academic/squizz: Added (A sequence/alignment format checker and converter)

Signed-off-by: Erik Hanson <erik@slackbuilds.org>

4 files changed, 139 insertions, 0 deletions

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"