.1-patched/jemboss/Makefile.in Tue Jun 18 22:40:36 2002
@@ -396,12 +396,12 @@
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/soap.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:."
>> $(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/soap.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:."
+ >> $(DESTDIR)$(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
--- emboss-2.4.1/jemboss/resources/Makefile.in Tue May 14 14:07:32 2002
+++ emboss-2.4.1-patched/jemboss/resources/Makefile.in Wed Jun 19 04:37:55 2002
@@ -250,14 +250,14 @@
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-2.4.1/jemboss/org/emboss/jemboss/Makefile.in Tue May 14 14:07:32 2002
+++ emboss-2.4.1-patched/jemboss/org/emboss/jemboss/Makefile.in Wed Jun 19 03:49:47
+2002
@@ -375,9 +375,9 @@
@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.
--- emboss-2.4.1/jemboss/org/emboss/jemboss/soap/Makefile.in Tue May 14 14:07:32
2002
+++ emboss-2.4.1-patched/jemboss/org/emboss/jemboss/soap/Makefile.in Wed Jun 19
+03:52:11 2002
@@ -258,9 +258,9 @@
@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.
--- emboss-2.4.1/jemboss/org/emboss/jemboss/server/Makefile.in Tue May 14 14:07:32
2002
+++ emboss-2.4.1-patched/jemboss/org/emboss/jemboss/server/Makefile.in Wed Jun 19
+03:51:27 2002
@@ -254,9 +254,9 @@
@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.
--- emboss-2.4.1/jemboss/org/emboss/jemboss/programs/Makefile.in Tue May 14
14:07:32 2002
+++ emboss-2.4.1-patched/jemboss/org/emboss/jemboss/programs/Makefile.in Wed
+Jun 19 03:50:47 2002
@@ -253,9 +253,9 @@
@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.
--- emboss-2.4.1/jemboss/org/emboss/jemboss/parser/Makefile.in Tue May 14 14:07:32
2002
+++ emboss-2.4.1-patched/jemboss/org/emboss/jemboss/parser/Makefile.in Wed Jun 19
+03:50:10 2002
@@ -378,9 +378,9 @@
@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.
--- emboss-2.4.1/jemboss/org/emboss/jemboss/parser/acd/Makefile.in Tue May 14
14:07:32 2002
+++ emboss-2.4.1-patched/jemboss/org/emboss/jemboss/parser/acd/Makefile.in Wed
+Jun 19 03:50:27 2002
@@ -251,9 +251,9 @@
@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.
--- emboss-2.4.1/jemboss/org/emboss/jemboss/gui/Makefile.in Tue May 14 14:07:32
2002
+++ emboss-2.4.1-patched/jemboss/org/emboss/jemboss/gui/Makefile.in Wed Jun 19
+03:48:56 2002
@@ -380,9 +380,9 @@
@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.
--- emboss-2.4.1/jemboss/org/emboss/jemboss/gui/startup/Makefile.in Tue May 14
14:07:32 2002
+++ emboss-2.4.1-patched/jemboss/org/emboss/jemboss/gui/startup/Makefile.in Wed
+Jun 19 04:11:03 2002
@@ -251,9 +251,9 @@
@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.
--- emboss-2.4.1/jemboss/org/emboss/jemboss/gui/sequenceChooser/Makefile.in Tue
May 14 14:07:32 2002
+++ emboss-2.4.1-patched/jemboss/org/emboss/jemboss/gui/sequenceChooser/Makefile.in
+ Wed Jun 19 04:10:24 2002
@@ -254,9 +254,9 @@
@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.
--- emboss-2.4.1/jemboss/org/emboss/jemboss/gui/form/Makefile.in Tue May 14
14:07:32 2002
+++ emboss-2.4.1-patched/jemboss/org/emboss/jemboss/gui/form/Makefile.in Wed
+Jun 19 03:48:09 2002
@@ -255,9 +255,9 @@
@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.
--- emboss-2.4.1/jemboss/org/emboss/jemboss/gui/filetree/Makefile.in Tue May 14
14:07:32 2002
+++ emboss-2.4.1-patched/jemboss/org/emboss/jemboss/gui/filetree/Makefile.in Wed
+Jun 19 03:25:48 2002
@@ -254,9 +254,9 @@
@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.
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