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| -rw-r--r-- | academic/genpak/README | 10 | ||||
| -rw-r--r-- | academic/genpak/genpak.SlackBuild | 118 | ||||
| -rw-r--r-- | academic/genpak/genpak.info | 10 | ||||
| -rw-r--r-- | academic/genpak/slack-desc | 19 |
4 files changed, 157 insertions, 0 deletions
diff --git a/academic/genpak/README b/academic/genpak/README new file mode 100644 index 0000000000..39ec806ab9 --- /dev/null +++ b/academic/genpak/README @@ -0,0 +1,10 @@ +The GenPak (GP) package contains many command-line utilities which +fullfill a whole bunch of tasks, from DNA sequence searches to +restriction analysis and determining the melting temperature of +oligonucleotides. GP utilities can convert DNA / RNA to protein, +determine codon usage / GC contents, do promotor searches, calculate +Tm, search for restriction sites, convert sequences into numerical +representations and much more. + +You most likely want to install arka, which provides a GUI for genpak. +arka is also available at SlackBuilds.org. diff --git a/academic/genpak/genpak.SlackBuild b/academic/genpak/genpak.SlackBuild new file mode 100644 index 0000000000..37a42407ac --- /dev/null +++ b/academic/genpak/genpak.SlackBuild @@ -0,0 +1,118 @@ +#!/bin/sh + +# Slackware build script for genpak +# Written by Petar Petrov, <ppetrov@paju.oulu.fi> and +# hereby submitted to the public domain + +# THIS SLACKBUILD IS DISTRIBUTETD IN THE HOPE OF BEING +# USEFUL BUT WITHOUT ANY WARRANTY. THE AUTHOR IS _NOT_ +# RESPONSIBLE FOR ANY DAMAGE OR DATA LOSS CAUSED BY IT. + +PRGNAM=genpak +VERSION=${VERSION:-0.26} +BUILD=${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 $TMP +rm -rf gp-$VERSION +tar xvf $CWD/gp-$VERSION.tgz +cd gp-$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 {} \; + +#Use our CFLAGS +sed -i "/^CFLAGS/s/=/+=/" Makefile + +CFLAGS="$SLKCFLAGS" \ +CXXFLAGS="$SLKCFLAGS" \ + make + +# Makefile does not support "make DESTDIR install". So... +cd ./src +install -D -m755 gp_acc $PKG/usr/bin/gp_acc +install -D -m755 gp_adjust $PKG/usr/bin/gp_adjust +install -D -m755 gp_cdndev $PKG/usr/bin/gp_cdndev +install -D -m755 gp_cusage $PKG/usr/bin/gp_cusage +install -D -m755 gp_digest $PKG/usr/bin/gp_digest +install -D -m755 gp_dimer $PKG/usr/bin/gp_dimer +install -D -m755 gp_findorf $PKG/usr/bin/gp_findorf +install -D -m755 gp_getseq $PKG/usr/bin/gp_getseq +install -D -m755 gp_matrix $PKG/usr/bin/gp_matrix +install -D -m755 gp_mkmtx $PKG/usr/bin/gp_mkmtx +install -D -m755 gp_pars $PKG/usr/bin/gp_pars +install -D -m755 gp_pattern $PKG/usr/bin/gp_pattern +install -D -m755 gp_primer $PKG/usr/bin/gp_primer +install -D -m755 gp_qs $PKG/usr/bin/gp_qs +install -D -m755 gp_randseq $PKG/usr/bin/gp_randseq +install -D -m755 gp_scan $PKG/usr/bin/gp_scan +install -D -m755 gp_seq2prot $PKG/usr/bin/gp_seq2prot +install -D -m755 gp_shift $PKG/usr/bin/gp_shift +install -D -m755 gp_slen $PKG/usr/bin/gp_slen +install -D -m755 gp_tm $PKG/usr/bin/gp_tm +install -D -m755 gp_trimer $PKG/usr/bin/gp_trimer + +cd ../data +install -D -m644 ecoli.mtx $PKG/usr/lib/genpak/ecoli.mtx +install -D -m644 enzyme.enz $PKG/usr/lib/genpak/enzyme.enz +install -D -m644 myco.cdn $PKG/usr/lib/genpak/myco.cdn +install -D -m644 sample.seq $PKG/usr/lib/genpak/sample.seq +install -D -m644 standard.cdn $PKG/usr/lib/genpak/standard.cdn +install -D -m644 mporfs.seq $PKG/usr/lib/genpak/mporfs.seq + +# Put man pages to their proper place +mkdir -p $PKG/usr/man/man1 +cp ../man1/* $PKG/usr/man/man1 +cd .. + +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 \ + CHANGES.TXT INSTALL.TXT LICENSE.TXT README.TXT \ + $PKG/usr/doc/$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/genpak/genpak.info b/academic/genpak/genpak.info new file mode 100644 index 0000000000..0a3511afad --- /dev/null +++ b/academic/genpak/genpak.info @@ -0,0 +1,10 @@ +PRGNAM="genpak" +VERSION="0.26" +HOMEPAGE="http://www.bioinformatics.org/genpak/" +DOWNLOAD="http://www.bioinformatics.org/genpak/download/gp-0.26.tgz" +MD5SUM="34e2942ff6b27eeb6116b9dea87285b6" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +MAINTAINER="Petar Petrov" +EMAIL="ppetrov@paju.oulu.fi" +APPROVED="Niels Horn" diff --git a/academic/genpak/slack-desc b/academic/genpak/slack-desc new file mode 100644 index 0000000000..4df3bad496 --- /dev/null +++ b/academic/genpak/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 ':'. + + |-----handy-ruler------------------------------------------------------| +genpak: genpak (Utilities to manipulate DNA sequences) +genpak: +genpak: Genpak is a set of small utilities written in ANSI C to manipulate +genpak: DNA sequences in a Unix fashion, fit for combining within shell +genpak: and cgi scripts. +genpak: +genpak: +genpak: +genpak: +genpak: +genpak: Home: http://www.bioinformatics.org/genpak/
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