[med-svn] r5172 - in trunk/packages/ensembl: . ensembl/57/debian libwww-perl5.808-perl/trunk/debian
Steffen Möller
moeller at alioth.debian.org
Fri Aug 20 14:37:16 UTC 2010
Author: moeller
Date: 2010-08-20 14:37:11 +0000 (Fri, 20 Aug 2010)
New Revision: 5172
Added:
trunk/packages/ensembl/ensembl/57/debian/postinst
trunk/packages/ensembl/ensembl/57/debian/postrm
trunk/packages/ensembl/prepare_ensembl_source_packages.sh
Removed:
trunk/packages/ensembl/ensembl/57/debian/ensembl.substvars
trunk/packages/ensembl/ensembl/57/debian/files
trunk/packages/ensembl/ensembl/57/debian/postinst.ex
trunk/packages/ensembl/ensembl/57/debian/postrm.ex
Modified:
trunk/packages/ensembl/ensembl/57/debian/README.Debian
trunk/packages/ensembl/ensembl/57/debian/ensembl.debhelper.log
trunk/packages/ensembl/ensembl/57/debian/rules
trunk/packages/ensembl/libwww-perl5.808-perl/trunk/debian/control
Log:
Got postinst commands done.
Modified: trunk/packages/ensembl/ensembl/57/debian/README.Debian
===================================================================
--- trunk/packages/ensembl/ensembl/57/debian/README.Debian 2010-08-20 14:10:25 UTC (rev 5171)
+++ trunk/packages/ensembl/ensembl/57/debian/README.Debian 2010-08-20 14:37:11 UTC (rev 5172)
@@ -1,6 +1,13 @@
ensembl for Debian
------------------
-Apache modules enabled in postinst include perl, headers, expires and deflate. These do not get disabled again on uninstall.
+Apache modules enabled in postinst include perl, headers, expires and
+deflate. These do not get disabled again on uninstall.
+The (current) focus of this packaging is a running local web site.
+The genomic data remains on the remote servers. And it was produced
+there from sequence, not with this local host. This may change, but
+for now, to end somewhere, all the extra bits are left as they are
+upstream, i.e. no further paths adjusted than ultimately required.
+
-- Richard Holland <holland at eaglegenomics.com> Fri, 20 Aug 2010 14:46:17 +0200
Modified: trunk/packages/ensembl/ensembl/57/debian/ensembl.debhelper.log
===================================================================
--- trunk/packages/ensembl/ensembl/57/debian/ensembl.debhelper.log 2010-08-20 14:10:25 UTC (rev 5171)
+++ trunk/packages/ensembl/ensembl/57/debian/ensembl.debhelper.log 2010-08-20 14:37:11 UTC (rev 5172)
@@ -12,3 +12,16 @@
dh_gencontrol
dh_md5sums
dh_builddeb
+dh_installchangelogs
+dh_installdocs
+dh_installexamples
+dh_install
+dh_installman
+dh_strip
+dh_compress
+dh_fixperms
+dh_perl
+dh_installdeb
+dh_gencontrol
+dh_md5sums
+dh_builddeb
Deleted: trunk/packages/ensembl/ensembl/57/debian/ensembl.substvars
===================================================================
--- trunk/packages/ensembl/ensembl/57/debian/ensembl.substvars 2010-08-20 14:10:25 UTC (rev 5171)
+++ trunk/packages/ensembl/ensembl/57/debian/ensembl.substvars 2010-08-20 14:37:11 UTC (rev 5172)
@@ -1,2 +0,0 @@
-perl:Depends=perl
-misc:Depends=
Deleted: trunk/packages/ensembl/ensembl/57/debian/files
===================================================================
--- trunk/packages/ensembl/ensembl/57/debian/files 2010-08-20 14:10:25 UTC (rev 5171)
+++ trunk/packages/ensembl/ensembl/57/debian/files 2010-08-20 14:37:11 UTC (rev 5172)
@@ -1 +0,0 @@
-ensembl_57-1_amd64.deb unknown extra
Copied: trunk/packages/ensembl/ensembl/57/debian/postinst (from rev 5171, trunk/packages/ensembl/ensembl/57/debian/postinst.ex)
===================================================================
--- trunk/packages/ensembl/ensembl/57/debian/postinst (rev 0)
+++ trunk/packages/ensembl/ensembl/57/debian/postinst 2010-08-20 14:37:11 UTC (rev 5172)
@@ -0,0 +1,43 @@
+#!/bin/sh
+# postinst script for ensembl
+#
+# see: dh_installdeb(1)
+
+set -e
+
+# summary of how this script can be called:
+# * <postinst> `configure' <most-recently-configured-version>
+# * <old-postinst> `abort-upgrade' <new version>
+# * <conflictor's-postinst> `abort-remove' `in-favour' <package>
+# <new-version>
+# * <postinst> `abort-remove'
+# * <deconfigured's-postinst> `abort-deconfigure' `in-favour'
+# <failed-install-package> <version> `removing'
+# <conflicting-package> <version>
+# for details, see http://www.debian.org/doc/debian-policy/ or
+# the debian-policy package
+
+
+case "$1" in
+ configure)
+ a2enmod perl
+ a2enmod deflate
+ a2enmod expires
+ a2enmod headers
+ ;;
+
+ abort-upgrade|abort-remove|abort-deconfigure)
+ ;;
+
+ *)
+ echo "postinst called with unknown argument \`$1'" >&2
+ exit 1
+ ;;
+esac
+
+# dh_installdeb will replace this with shell code automatically
+# generated by other debhelper scripts.
+
+#DEBHELPER#
+
+exit 0
Deleted: trunk/packages/ensembl/ensembl/57/debian/postinst.ex
===================================================================
--- trunk/packages/ensembl/ensembl/57/debian/postinst.ex 2010-08-20 14:10:25 UTC (rev 5171)
+++ trunk/packages/ensembl/ensembl/57/debian/postinst.ex 2010-08-20 14:37:11 UTC (rev 5172)
@@ -1,39 +0,0 @@
-#!/bin/sh
-# postinst script for ensembl
-#
-# see: dh_installdeb(1)
-
-set -e
-
-# summary of how this script can be called:
-# * <postinst> `configure' <most-recently-configured-version>
-# * <old-postinst> `abort-upgrade' <new version>
-# * <conflictor's-postinst> `abort-remove' `in-favour' <package>
-# <new-version>
-# * <postinst> `abort-remove'
-# * <deconfigured's-postinst> `abort-deconfigure' `in-favour'
-# <failed-install-package> <version> `removing'
-# <conflicting-package> <version>
-# for details, see http://www.debian.org/doc/debian-policy/ or
-# the debian-policy package
-
-
-case "$1" in
- configure)
- ;;
-
- abort-upgrade|abort-remove|abort-deconfigure)
- ;;
-
- *)
- echo "postinst called with unknown argument \`$1'" >&2
- exit 1
- ;;
-esac
-
-# dh_installdeb will replace this with shell code automatically
-# generated by other debhelper scripts.
-
-#DEBHELPER#
-
-exit 0
Copied: trunk/packages/ensembl/ensembl/57/debian/postrm (from rev 5171, trunk/packages/ensembl/ensembl/57/debian/postrm.ex)
===================================================================
--- trunk/packages/ensembl/ensembl/57/debian/postrm (rev 0)
+++ trunk/packages/ensembl/ensembl/57/debian/postrm 2010-08-20 14:37:11 UTC (rev 5172)
@@ -0,0 +1,45 @@
+#!/bin/sh
+# postrm script for ensembl
+#
+# see: dh_installdeb(1)
+
+set -e
+
+# summary of how this script can be called:
+# * <postrm> `remove'
+# * <postrm> `purge'
+# * <old-postrm> `upgrade' <new-version>
+# * <new-postrm> `failed-upgrade' <old-version>
+# * <new-postrm> `abort-install'
+# * <new-postrm> `abort-install' <old-version>
+# * <new-postrm> `abort-upgrade' <old-version>
+# * <disappearer's-postrm> `disappear' <overwriter>
+# <overwriter-version>
+# for details, see http://www.debian.org/doc/debian-policy/ or
+# the debian-policy package
+
+
+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)
+ ;;
+
+ *)
+ echo "postrm called with unknown argument \`$1'" >&2
+ exit 1
+ ;;
+esac
+
+# dh_installdeb will replace this with shell code automatically
+# generated by other debhelper scripts.
+
+#DEBHELPER#
+
+exit 0
Deleted: trunk/packages/ensembl/ensembl/57/debian/postrm.ex
===================================================================
--- trunk/packages/ensembl/ensembl/57/debian/postrm.ex 2010-08-20 14:10:25 UTC (rev 5171)
+++ trunk/packages/ensembl/ensembl/57/debian/postrm.ex 2010-08-20 14:37:11 UTC (rev 5172)
@@ -1,37 +0,0 @@
-#!/bin/sh
-# postrm script for ensembl
-#
-# see: dh_installdeb(1)
-
-set -e
-
-# summary of how this script can be called:
-# * <postrm> `remove'
-# * <postrm> `purge'
-# * <old-postrm> `upgrade' <new-version>
-# * <new-postrm> `failed-upgrade' <old-version>
-# * <new-postrm> `abort-install'
-# * <new-postrm> `abort-install' <old-version>
-# * <new-postrm> `abort-upgrade' <old-version>
-# * <disappearer's-postrm> `disappear' <overwriter>
-# <overwriter-version>
-# for details, see http://www.debian.org/doc/debian-policy/ or
-# the debian-policy package
-
-
-case "$1" in
- purge|remove|upgrade|failed-upgrade|abort-install|abort-upgrade|disappear)
- ;;
-
- *)
- echo "postrm called with unknown argument \`$1'" >&2
- exit 1
- ;;
-esac
-
-# dh_installdeb will replace this with shell code automatically
-# generated by other debhelper scripts.
-
-#DEBHELPER#
-
-exit 0
Modified: trunk/packages/ensembl/ensembl/57/debian/rules
===================================================================
--- trunk/packages/ensembl/ensembl/57/debian/rules 2010-08-20 14:10:25 UTC (rev 5171)
+++ trunk/packages/ensembl/ensembl/57/debian/rules 2010-08-20 14:37:11 UTC (rev 5172)
@@ -19,7 +19,9 @@
# nothing to be built
touch build-stamp
-install:
+install: install-copying install-paths
+
+install-copying:
dh_testdir
dh_testroot
dh_prep
@@ -33,8 +35,20 @@
ensembl-functgenomics ensembl-variation \
htdocs modules perl public-plugins utils \
$$d
+ touch $@
+install-paths: install-copying
+ d=$(CURDIR)/debian/ensembl/usr/share/ensembl ; \
+ if [ ! -d "$$d" ]; then \
+ echo "Directory '$$d' not existing. Quitting." ; \
+ exit 1; \
+ fi; \
+ echo ; \
+ echo "Adjusting path to Perl" ; \
+ egrep -rl "usr/local.*/bin/perl" $$d | xargs -r sed -i 's%^#!\s*/usr/.*/perl%#!/usr/bin/perl%'
+ touch $@
+
binary-indep:
# nothing to do for binary-indep
@@ -56,7 +70,7 @@
dh_builddeb
clean:
- dh_clean
+ dh_clean install-paths install-copying
binary: binary-indep binary-arch
Modified: trunk/packages/ensembl/libwww-perl5.808-perl/trunk/debian/control
===================================================================
--- trunk/packages/ensembl/libwww-perl5.808-perl/trunk/debian/control 2010-08-20 14:10:25 UTC (rev 5171)
+++ trunk/packages/ensembl/libwww-perl5.808-perl/trunk/debian/control 2010-08-20 14:37:11 UTC (rev 5172)
@@ -14,6 +14,7 @@
Architecture: all
Provides: libwww-perl
Conflicts: libwww-perl
+Replaces: libwww-perl
Depends: ${misc:Depends}, ${perl:Depends}, liburi-perl, libhtml-parser-perl, libhtml-tree-perl, libhtml-tagset-perl, netbase
Recommends: libmailtools-perl, libhtml-format-perl, perl (>= 5.10.1) | libio-compress-perl
Suggests: libcrypt-ssleay-perl | libio-socket-ssl-perl
Added: trunk/packages/ensembl/prepare_ensembl_source_packages.sh
===================================================================
--- trunk/packages/ensembl/prepare_ensembl_source_packages.sh (rev 0)
+++ trunk/packages/ensembl/prepare_ensembl_source_packages.sh 2010-08-20 14:37:11 UTC (rev 5172)
@@ -0,0 +1,50 @@
+#!/bin/bash
+
+set -e
+
+# All libraries must be of the same version - update them all or none
+ensemblversion=57
+
+if [ -d "$ensemblversion" ] ; then cd $ensemblversion; else
+ echo "No dir $ensemblversion"
+ exit;
+fi
+
+export CVSROOT=":pserver:cvsuser at cvs.sanger.ac.uk:/cvsroot/ensembl"
+
+echo "Logging in to Sanger CVS, type password CVSUSER"
+cvs login
+
+echo
+echo " Performing checkout"
+echo
+
+#ensembl # Install the Ensembl Core Perl API for version 50
+#ensembl-variation # If required, install the Ensembl Variation Perl API for version 50
+#ensembl-functgenomics # If required, install the Ensembl Functional Genomics Perl API for version 50
+#ensembl-compara # If required, install the Ensembl Compara Perl API for verion 50
+
+
+for package in ensembl-api ensembl-website # ensembl ensembl-functgenomics ensembl-compara ensembl-variation
+do
+ echo "----------------------------------------------------"
+ echo " $package"
+ echo "----------------------------------------------------"
+ if [ -d "$dname" ]; then
+ echo "Skipping fetch of package '$dname', directory is already existing."
+ #(cd $i && cvs -z 3 update .)
+ else
+ cvs -z 3 checkout -r branch-ensembl-${ensemblversion} ${package}
+ fi
+ echo
+done
+
+#for package in ensembl-api ensembl-website ensembl ensembl-functgenomics ensembl-compara ensembl-variation
+#do
+# dname="$package-$ensemblversion"
+# tar --exclude CVS --exclude CVSROOT -czvf ${package}_${ensemblversion}.orig.tar.gz $dname
+#done
+
+echo
+echo "Success."
+echo
Property changes on: trunk/packages/ensembl/prepare_ensembl_source_packages.sh
___________________________________________________________________
Added: svn:executable
+ *
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