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academic/genpak: Added (Utilities to manipulate DNA sequences)
Signed-off-by: Niels Horn <niels.horn@slackbuilds.org>
This commit is contained in:
Petar Petrov
Niels Horn
parent
e99cd4194e
commit
5d75fedb2e
4 changed files with 157 additions and 0 deletions
10
academic/genpak/README
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10
academic/genpak/README
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The GenPak (GP) package contains many command-line utilities which
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fullfill a whole bunch of tasks, from DNA sequence searches to
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restriction analysis and determining the melting temperature of
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oligonucleotides. GP utilities can convert DNA / RNA to protein,
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determine codon usage / GC contents, do promotor searches, calculate
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Tm, search for restriction sites, convert sequences into numerical
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representations and much more.
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You most likely want to install arka, which provides a GUI for genpak.
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arka is also available at SlackBuilds.org.
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118
academic/genpak/genpak.SlackBuild
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118
academic/genpak/genpak.SlackBuild
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#!/bin/sh
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# Slackware build script for genpak
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# Written by Petar Petrov, <ppetrov@paju.oulu.fi> and
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# hereby submitted to the public domain
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# THIS SLACKBUILD IS DISTRIBUTETD IN THE HOPE OF BEING
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# USEFUL BUT WITHOUT ANY WARRANTY. THE AUTHOR IS _NOT_
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# RESPONSIBLE FOR ANY DAMAGE OR DATA LOSS CAUSED BY IT.
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PRGNAM=genpak
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VERSION=${VERSION:-0.26}
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BUILD=${BUILD:-1}
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TAG=${TAG:-_SBo}
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if [ -z "$ARCH" ]; then
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case "$( uname -m )" in
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i?86) ARCH=i486 ;;
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arm*) ARCH=arm ;;
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*) ARCH=$( uname -m ) ;;
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esac
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fi
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CWD=$(pwd)
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TMP=${TMP:-/tmp/SBo}
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PKG=$TMP/package-$PRGNAM
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OUTPUT=${OUTPUT:-/tmp}
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if [ "$ARCH" = "i486" ]; then
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SLKCFLAGS="-O2 -march=i486 -mtune=i686"
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LIBDIRSUFFIX=""
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elif [ "$ARCH" = "i686" ]; then
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SLKCFLAGS="-O2 -march=i686 -mtune=i686"
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LIBDIRSUFFIX=""
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elif [ "$ARCH" = "x86_64" ]; then
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SLKCFLAGS="-O2 -fPIC"
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LIBDIRSUFFIX="64"
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else
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SLKCFLAGS="-O2"
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LIBDIRSUFFIX=""
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fi
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set -e
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rm -rf $PKG
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mkdir -p $TMP $PKG $OUTPUT
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cd $TMP
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rm -rf gp-$VERSION
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tar xvf $CWD/gp-$VERSION.tgz
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cd gp-$VERSION
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chown -R root:root .
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find . \
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\( -perm 777 -o -perm 775 -o -perm 711 -o -perm 555 -o -perm 511 \) \
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-exec chmod 755 {} \; -o \
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\( -perm 666 -o -perm 664 -o -perm 600 -o -perm 444 -o -perm 440 -o -perm 400 \) \
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-exec chmod 644 {} \;
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#Use our CFLAGS
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sed -i "/^CFLAGS/s/=/+=/" Makefile
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CFLAGS="$SLKCFLAGS" \
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CXXFLAGS="$SLKCFLAGS" \
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make
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# Makefile does not support "make DESTDIR install". So...
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cd ./src
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install -D -m755 gp_acc $PKG/usr/bin/gp_acc
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install -D -m755 gp_adjust $PKG/usr/bin/gp_adjust
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install -D -m755 gp_cdndev $PKG/usr/bin/gp_cdndev
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install -D -m755 gp_cusage $PKG/usr/bin/gp_cusage
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install -D -m755 gp_digest $PKG/usr/bin/gp_digest
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install -D -m755 gp_dimer $PKG/usr/bin/gp_dimer
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install -D -m755 gp_findorf $PKG/usr/bin/gp_findorf
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install -D -m755 gp_getseq $PKG/usr/bin/gp_getseq
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install -D -m755 gp_matrix $PKG/usr/bin/gp_matrix
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install -D -m755 gp_mkmtx $PKG/usr/bin/gp_mkmtx
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install -D -m755 gp_pars $PKG/usr/bin/gp_pars
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install -D -m755 gp_pattern $PKG/usr/bin/gp_pattern
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install -D -m755 gp_primer $PKG/usr/bin/gp_primer
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install -D -m755 gp_qs $PKG/usr/bin/gp_qs
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install -D -m755 gp_randseq $PKG/usr/bin/gp_randseq
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install -D -m755 gp_scan $PKG/usr/bin/gp_scan
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install -D -m755 gp_seq2prot $PKG/usr/bin/gp_seq2prot
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install -D -m755 gp_shift $PKG/usr/bin/gp_shift
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install -D -m755 gp_slen $PKG/usr/bin/gp_slen
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install -D -m755 gp_tm $PKG/usr/bin/gp_tm
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install -D -m755 gp_trimer $PKG/usr/bin/gp_trimer
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cd ../data
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install -D -m644 ecoli.mtx $PKG/usr/lib/genpak/ecoli.mtx
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install -D -m644 enzyme.enz $PKG/usr/lib/genpak/enzyme.enz
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install -D -m644 myco.cdn $PKG/usr/lib/genpak/myco.cdn
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install -D -m644 sample.seq $PKG/usr/lib/genpak/sample.seq
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install -D -m644 standard.cdn $PKG/usr/lib/genpak/standard.cdn
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install -D -m644 mporfs.seq $PKG/usr/lib/genpak/mporfs.seq
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# Put man pages to their proper place
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mkdir -p $PKG/usr/man/man1
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cp ../man1/* $PKG/usr/man/man1
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cd ..
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find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \
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| cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true
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find $PKG/usr/man -type f -exec gzip -9 {} \;
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for i in $( find $PKG/usr/man -type l ) ; do ln -s $( readlink $i ).gz $i.gz ; rm $i ; done
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mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION
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cp -a \
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CHANGES.TXT INSTALL.TXT LICENSE.TXT README.TXT \
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$PKG/usr/doc/$PRGNAM-$VERSION/
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cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild
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mkdir -p $PKG/install
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cat $CWD/slack-desc > $PKG/install/slack-desc
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cd $PKG
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/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz}
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10
academic/genpak/genpak.info
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10
academic/genpak/genpak.info
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PRGNAM="genpak"
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VERSION="0.26"
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HOMEPAGE="http://www.bioinformatics.org/genpak/"
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DOWNLOAD="http://www.bioinformatics.org/genpak/download/gp-0.26.tgz"
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MD5SUM="34e2942ff6b27eeb6116b9dea87285b6"
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DOWNLOAD_x86_64=""
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MD5SUM_x86_64=""
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MAINTAINER="Petar Petrov"
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EMAIL="ppetrov@paju.oulu.fi"
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APPROVED="Niels Horn"
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19
academic/genpak/slack-desc
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19
academic/genpak/slack-desc
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# HOW TO EDIT THIS FILE:
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# The "handy ruler" below makes it easier to edit a package description. Line
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# up the first '|' above the ':' following the base package name, and the '|'
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# on the right side marks the last column you can put a character in. You must
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# make exactly 11 lines for the formatting to be correct. It's also
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# customary to leave one space after the ':'.
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|-----handy-ruler------------------------------------------------------|
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genpak: genpak (Utilities to manipulate DNA sequences)
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genpak:
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genpak: Genpak is a set of small utilities written in ANSI C to manipulate
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genpak: DNA sequences in a Unix fashion, fit for combining within shell
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genpak: and cgi scripts.
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genpak:
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genpak:
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genpak:
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genpak:
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genpak:
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genpak: Home: http://www.bioinformatics.org/genpak/
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