From 178b7046dd3945f801c3d17cde2d75d69c2b7987 Mon Sep 17 00:00:00 2001 From: Petar Petrov Date: Sat, 13 Jul 2013 11:47:24 -0500 Subject: academic/squizz: Added (A sequence/alignment format checker and converter) Signed-off-by: Erik Hanson --- academic/squizz/README | 8 +++ academic/squizz/slack-desc | 19 +++++++ academic/squizz/squizz.SlackBuild | 102 ++++++++++++++++++++++++++++++++++++++ academic/squizz/squizz.info | 10 ++++ 4 files changed, 139 insertions(+) create mode 100644 academic/squizz/README create mode 100644 academic/squizz/slack-desc create mode 100644 academic/squizz/squizz.SlackBuild create mode 100644 academic/squizz/squizz.info diff --git a/academic/squizz/README b/academic/squizz/README new file mode 100644 index 0000000000..18dbd3fc4f --- /dev/null +++ b/academic/squizz/README @@ -0,0 +1,8 @@ +Squizz is a sequence/alignment format checker, but it has some +conversion capabilities too. + +Most common sequence and alignment formats are supported : +- EMBL, FASTA, GCG, GDE, GENBANK, IG, NBRF, PIR (codata), RAW, and + SWISSPROT. +- CLUSTAL, FASTA, MEGA, MSF, NEXUS, PHYLIP (interleaved / sequential) + and STOCKHOLM. diff --git a/academic/squizz/slack-desc b/academic/squizz/slack-desc new file mode 100644 index 0000000000..b179c3078a --- /dev/null +++ b/academic/squizz/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 ':' except on otherwise blank lines. + + |-----handy-ruler------------------------------------------------------| +squizz: squizz (A sequence/alignment format checker and converter) +squizz: +squizz: Squizz is a sequence/alignment format checker, but it has +squizz: some conversion capabilities too. Most common sequence and +squizz: alignment formats are supported: EMBL, FASTA, GCG, GDE, +squizz: GENBANK, IG, NBRF, PIR (codata), RAW, SWISSPROT and CLUSTAL, +squizz: FASTA, MEGA, MSF, NEXUS, PHYLIP (interleaved and sequential) +squizz: and STOCKHOLM. +squizz: +squizz: Home: http://pbil.univ-lyon1.fr/pf_bioinfo/article313.html +squizz: diff --git a/academic/squizz/squizz.SlackBuild b/academic/squizz/squizz.SlackBuild new file mode 100644 index 0000000000..763fda8329 --- /dev/null +++ b/academic/squizz/squizz.SlackBuild @@ -0,0 +1,102 @@ +#!/bin/sh + +# Slackware build script for squizz + +# Copyright 2013 Petar Petrov, ppetrov@paju.oulu.fi +# All rights reserved. +# +# Redistribution and use of this script, with or without modification, 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. + +PRGNAM=squizz +VERSION=${VERSION:-0.99b} +BUILD=${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${LIBDIRSUFFIX} \ + --sysconfdir=/etc \ + --localstatedir=/var \ + --mandir=/usr/man \ + --docdir=/usr/doc/$PRGNAM-$VERSION \ + --build=$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 + +find $PKG/usr/man -type f -exec gzip -9 {} \; +for i in $( find $PKG/usr/man -type l ) ; do ln -s $( readlink $i ).gz $i.gz ; rm $i ; done + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp -a \ + AUTHORS ChangeLog COPYING INSTALL NEWS README TODO \ + $PKG/usr/doc/$PRGNAM-$VERSION +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild + +mkdir -p $PKG/install +cat $CWD/slack-desc > $PKG/install/slack-desc + +cd $PKG +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} diff --git a/academic/squizz/squizz.info b/academic/squizz/squizz.info new file mode 100644 index 0000000000..78be297b90 --- /dev/null +++ b/academic/squizz/squizz.info @@ -0,0 +1,10 @@ +PRGNAM="squizz" +VERSION="0.99b" +HOMEPAGE="http://pbil.univ-lyon1.fr/pf_bioinfo/article313.html" +DOWNLOAD="ftp://ftp.pasteur.fr/pub/gensoft/projects/squizz/squizz-0.99b.tar.gz" +MD5SUM="ca02757a592cf4ee5c5056a1f6113de0" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="" +MAINTAINER="Petar Petrov" +EMAIL="ppetrov@paju.oulu.fi" -- cgit v1.2.3