[med-svn] r5441 - trunk/packages/ensembl/ensembl/57/debian

[Steffen Möller]

Author: moeller
Date: 2010-11-17 00:13:31 +0000 (Wed, 17 Nov 2010)
New Revision: 5441

Modified:
   trunk/packages/ensembl/ensembl/57/debian/adjust_shebang_line.sh
   trunk/packages/ensembl/ensembl/57/debian/control
   trunk/packages/ensembl/ensembl/57/debian/rules
Log:
No more lintian errors. 59 warnings, still.


Modified: trunk/packages/ensembl/ensembl/57/debian/adjust_shebang_line.sh
===================================================================
--- trunk/packages/ensembl/ensembl/57/debian/adjust_shebang_line.sh	2010-11-16 16:22:56 UTC (rev 5440)
+++ trunk/packages/ensembl/ensembl/57/debian/adjust_shebang_line.sh	2010-11-17 00:13:31 UTC (rev 5441)
@@ -3,7 +3,7 @@
 for i in "$@"
 do
 
-	if head -n 1 "$i" | egrep -q '^#!\s*(/usr/bin/perl|/bin/bash)'; then 
+	if head -n 1 "$i" | egrep -q '^#!\s*(/usr/bin/perl(\s+-w)?|/bin/bash|/usr/bin/wish)\s*$'; then 
 		if echo "$i" | egrep -q '.pm$'; then
 			echo "Remove: '$i'"
 			sed -i '1d' $i
@@ -35,9 +35,15 @@
 		echo "Substitute: '$i'"
 		if head -n 1 "$i" | grep -q perl; then
 			echo Perl
+			# remove version from Perl
+			sed -i '1s%perl5[0-9.]*%perl%' $i
+			# now the path substitution, keeping arguments to Perl intact
 			sed -i '1s%#!\s*/.*/perl%#!/usr/bin/perl%' $i
 			# also seen
 			sed -i '1s%#!perl%#!/usr/bin/perl%' $i
+		elif head -n 1 "$i" | grep -q wish; then
+			echo Tcl/Tk
+			sed -i '1s%#!\s*/.*/wish.*%#!/usr/bin/wish%' $i
 		else
 			echo BASH
 			sed -i '1s%#!\s*/.*/bash%#!/bin/bash%' $i
@@ -57,6 +63,9 @@
 		if echo "$i" | egrep -q '.(pl|t)$' || egrep -q "use\s\s*strict\s*;" $i; then
 			sed -i '1i#!/usr/bin/perl\n' $i
 			chmod 755 "$i"
+		elif (echo "$i" | grep -q ".tcl" ) ; then
+			sed -i '1i#!/usr/bin/wish\n' $i
+			chmod 755 "$i"
 		elif (echo "$i" | grep -q ".sh" ) ; then
 			sed -i '1i#!/bin/bash\n' $i
 			chmod 755 "$i"

Modified: trunk/packages/ensembl/ensembl/57/debian/control
===================================================================
--- trunk/packages/ensembl/ensembl/57/debian/control	2010-11-16 16:22:56 UTC (rev 5440)
+++ trunk/packages/ensembl/ensembl/57/debian/control	2010-11-17 00:13:31 UTC (rev 5441)
@@ -53,7 +53,7 @@
 Package: libensembl-core-perl
 Architecture: all
 Depends: ${misc:Depends},bioperl1.2.3|bioperl
-Suggests: ksh | mksh | pdksh | zsh
+Suggests: ksh | mksh | pdksh | zsh, tk
 Description: core libraries of Ensembl API
  The Ensembl project presents the sequence data for the yet
  available complete genomes of many vertebrates and is helped by many

Modified: trunk/packages/ensembl/ensembl/57/debian/rules
===================================================================
--- trunk/packages/ensembl/ensembl/57/debian/rules	2010-11-16 16:22:56 UTC (rev 5440)
+++ trunk/packages/ensembl/ensembl/57/debian/rules	2010-11-17 00:13:31 UTC (rev 5441)
@@ -35,7 +35,9 @@
 	find . -name ".cvsignore" | xargs -r rm
 
 	# First round of updates
-	find . -name "*.pl" -o -name "*.sh" -o -name "*.t" -o -name "*.pm" | grep -v "/.pc/" | xargs -r --max-args 1 debian/adjust_shebang_line.sh
+	find . -name "*.pl" -o -name "*.sh" -o -name "*.t" -o -name "*.pm" -o \
+		-name "do_flatfile_dump_registry" -o -name "parse_snp_to_ensembl_mouse" \
+				| grep -v "/.pc/" | xargs -r --max-args 1 debian/adjust_shebang_line.sh
 
 	#d=$(DESTDIR)/usr/share/ensembl
 	echo "Adjusting path to Perl wherever it may be found" ; \
@@ -70,7 +72,10 @@
 	cp debian/ensembl.overwrites/Plugins.pm        "$(DESTDIR)/etc/default/ensembl.d/"
 	cp debian/ensembl.overwrites/confSiteDefs.pm   "$(DESTDIR)/etc/default/ensembl.d/"
 	cp debian/ensembl.overwrites/pluginSiteDefs.pm "$(DESTDIR)/etc/default/ensembl.d/"
+	find debian/ensembl -name config.guess -o -name config.sub -o -name configure -o \
+		-name depcomp -o -name install-sh -o -name missing -o -name Makefile.PL | xargs -r rm
 
+
 install-indep-copying:
 	dh_testdir
 	dh_testroot