extra/biopython: Added.

extra/biopython/biopython-1.49.tar.gz.sha1

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+f2ea7f3b8985facdf8f4d4c86ee300e4a8f1a5fb  biopython-1.49.tar.gz

extra/biopython/biopython.SlackBuild

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+#!/bin/bash
+# Build script for Slackware
+# Damien Goutte-Gattat "gouttegd" <damien.goutte-gattat at e.ujf-grenoble.fr>
+#
+# 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 biopython sourcecode is available at:
+# http://www.biopython.org/
+#
+# Recommmends: extra/numpy, extra/reportlab, extra/psycopg2
+
+# Source package infos
+NAMESRC=${NAMESRC:-biopython}
+VERSION=${VERSION:-1.49}
+ARCHIVE=${ARCHIVE:-$NAMESRC-$VERSION.tar.gz}
+WGET=${WGET:-http://biopython.org/DIST/$ARCHIVE}
+SHA1=${SHA1:-838aea352d1b78a013b50dfab4a6363a5027edd0}
+
+# Built package infos
+NAMETGZ=${NAMETGZ:-biopython}
+BUILD=${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 check
+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 source archive
+if [ ! -r $ARCHIVE ]; then
+    wget "$WGET"
+fi
+sha1sum -c $ARCHIVE.sha1
+NAME=$(tar ft $ARCHIVE | head -1 | cut -d / -f 1)
+
+# Compile
+cd $TMP
+echo "Building $ARCHIVE..."
+tar xf $CWD/$ARCHIVE
+cd $NAME
+CFLAGS=$CPUOPT \
+CXXFLAGS=$CPUOPT \
+python setup.py build
+python setup.py install --prefix=$PKG/usr
+
+# Install the documentation
+mkdir -p $PKG/usr/doc/$NAME
+install -m 644 \
+  CONTRIB DEPRECATED LICENSE NEWS README \
+  $PKG/usr/doc/$NAME
+cp -r Doc $PKG/usr/doc/$NAME/docs
+
+# Copy slack-desc file
+install -D -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 $TMP/$NAME
+"
+if type -p fakeroot ; then
+    echo "$PACKAGING" | fakeroot
+else
+    su -c "$PACKAGING"
+fi

extra/biopython/slack-desc

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+         |-----handy-ruler------------------------------------------------------|
+biopython: biopython (Python libraries for biology-related computations)
+biopython: 
+biopython: The Biopython project is an international associations of
+biopython: developers of freely available Python tools for computational
+biopython: molecular biology. Is is a distributed collaborative effort to
+biopython: develop Python libraries and applications which address the needs
+biopython: of current and future work in bioinformatics.
+biopython: 
+biopython: The source code is made available under the Biopython License,
+biopython: which is extremely liberal and compatible with almost every license
+biopython: in the world.