For EMBOSS:

	This patch brings EMBOSS up to date with the current version.

	i.   The patches included in files/ are bugfixes for files in
	     EMBOSS-3.0.0 that appeared after the release. They are
   	     documented in ftp://emboss.open-bio.org/pub/EMBOSS/fixes/README

	     This is just 'for the record' so that we remember to remove these
	     patches in the next update.

	ii.  EMBOSS is now installed by default in LOCALBASE/emboss
	     This is to avoid CONFLICTS with other ports that install files
	     with the same names. Installing EMBOSS to another PREFIX is also
	     possible.

	iii. now EMBASSY and EMBOSS both store their distfiles in the same
	     DIST_SUBDIR

	iv.  use built-in PKGMESSAGE and SUB_FILES instead of doing it the old
	     (manual) way

	For EMBASSY:

	This update brings embassy in sync with the update of EMBOSS to 3.0.0.

	Things that changed from previous version of the port:

	i.  embassy now installs by default in $LOCALBASE/emboss (the
	    new default PREFIX for emboss as well).

	ii. changed DIST_SUBDIR so that all the distfiles are put together with
	    emboss. This makes sense(TM)

	iii. incorporated new EMBASSY apps (this accounts for the changes in
	     OPTIONS and pkg-plist)

	iv.  removed obsoleted patches

	Finally, I included a sample text that could go in UPDATING.

PR:		93053
Submitted by:	Fernan Aguero <fernan (at) iib.unsam.edu.ar> (maintainer)

1 files changed, 20 insertions, 0 deletions

diff --git a/biology/emboss/files/patch-emboss.default.template b/biology/emboss/files/patch-emboss.default.template
new file mode 100644
index 000000000000..04ee586b4bfb
--- /dev/null
+++ b/biology/emboss/files/patch-emboss.default.template
@@ -0,0 +1,20 @@
+--- emboss/emboss.default.template.orig	Wed Feb  8 00:43:42 2006
++++ emboss/emboss.default.template	Wed Feb  8 00:40:34 2006
+@@ -4,7 +4,7 @@
+ # By default this is /usr/local/share/EMBOSS/test but the directory can
+ # be changed with --prefix when you configure EMBOSS.
+ 
+-# SET emboss_tempdata path_to_directory_$EMBOSS/test
++# SET emboss_tempdata %%DATADIR%%/test
+ 
+ # Proxy - set this if any databases are accessed through a proxy web server.
+ # Turn off in the DB definition with proxy: ":" for any
+@@ -15,7 +15,7 @@
+ # Logfile - set this to a file that any user can append to
+ # and EMBOSS applications will automatically write log information
+ 
+-# SET emboss_logfile /packages/emboss/emboss/log
++# SET emboss_logfile /var/log/emboss.log
+ 
+ # Pagesize - this is the size of disc page blocks and is
+ # required by the 'dbx' indexing programs and 'method: emboss'