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 <[email protected]> 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:[email protected]:/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 + * _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/mailman/listinfo/debian-med-commit
