From e13451b0c2f46cd1c9d8f366b6e2081aa5f24ff6 Mon Sep 17 00:00:00 2001 From: Damien Goutte-Gattat Date: Sat, 13 Dec 2008 23:41:15 +0100 Subject: [PATCH] ap/acedb: Added. --- ap/acedb/acedb.SlackBuild | 120 ++++++++++++++++++++++++++++++++++++++ ap/acedb/doinst.sh | 11 ++++ ap/acedb/sha1sums | 5 ++ ap/acedb/slack-desc | 12 ++++ 4 files changed, 148 insertions(+) create mode 100755 ap/acedb/acedb.SlackBuild create mode 100644 ap/acedb/doinst.sh create mode 100644 ap/acedb/sha1sums create mode 100644 ap/acedb/slack-desc diff --git a/ap/acedb/acedb.SlackBuild b/ap/acedb/acedb.SlackBuild new file mode 100755 index 00000000..6ef7df82 --- /dev/null +++ b/ap/acedb/acedb.SlackBuild @@ -0,0 +1,120 @@ +#!/bin/bash +# Build script for Slackware +# Damien Goutte-Gattat "gouttegd" +# +# Redistribution and use of this script, with or without modifications, is +# permitted provided that the following conditions are met: +# +# 1. Redistributions of this script must retain the above copyright +# notice, this list of conditions and the following disclaimer. +# +# THIS SOFTWARE IS PROVIDED BY THE AUTHOR AS IS'' AND ANY EXPRESS OR IMPLIED +# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO +# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +# +# Latest acedb sourcecode is available at: +# http://www.acedb.org/Software/Downloads/ + +# Source package infos +VERSION=${VERSION:-4.9.39} +SOURCE=${SOURCE:-ACEDB-source.$VERSION.tar.gz} +DEMODB=${DEMODB:-ACEDB-demo.$VERSION.tar.gz} +DEVDOC=${DEVDOC:-ACEDB-doc.$VERSION.tar.gz} +HELP=${HELP:-ACEDB-help.$VERSION.tar.gz} +TOOLS=${TOOLS:-ACEDB-tools.$VERSION.tar.gz} +BASEURL=${BASEURL:-ftp://ftp.sanger.ac.uk/pub/acedb/SUPPORTED} + +# Built package infos +NAMETGZ=${NAMETGZ:-acedb} +BUILD=${BUILD:-1GGD} +ARCH=${ARCH:-i486} +TARGET=${TARGET:-i486} + +# Directories +TMP=${TMP:-/tmp} +OUT=${OUT:-$TMP/build} +PKG=${PKG:-$OUT/$NAMETGZ} +CWD=$(pwd) + +set -e # Quit if a command returns non-zero + +# Sanity checks +if [ $UID -eq 0 ]; then + echo "You should NOT run this script as ROOT!" + exit 1 +fi +if [ ! -d $TMP ]; then + echo "$TMP does not exist or is not a directory!" + exit 1 +fi + +# Compilation flags +case "$ARCH" in +i?86) + CPUOPT="-O2 -march=$ARCH -mtune=i686" + ;; +*) + CPUOPT="-O2" + ;; +esac + +# Get and verify the archives +# (beware when extracting them, they are tar bombs!) +for ARCHIVE in $SOURCE $DEMODB $DEVDOC $HELP $TOOLS; do + if [ ! -r $ARCHIVE ]; then + wget "$BASEURL/$ARCHIVE" + fi +done +sha1sum -c sha1sums + +# Build and install the binaries +mkdir -p $TMP/$NAMETGZ +tar xf $CWD/$SOURCE -C $TMP/$NAMETGZ +cd $TMP/$NAMETGZ +ACEDB_MACHINE=LINUX_4 make -j 3 COPT="$CPUOPT" || true +mkdir -p $PKG/usr/bin +find bin.LINUX_4 -type f -perm 755 -exec install -m 755 '{}' $PKG/usr/bin \; +find $PKG/usr/bin -exec strip --strip-unneeded '{}' \; + +# Install the sample database and the helper scripts +mkdir -p $PKG/usr/share/$NAMETGZ/{demo,tools} +tar xf $CWD/$DEMODB -C $PKG/usr/share/$NAMETGZ/demo +tar xf $CWD/$TOOLS -C $PKG/usr/share/$NAMETGZ/tools + +# Install the docs +mkdir -p $PKG/usr/doc/$NAMETGZ-$VERSION/{developers,users} +tar xf $CWD/$DEVDOC -C $PKG/usr/doc/$NAMETGZ-$VERSION/developers +tar xf $CWD/$HELP -C $PKG/usr/doc/$NAMETGZ-$VERSION/users + +# Get rid of the various CVS directories, and sanitize permissions +# for all files except the binaries +find $PKG -type d -name CVS | xargs rm -rf +find $PKG/usr/doc -type f -exec chmod 644 '{}' \; +find $PKG/usr/share -type f -exec chmod 644 '{}' \; + +# Copy slack-desc file +mkdir -p $PKG/install +install -m 644 $CWD/slack-desc $PKG/install/slack-desc + +# Package the tree +cd $PKG +mkdir -p $OUT +PACKAGING=" +chown root:root . -R +/sbin/makepkg -l y -c n $OUT/$NAMETGZ-$VERSION-$ARCH-$BUILD.tgz +rm -rf $PKG +rm -rf $TMP/$NAMETGZ +" + +if type -p fakeroot ; then + echo "$PACKAGING" | fakeroot +else + su -c "$PACKAGING" +fi diff --git a/ap/acedb/doinst.sh b/ap/acedb/doinst.sh new file mode 100644 index 00000000..d51b64df --- /dev/null +++ b/ap/acedb/doinst.sh @@ -0,0 +1,11 @@ +#!/bin/sh +config() +{ + NEW="$1" + OLD="`dirname $NEW`/`basename $NEW .new`" + if [ ! -r $OLD ]; then + mv $NEW $OLD + elif [ "`cat $OLD | md5sum`" = "`cat $NEW | md5sum`" ]; then + rm $NEW + fi +} diff --git a/ap/acedb/sha1sums b/ap/acedb/sha1sums new file mode 100644 index 00000000..cfe6887a --- /dev/null +++ b/ap/acedb/sha1sums @@ -0,0 +1,5 @@ +598bf67f83d3fdbb257e418be2c16570ac5c6343 ACEDB-demo.4.9.39.tar.gz +64f70fde157fb7194a1cacd733c2c12332182fb1 ACEDB-doc.4.9.39.tar.gz +8efd1d0c8e87533241fd6946019bf8982cff00a2 ACEDB-help.4.9.39.tar.gz +84bd885fa2300933fce31f6ebe38b936918f30d2 ACEDB-source.4.9.39.tar.gz +1ba2dd989efc7c846cd251c9521cd5fc87bf5205 ACEDB-tools.4.9.39.tar.gz diff --git a/ap/acedb/slack-desc b/ap/acedb/slack-desc new file mode 100644 index 00000000..1b0f0a93 --- /dev/null +++ b/ap/acedb/slack-desc @@ -0,0 +1,12 @@ + |-----handy-ruler------------------------------------------------------| +acedb: acedb (A C.elegans Database) +acedb: +acedb: Acedb is a genome database system. It provides a custom database +acedb: kernel, with a non-standard data model designed specifically for +acedb: handling scientific data flexibly, and a graphical user interface +acedb: with many specific displays and tools for genomic data. +acedb: +acedb: Acedb was originally developed for the C.elegans genome project, from +acedb: which its name was derived. +acedb: +acedb: