From 4e126c8b5708625bb18bef90d10eed6329a14de9 Mon Sep 17 00:00:00 2001 From: Petar Petrov Date: Fri, 2 Sep 2011 21:57:45 -0300 Subject: academic/EMBOSS: Added (European Molecular Biology OSS) Signed-off-by: Niels Horn --- academic/EMBOSS/EMBOSS.SlackBuild | 90 ++++++++++++++++++++++++++++++++++++++ academic/EMBOSS/EMBOSS.info | 10 +++++ academic/EMBOSS/README | 20 +++++++++ academic/EMBOSS/References | 4 ++ academic/EMBOSS/doinst.sh | 3 ++ academic/EMBOSS/emboss.desktop | 8 ++++ academic/EMBOSS/emboss.png | Bin 0 -> 1269 bytes academic/EMBOSS/slack-desc | 19 ++++++++ 8 files changed, 154 insertions(+) create mode 100644 academic/EMBOSS/EMBOSS.SlackBuild create mode 100644 academic/EMBOSS/EMBOSS.info create mode 100644 academic/EMBOSS/README create mode 100644 academic/EMBOSS/References create mode 100644 academic/EMBOSS/doinst.sh create mode 100644 academic/EMBOSS/emboss.desktop create mode 100644 academic/EMBOSS/emboss.png create mode 100644 academic/EMBOSS/slack-desc diff --git a/academic/EMBOSS/EMBOSS.SlackBuild b/academic/EMBOSS/EMBOSS.SlackBuild new file mode 100644 index 0000000000..3ef67501d8 --- /dev/null +++ b/academic/EMBOSS/EMBOSS.SlackBuild @@ -0,0 +1,90 @@ +#!/bin/sh + +# Slackware build script for EMBOSS +# Written by Petar Petrov, and +# hereby submitted to the public domain + +# THIS SLACKBUILD IS DISTRIBUTETD IN THE HOPE OF BEING +# USEFUL BUT WITHOUT ANY WARRANTY. THE AUTHOR IS _NOT_ +# RESPONSIBLE FOR ANY DAMAGE OR DATA LOSS CAUSED BY IT. + +PRGNAM=EMBOSS +VERSION=${VERSION:-6.4.0} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i486 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +CWD=$(pwd) +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +if [ "$ARCH" = "i486" ]; then + SLKCFLAGS="-O2 -march=i486 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "i686" ]; then + SLKCFLAGS="-O2 -march=i686 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "x86_64" ]; then + SLKCFLAGS="-O2 -fPIC" + LIBDIRSUFFIX="64" +else + SLKCFLAGS="-O2" + LIBDIRSUFFIX="" +fi + +set -e + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP +rm -rf $PRGNAM-$VERSION +tar xvf $CWD/$PRGNAM-$VERSION.tar.gz +cd $PRGNAM-$VERSION +chown -R root:root . +find . \ + \( -perm 777 -o -perm 775 -o -perm 711 -o -perm 555 -o -perm 511 \) \ + -exec chmod 755 {} \; -o \ + \( -perm 666 -o -perm 664 -o -perm 600 -o -perm 444 -o -perm 440 -o -perm 400 \) \ + -exec chmod 644 {} \; + +CFLAGS="$SLKCFLAGS" \ +CXXFLAGS="$SLKCFLAGS" \ +./configure \ + --prefix=/usr \ + --libdir=/usr/lib${LIBDIRSUFFIX} \ + --with-x \ + --sysconfdir=/etc \ + --localstatedir=/var \ + --build=$ARCH-slackware-linux + +make +make install DESTDIR=$PKG + +find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ + | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp -a \ + AUTHORS ChangeLog COPYING FAQ INSTALL NEWS README THANKS \ + $PKG/usr/doc/$PRGNAM-$VERSION +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild +cat $CWD/References > $PKG/usr/doc/$PRGNAM-$VERSION/References + +mkdir -p $PKG/usr/share/{applications,pixmaps} +cp $CWD/emboss.desktop $PKG/usr/share/applications +cp $CWD/emboss.png $PKG/usr/share/pixmaps + +mkdir -p $PKG/install +cat $CWD/slack-desc > $PKG/install/slack-desc +cat $CWD/doinst.sh > $PKG/install/doinst.sh + +cd $PKG +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} diff --git a/academic/EMBOSS/EMBOSS.info b/academic/EMBOSS/EMBOSS.info new file mode 100644 index 0000000000..52e4178984 --- /dev/null +++ b/academic/EMBOSS/EMBOSS.info @@ -0,0 +1,10 @@ +PRGNAM="EMBOSS" +VERSION="6.4.0" +HOMEPAGE="http://emboss.sourceforge.net/" +DOWNLOAD="ftp://emboss.open-bio.org/pub/EMBOSS/EMBOSS-6.4.0.tar.gz" +MD5SUM="54993a22064222b01bd4fc8086f7684d" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +MAINTAINER="Petar Petrov" +EMAIL="ppetrov@paju.oulu.fi" +APPROVED="Niels Horn" diff --git a/academic/EMBOSS/README b/academic/EMBOSS/README new file mode 100644 index 0000000000..b3bb191db2 --- /dev/null +++ b/academic/EMBOSS/README @@ -0,0 +1,20 @@ +EMBOSS is "The European Molecular Biology Open Software Suite". + +EMBOSS is a free Open Source software analysis package specially +developed for the needs of the molecular biology (e.g. EMBnet) user +community. The software automatically copes with data in a variety of +formats and even allows transparent retrieval of sequence data from +the web. Also, as extensive libraries are provided with the package, +it is a platform to allow other scientists to develop and release +software in true open source spirit. EMBOSS also integrates a range of +currently available packages and tools for sequence analysis into a +seamless whole. EMBOSS breaks the historical trend towards commercial +software packages. + +For details and citation: +EMBOSS: The European Molecular Biology Open Software Suite (2000) +Rice,P. Longden,I. and Bleasby,A. Trends in Genetics 16, (6) pp276-277 + +If you want to use eprimer3 and multiple sequence alignment programs +like emma, you should install primer3 and clustalw, both of which are +available at SlackBuilds.org. \ No newline at end of file diff --git a/academic/EMBOSS/References b/academic/EMBOSS/References new file mode 100644 index 0000000000..05d39457f4 --- /dev/null +++ b/academic/EMBOSS/References @@ -0,0 +1,4 @@ +References + +EMBOSS: The European Molecular Biology Open Software Suite (2000) +Rice,P. Longden,I. and Bleasby,A. Trends in Genetics 16, (6) pp276--277 diff --git a/academic/EMBOSS/doinst.sh b/academic/EMBOSS/doinst.sh new file mode 100644 index 0000000000..5fb28930db --- /dev/null +++ b/academic/EMBOSS/doinst.sh @@ -0,0 +1,3 @@ +if [ -x /usr/bin/update-desktop-database ]; then + /usr/bin/update-desktop-database -q usr/share/applications >/dev/null 2>&1 +fi diff --git a/academic/EMBOSS/emboss.desktop b/academic/EMBOSS/emboss.desktop new file mode 100644 index 0000000000..249650b343 --- /dev/null +++ b/academic/EMBOSS/emboss.desktop @@ -0,0 +1,8 @@ +[Desktop Entry] +Categories=Education; +Comment=Bioinformatics suite +Exec=runJemboss.csh +Icon=emboss.png +Name=EMBOSS +StartupNotify=false +Type=Application diff --git a/academic/EMBOSS/emboss.png b/academic/EMBOSS/emboss.png new file mode 100644 index 0000000000..c9fd651eec Binary files /dev/null and b/academic/EMBOSS/emboss.png differ diff --git a/academic/EMBOSS/slack-desc b/academic/EMBOSS/slack-desc new file mode 100644 index 0000000000..ee0f082ba5 --- /dev/null +++ b/academic/EMBOSS/slack-desc @@ -0,0 +1,19 @@ +# HOW TO EDIT THIS FILE: +# The "handy ruler" below makes it easier to edit a package description. Line +# up the first '|' above the ':' following the base package name, and the '|' +# on the right side marks the last column you can put a character in. You must +# make exactly 11 lines for the formatting to be correct. It's also +# customary to leave one space after the ':'. + + |-----handy-ruler------------------------------------------------------| +EMBOSS: EMBOSS (European Molecular Biology Open Software Suite) +EMBOSS: +EMBOSS: EMBOSS is a free Open Source software analysis package specially +EMBOSS: developed for the needs of the molecular biology (e.g. EMBnet) +EMBOSS: user community. +EMBOSS: +EMBOSS: +EMBOSS: +EMBOSS: +EMBOSS: References: /usr/doc/EMBOSS-$VERSION/References +EMBOSS: Home: http://emboss.sourceforge.net/ -- cgit v1.2.3-80-g2a13