Author: moeller
Date: 2010-11-11 14:31:40 +0000 (Thu, 11 Nov 2010)
New Revision: 5420
Added:
trunk/packages/ensembl/ensembl/57/debian/ensembl.cron.d
Removed:
trunk/packages/ensembl/ensembl/57/debian/ensembl.cron.d.ex
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:
Further deborkation and upload.
Modified: trunk/packages/ensembl/ensembl/57/debian/adjust_shebang_line.sh
===================================================================
--- trunk/packages/ensembl/ensembl/57/debian/adjust_shebang_line.sh
2010-11-11 13:30:47 UTC (rev 5419)
+++ trunk/packages/ensembl/ensembl/57/debian/adjust_shebang_line.sh
2010-11-11 14:31:40 UTC (rev 5420)
@@ -2,38 +2,58 @@
for i in "$@"
do
- if head -n 1 "$i" | egrep -q '^#!(/usr/bin/perl|/bin/bash)'; then
- if ! echo "$i" | egrep -q '.pm$'; then
+
+ if head -n 1 "$i" | egrep -q '^#!\s*(/usr/bin/perl|/bin/bash)'; then
+ if echo "$i" | egrep -q '.pm$'; then
+ echo "Remove: '$i'"
+ sed -i '1d' $i
+ chmod -x "$i"
+ else
chmod 755 "$i"
echo "OK: '$i'"
- continue;
- fi
+ fi
+ continue
+ elif echo "$i" | egrep -q '.pm$'; then
+ echo "OK: '$i'"
+ chmod 644 "$i"
+ continue
fi
+
if head -n 1 "$1" | grep -q '^#!'; then
if echo "$i" | egrep -q '.pm$'; then
- echo "Remove: '$i'"
- sed -i '1d' $i
- chmod -x "$i"
- else
- echo "Substitute: '$i'"
- if head -n 1 "$i" | grep -q perl; then
- echo Perl
- sed -i '1s%#!\s*/.*/perl%#!/usr/bin/perl%' $i
- # also seen
- sed -i '1s%#!perl%#!/usr/bin/perl%' $i
- else
- echo BASH
- sed -i '1s%#!\s*/.*/bash%#!/bin/bash%' $i
+ echo "This script should have performed the removal for
.pm files already."
+ exit -1
+ elif echo "$i" | egrep -q '*.t$'; then
+ if [ ! -x "$i" ]; then
+ echo "Remove for non-executable .t: '$i'"
+ # not executable, should then lose shebang line
+ # well, it should not have one in the first
place
+ sed -i '1s%^#!.*$%%' $i
+ continue
fi
fi
+ echo "Substitute: '$i'"
+ if head -n 1 "$i" | grep -q perl; then
+ echo Perl
+ sed -i '1s%#!\s*/.*/perl%#!/usr/bin/perl%' $i
+ # also seen
+ sed -i '1s%#!perl%#!/usr/bin/perl%' $i
+ else
+ echo BASH
+ sed -i '1s%#!\s*/.*/bash%#!/bin/bash%' $i
+ fi
+ chmod 755 "$i"
else
- echo "Insert: '$i'"
if echo "$i" | egrep -q '*.t$'; then
if [ ! -x "$i" ]; then
+ echo "Leave without: '$i'"
# not executable, should then lose shebang line
- sed -i '1s%^#!.*$//' $i
+ # well, it should not have one in the first
place
+ sed -i '1s%^#!.*$%%' $i
+ continue
fi
fi
+ echo "Insert: '$i'"
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"
Modified: trunk/packages/ensembl/ensembl/57/debian/control
===================================================================
--- trunk/packages/ensembl/ensembl/57/debian/control 2010-11-11 13:30:47 UTC
(rev 5419)
+++ trunk/packages/ensembl/ensembl/57/debian/control 2010-11-11 14:31:40 UTC
(rev 5420)
@@ -53,6 +53,7 @@
Package: libensembl-core-perl
Architecture: all
Depends: ${misc:Depends},bioperl1.2.3|bioperl
+Suggests: ksh | mksh | pdksh | zsh
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
Copied: trunk/packages/ensembl/ensembl/57/debian/ensembl.cron.d (from rev 5357,
trunk/packages/ensembl/ensembl/57/debian/ensembl.cron.d.ex)
===================================================================
--- trunk/packages/ensembl/ensembl/57/debian/ensembl.cron.d
(rev 0)
+++ trunk/packages/ensembl/ensembl/57/debian/ensembl.cron.d 2010-11-11
14:31:40 UTC (rev 5420)
@@ -0,0 +1,6 @@
+#
+# Regular cron jobs for the ensembl package
+# the web server creates many temporary images which should be removed
+# on a regular basis
+#
+#0 4 * * * root [ -x /usr/bin/ensembl_maintenance ] &&
/usr/bin/ensembl_maintenance
Deleted: trunk/packages/ensembl/ensembl/57/debian/ensembl.cron.d.ex
===================================================================
--- trunk/packages/ensembl/ensembl/57/debian/ensembl.cron.d.ex 2010-11-11
13:30:47 UTC (rev 5419)
+++ trunk/packages/ensembl/ensembl/57/debian/ensembl.cron.d.ex 2010-11-11
14:31:40 UTC (rev 5420)
@@ -1,4 +0,0 @@
-#
-# Regular cron jobs for the ensembl package
-#
-0 4 * * * root [ -x /usr/bin/ensembl_maintenance ] &&
/usr/bin/ensembl_maintenance
Modified: trunk/packages/ensembl/ensembl/57/debian/rules
===================================================================
--- trunk/packages/ensembl/ensembl/57/debian/rules 2010-11-11 13:30:47 UTC
(rev 5419)
+++ trunk/packages/ensembl/ensembl/57/debian/rules 2010-11-11 14:31:40 UTC
(rev 5420)
@@ -27,23 +27,30 @@
# well, those bits should already have been fixed in the source tree,
but, who knows...
find . -name CVS -a -type d | xargs -r rm -r
find . -name "*.pm" -o -name "*.png" -o -name "*.gif" -o -name README \
- -o -name "*.sql" -o -name "*.pdf" -o -name "*.html" | xargs
-r chmod 644
- find . -name "*.pl" -o -name "*.t" | xargs -r chmod 755
+ -o -name "*.sql" -o -name "*.pdf" -o -name "*.html" \
+ -o -name "*.sxw" -o -name "*.conf*" -o -name "*.guess" -o -name
"*.sub" \
+ -o -name "*.h" -o -name "*.cpp" -o -name "*.txt" \
+ | grep -v "/.pc/" | xargs -r --max-args 10
chmod 644
+ #find . -name "*.pl" | xargs -r chmod 755
+ find . -name ".cvsignore" | xargs -r rm
# First round of updates
- find . -name "*.pl" -o -name "*.sh" -o -name "*.t" | xargs -r
debian/adjust_shebang_line.sh
+ 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
#d=$(DESTDIR)/usr/share/ensembl
echo "Adjusting path to Perl wherever it may be found" ; \
- egrep -rl "^#!\s*/.*/perl" . | xargs -r sed -i
'1s%^#!\s*/\(usr\|localsw\)/.*/perl%#!/usr/bin/perl%' ; \
+ egrep -rl "^#!\s*/.*/perl" . | grep -v "/.pc/" | xargs -r --max-args 1
sed -i '1s%^#!\s*/\(usr\|localsw\)/.*/perl%#!/usr/bin/perl%' ; \
echo "Adjusting path to Bash wherever it may be found" ; \
- egrep -rl "^#!\s*/.*/bash" . | xargs -r sed -i
'1s%^#!\s*/\(usr\|localsw\)/.*/bash%#!/bin/bash%' ; \
+ egrep -rl "^#!\s*/.*/bash" . | grep -v "/.pc/" | xargs -r --max-args 1
sed -i '1s%^#!\s*/\(usr\|localsw\)/.*/bash%#!/bin/bash%' ; \
+ egrep -rl "^#!.*ENV.*PERL" . | grep -v "/.pc/" | xargs -r --max-args 1
sed -i '1s%^#!.*%#!/usr/bin/perl%' ; \
# First round of updates
- find . -name "*.pl" -o -name "*.sh" -o -name "*.t" | xargs -r
debian/adjust_chmod.sh
+ #find . -name "*.pl" -o -name "*.sh" | xargs -r debian/adjust_chmod.sh
+ touch $@
+
install-arch: build-arch
dh_testdir
dh_testroot
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