- Update EMBOSS (biology/emboss) from 1.9.0 to 1.9.1

- Update the EMBASSY package EMNU from 1.0.2 to 1.0.3
- Merged the four pkg-plist* files into one

PR: 24717
Submitted by: MAINTAINER

3 files changed, 44 insertions, 1 deletions

diff --git a/biology/emboss/files/patch-aa b/biology/emboss/files/patch-aa
index f4b1bc46f7a1..d8bdbf96f9fb 100644
--- a/biology/emboss/files/patch-aa
+++ b/biology/emboss/files/patch-aa
@@ -17,7 +17,7 @@ The port installs ${PREFIX}/etc/emboss.default.sample
 +    if (!prefixRootFile)
 +    {
 +      ajFmtPrintS (&namRootStr, "%s/etc/%s.default",
-+		   namInstallRoot, prefixCap, prefix);
++		   namInstallRoot, prefix);
 +      prefixRootFile = fopen (ajStrStr(namRootStr), "r");
 +    }
 +
diff --git a/biology/emboss/files/patch-configure b/biology/emboss/files/patch-configure
new file mode 100644
index 000000000000..da46a3c60faa
--- /dev/null
+++ b/biology/emboss/files/patch-configure
@@ -0,0 +1,11 @@
+--- configure.orig	Mon Jan 22 23:28:17 2001
++++ configure	Thu Jan 25 19:07:33 2001
+@@ -1473,7 +1473,7 @@
+ 
+ 
+ 
+-AJAX_FIXED_ROOT="\\\"`pwd`/emboss\\\""
++AJAX_FIXED_ROOT="\\\"${datadir}/${PACKAGE}\\\""
+ 
+ #AC_PROG_CXX
+ for ac_prog in mawk gawk nawk awk
diff --git a/biology/emboss/files/patch-emboss-acd-emboss.default b/biology/emboss/files/patch-emboss-acd-emboss.default
new file mode 100644
index 000000000000..8311f5b23837
--- /dev/null
+++ b/biology/emboss/files/patch-emboss-acd-emboss.default
@@ -0,0 +1,32 @@
+--- emboss/acd/emboss.default.orig	Mon Jan 22 23:26:54 2001
++++ emboss/acd/emboss.default	Mon Jan 29 16:23:15 2001
+@@ -1,9 +1,26 @@
+-SET emboss_tempdata /nfs/WWW/data/EMBOSS/test
++#####################################################
++### Configuration options for FreeBSD EMBOSS port ###
++#####################################################
+ 
+-# Logfile - set this to a file that any user can append to
+-# and EMBOSS applications will automatically write log information
++# This is the compiled-in default.  Change only if
++# you know what you're doing!
++#
++#SET emboss_data /usr/local/share/EMBOSS/data
+ 
++# This is where your local databases reside
++# (this will differ from site to site):
++#
++SET emboss_tempdata /var/db/bio
++
++# 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
++
++
++###########################################
++### Configuration options for databases ###
++###########################################
+ 
+ # swissprot (Puffer fish entries)
+ # =========