Author: moeller
Date: 2010-08-20 20:24:10 +0000 (Fri, 20 Aug 2010)
New Revision: 5176
Modified:
trunk/packages/ensembl/ensembl/57/debian/ensembl.debhelper.log
trunk/packages/ensembl/ensembl/57/debian/init.d
trunk/packages/ensembl/ensembl/57/debian/postinst
trunk/packages/ensembl/ensembl/57/debian/postrm
trunk/packages/ensembl/ensembl/57/debian/rules
trunk/packages/ensembl/libbio-das-lite-perl/trunk/debian/control
Log:
Further work towards ensembl.
Modified: trunk/packages/ensembl/ensembl/57/debian/ensembl.debhelper.log
===================================================================
--- trunk/packages/ensembl/ensembl/57/debian/ensembl.debhelper.log
2010-08-20 19:58:59 UTC (rev 5175)
+++ trunk/packages/ensembl/ensembl/57/debian/ensembl.debhelper.log
2010-08-20 20:24:10 UTC (rev 5176)
@@ -4,6 +4,7 @@
dh_installexamples
dh_install
dh_installman
+dh_installinit
dh_strip
dh_compress
dh_fixperms
@@ -17,6 +18,7 @@
dh_installexamples
dh_install
dh_installman
+dh_installinit
dh_strip
dh_compress
dh_fixperms
@@ -25,3 +27,17 @@
dh_gencontrol
dh_md5sums
dh_builddeb
+dh_installchangelogs
+dh_installdocs
+dh_installexamples
+dh_install
+dh_installman
+dh_installinit
+dh_strip
+dh_compress
+dh_fixperms
+dh_perl
+dh_installdeb
+dh_gencontrol
+dh_md5sums
+dh_builddeb
Modified: trunk/packages/ensembl/ensembl/57/debian/init.d
===================================================================
--- trunk/packages/ensembl/ensembl/57/debian/init.d 2010-08-20 19:58:59 UTC
(rev 5175)
+++ trunk/packages/ensembl/ensembl/57/debian/init.d 2010-08-20 20:24:10 UTC
(rev 5176)
@@ -6,10 +6,154 @@
# Default-Start: 2 3 4 5
# Default-Stop: 0 1 6
# X-Interactive: true
-# Short-Description: Start/stop apache2-ensembl web server
+# Short-Description: Start/stop ensembl web server
### END INIT INFO
set -e
-APACHE_CONFDIR=/usr/share/ensembl /etc/init.d/apache2 $*
+ENSEMBL_CONFDIR=/usr/share/ensembl
+. /lib/lsb/init-functions
+
+PIDFILE=/var/run/ensembl.pid
+export APACHE_PID_FILE=$PIDFILE
+APACHE2CTL="/usr/sbin/apache2ctl -d $ENSEMBL_CONFDIR -f
$ENSEMBL_CONFDIR/conf/httpd.conf -k"
+
+pidof_ensembl() {
+ # if there is actually an apache2-ensembl process whose pid is in
PIDFILE,
+ # print it and return 0.
+ if [ -e "$PIDFILE" ]; then
+ if pidof apache2 | tr ' ' '\n' | grep -w $(cat $PIDFILE); then
+ return 0
+ fi
+ fi
+ return 1
+}
+
+ensembl_stop() {
+ if $APACHE2CTL configtest > /dev/null 2>&1; then
+ # if the config is ok than we just stop normaly
+ $APACHE2CTL stop 2>&1 | grep -v 'not running' >&2 || true
+ else
+ # if we are here something is broken and we need to try
+ # to exit as nice and clean as possible
+ PID=$(pidof_ensembl) || true
+
+ if [ "${PID}" ]; then
+ # in this case it is everything nice and dandy and we
kill apache2
+ echo
+ log_warning_msg "The ensembl configtest failed, so we
are trying to kill it manually. This is almost certainly suboptimal, so please
make sure your system is working as you'd expect now!"
+ kill $PID
+ elif [ "$(pidof apache2)" ]; then
+ if [ "$VERBOSE" != no ]; then
+ echo " ... failed!"
+ echo "You may still have some ensembl processes
running. There are"
+ echo "processes named 'apache2' which do not
match your pid file,"
+ echo "and in the name of safety, we've left
them alone. Please review"
+ echo "the situation by hand."
+ fi
+ return 1
+ fi
+ fi
+}
+
+ensembl_wait_stop() {
+ # running ?
+ PIDTMP=$(pidof_ensembl) || true
+ if kill -0 "${PIDTMP:-}" 2> /dev/null; then
+ PID=$PIDTMP
+ fi
+
+ ensembl_stop
+
+ # wait until really stopped
+ if [ -n "${PID:-}" ]; then
+ i=0
+ while kill -0 "${PID:-}" 2> /dev/null; do
+ if [ $i = '60' ]; then
+ break;
+ else
+ if [ $i = '0' ]; then
+ echo -n " ... waiting "
+ else
+ echo -n "."
+ fi
+ i=$(($i+1))
+ sleep 1
+ fi
+ done
+ fi
+}
+
+case $1 in
+ start)
+ log_daemon_msg "Starting web server" "ensembl"
+ if $APACHE2CTL start; then
+ log_end_msg 0
+ else
+ log_end_msg 1
+ fi
+ ;;
+ stop)
+ log_daemon_msg "Stopping web server" "ensembl"
+ if ensembl_wait_stop; then
+ log_end_msg 0
+ else
+ log_end_msg 1
+ fi
+ ;;
+ graceful-stop)
+ log_daemon_msg "Stopping web server" "ensembl"
+ if $APACHE2CTL graceful-stop; then
+ log_end_msg 0
+ else
+ log_end_msg 1
+ fi
+ ;;
+ reload | force-reload)
+ if ! $APACHE2CTL configtest > /dev/null 2>&1; then
+ $APACHE2CTL configtest || true
+ log_end_msg 1
+ exit 1
+ fi
+ log_daemon_msg "Reloading web server config" "ensembl"
+ if pidof_ensembl > /dev/null ; then
+ if $APACHE2CTL graceful $2 ; then
+ log_end_msg 0
+ else
+ log_end_msg 1
+ fi
+ fi
+ ;;
+ restart)
+ if ! $APACHE2CTL configtest > /dev/null 2>&1; then
+ $APACHE2CTL configtest || true
+ log_end_msg 1
+ exit 1
+ fi
+ log_daemon_msg "Restarting web server" "ensembl"
+ PID=$(pidof_ensembl) || true
+ if ! ensembl_wait_stop; then
+ log_end_msg 1 || true
+ fi
+ if $APACHE2CTL start; then
+ log_end_msg 0
+ else
+ log_end_msg 1
+ fi
+ ;;
+ status)
+ PID=$(pidof_ensembl) || true
+ if [ -n "$PID" ]; then
+ echo "Ensembl is running (pid $PID)."
+ exit 0
+ else
+ echo "Ensembl is NOT running."
+ exit 1
+ fi
+ ;;
+ *)
+ log_success_msg "Usage: /etc/init.d/ensembl
{start|stop|graceful-stop|restart|reload|force-reload|status}"
+ exit 1
+ ;;
+esac
Modified: trunk/packages/ensembl/ensembl/57/debian/postinst
===================================================================
--- trunk/packages/ensembl/ensembl/57/debian/postinst 2010-08-20 19:58:59 UTC
(rev 5175)
+++ trunk/packages/ensembl/ensembl/57/debian/postinst 2010-08-20 20:24:10 UTC
(rev 5176)
@@ -30,7 +30,7 @@
grant all privileges on ensembl_web_user_db.* to ensembl@'%' identified by
'ensembl';
grant all privileges on ensembl_web_user_db.* to ense...@localhost identified
by 'ensembl';
EOMYSQL
- zcat /usr/share/doc/ensembl_web_user_db.sql.gz | mysql -uensembl
-pensembl ensembl_web_user_db
+ zcat /usr/share/doc/ensembl/ensembl_web_user_db.sql.gz | mysql
-uensembl -pensembl ensembl_web_user_db
;;
abort-upgrade|abort-remove|abort-deconfigure)
Modified: trunk/packages/ensembl/ensembl/57/debian/postrm
===================================================================
--- trunk/packages/ensembl/ensembl/57/debian/postrm 2010-08-20 19:58:59 UTC
(rev 5175)
+++ trunk/packages/ensembl/ensembl/57/debian/postrm 2010-08-20 20:24:10 UTC
(rev 5176)
@@ -21,12 +21,6 @@
case "$1" in
purge|remove)
- cat <<EOMESSAGE
-We have enabled the apache modules
- perl deflate expires headers
-when we first installed the Ensembl packages. Please check if
-you want them to remain enabled.
-EOMESSAGE
;;
upgrade|failed-upgrade|abort-install|abort-upgrade|disappear)
;;
Modified: trunk/packages/ensembl/ensembl/57/debian/rules
===================================================================
--- trunk/packages/ensembl/ensembl/57/debian/rules 2010-08-20 19:58:59 UTC
(rev 5175)
+++ trunk/packages/ensembl/ensembl/57/debian/rules 2010-08-20 20:24:10 UTC
(rev 5176)
@@ -35,7 +35,12 @@
ensembl-functgenomics ensembl-variation \
htdocs modules perl public-plugins utils \
$$d
- mv ensembl-variation/C_code/calc_genotypes
$(CURDIR)/debian/ensembl/usr/bin/
+ d=$(CURDIR)/debian/ensembl/usr/bin ; \
+ if [ ! -d "$$d" ]; then \
+ echo "Creating directory '$$d'." ; \
+ mkdir -p "$$d" ; \
+ fi ; \
+ mv ensembl-variation/C_code/calc_genotypes $$d
touch $@
install-paths: install-copying
@@ -61,6 +66,7 @@
dh_installexamples
dh_install
dh_installman
+ dh_installinit
dh_strip
dh_compress
dh_fixperms
@@ -71,7 +77,7 @@
dh_builddeb
clean:
- dh_clean install-paths install-copying
+ dh_clean install-paths install-copying build-stamp
binary: binary-indep binary-arch
Modified: trunk/packages/ensembl/libbio-das-lite-perl/trunk/debian/control
===================================================================
--- trunk/packages/ensembl/libbio-das-lite-perl/trunk/debian/control
2010-08-20 19:58:59 UTC (rev 5175)
+++ trunk/packages/ensembl/libbio-das-lite-perl/trunk/debian/control
2010-08-20 20:24:10 UTC (rev 5176)
@@ -3,7 +3,7 @@
Priority: optional
Build-Depends: debhelper (>= 7), perl
Build-Depends-Indep: libio-stringy-perl (>= 2.110), libreadonly-perl (>= 1.03),
- libwww-curl-perl (>= 4.07), libwww-perl (>= 1.49),
+ libwww-curl-perl (>= 4.07), libwww-perl (>= 1.49) | libwww-perl5.808-perl,
libtest-pod-coverage-perl, libtest-distribution-perl,
perl (>= 5.10.1) | libtest-simple-perl (>= 0.8)
Maintainer: Richard Holland <[email protected]>
@@ -15,7 +15,7 @@
Package: libbio-das-lite-perl
Architecture: all
Depends: ${misc:Depends}, ${perl:Depends}, libio-stringy-perl (>= 2.110),
- libreadonly-perl (>= 1.03), libwww-curl-perl (>= 4.07), libwww-perl (>= 1.49),
+ libreadonly-perl (>= 1.03), libwww-curl-perl (>= 4.07), libwww-perl (>= 1.49)
| libwww-perl5.808-perl,
perl
Description: implementation of the BioDas protocol
Bio::Das::Lite is an implementation of the BioDas protocol
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