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| -rw-r--r-- | academic/biopython/README | 23 | ||||
| -rw-r--r-- | academic/biopython/References | 7 | ||||
| -rw-r--r-- | academic/biopython/biopython.SlackBuild | 86 | ||||
| -rw-r--r-- | academic/biopython/biopython.info | 10 | ||||
| -rw-r--r-- | academic/biopython/slack-desc | 19 |
5 files changed, 145 insertions, 0 deletions
diff --git a/academic/biopython/README b/academic/biopython/README new file mode 100644 index 0000000000..9c61e5c495 --- /dev/null +++ b/academic/biopython/README @@ -0,0 +1,23 @@ +The Biopython Project is an international association of developers of +freely available Python tools for computational molecular biology. + +The Biopython web site provides an online resource for modules, +scripts, and web links for developers of Python-based software for +bioinformatics use and research. Basically, the goal of Biopython is +to make it as easy as possible to use Python for bioinformatics by +creating high-quality, reusable modules and classes. Biopython +features include parsers for various Bioinformatics file formats +(BLAST, Clustalw, FASTA, Genbank,...), access to online services +(NCBI, Expasy,...), interfaces to common and not-so-common programs +(Clustalw, DSSP, MSMS,...), a standard sequence class, various +clustering modules, a KD tree data structure etc. and even +documentation. + +If you use Biopython in work contributing to a scientific publication, +please cite the application note (below) or one of the module specific +publications (listed on Biopython's website): + +Cock, P.J.A. et al. Biopython: freely available Python tools for +computational molecular biology and bioinformatics. Bioinformatics +2009 Jun 1; 25(11) 1422-3 +http://dx.doi.org/10.1093/bioinformatics/btp163 pmid:19304878 diff --git a/academic/biopython/References b/academic/biopython/References new file mode 100644 index 0000000000..cb4bbf6471 --- /dev/null +++ b/academic/biopython/References @@ -0,0 +1,7 @@ +If you use Biopython in work contributing to a scientific publication, we ask +that you cite our application note (below) or one of the module specific +publications (listed on our website): + +Cock, P.J.A. et al. Biopython: freely available Python tools for computational +molecular biology and bioinformatics. Bioinformatics 2009 Jun 1; 25(11) 1422-3 +http://dx.doi.org/10.1093/bioinformatics/btp163 pmid:19304878
\ No newline at end of file diff --git a/academic/biopython/biopython.SlackBuild b/academic/biopython/biopython.SlackBuild new file mode 100644 index 0000000000..22bd291d1f --- /dev/null +++ b/academic/biopython/biopython.SlackBuild @@ -0,0 +1,86 @@ +#!/bin/sh + +# Slackware build script for biopython + +# Copyright 2019 Petar Petrov slackalaxy@gmail.com +# 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=biopython +VERSION=${VERSION:-1.74} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +CWD=$(pwd) +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -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 -L . \ + \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ + -o -perm 511 \) -exec chmod 755 {} \; -o \ + \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; + +python setup.py install --root=$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 *.rst $PKG/usr/doc/$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/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/biopython/biopython.info b/academic/biopython/biopython.info new file mode 100644 index 0000000000..9906f1df81 --- /dev/null +++ b/academic/biopython/biopython.info @@ -0,0 +1,10 @@ +PRGNAM="biopython" +VERSION="1.74" +HOMEPAGE="https://biopython.org/" +DOWNLOAD="http://biopython.org/DIST/biopython-1.74.tar.gz" +MD5SUM="cead2bfe9e7be45267eba00635f68d5c" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="numpy" +MAINTAINER="Petar Petrov" +EMAIL="slackalaxy@gmail.com" diff --git a/academic/biopython/slack-desc b/academic/biopython/slack-desc new file mode 100644 index 0000000000..14374d1dfd --- /dev/null +++ b/academic/biopython/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------------------------------------------------------| +biopython: biopython (A set of Python tools for biological computation) +biopython: +biopython: Biopython is a set of freely available tools for biological +biopython: computation written in Python. Biopython features include parsers +biopython: for various Bioinformatics file formats (BLAST, Clustalw, FASTA, +biopython: Genbank), access to online services (NCBI, Expasy), interfaces to +biopython: common and not-so-common programs (Clustalw, DSSP, MSMS), a +biopython: standard sequence class, various clustering modules, a KD tree +biopython: data structure etc. and even documentation. +biopython: +biopython: https://biopython.org/ |