diff options
Diffstat (limited to 'academic/genpak')
| -rw-r--r-- | academic/genpak/README | 3 | ||||
| -rw-r--r-- | academic/genpak/genpak.SlackBuild | 101 | ||||
| -rw-r--r-- | academic/genpak/genpak.info | 2 | ||||
| -rw-r--r-- | academic/genpak/slack-desc | 2 |
4 files changed, 43 insertions, 65 deletions
diff --git a/academic/genpak/README b/academic/genpak/README index 583261ae98804..6b257d0ebe28c 100644 --- a/academic/genpak/README +++ b/academic/genpak/README @@ -6,5 +6,4 @@ 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. +You most likely want to install Arka, which provides a GUI for GenPak. diff --git a/academic/genpak/genpak.SlackBuild b/academic/genpak/genpak.SlackBuild index 84509b70853d4..87c2f2c2dff25 100644 --- a/academic/genpak/genpak.SlackBuild +++ b/academic/genpak/genpak.SlackBuild @@ -1,16 +1,30 @@ #!/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. +# Copyright 2011 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=genpak VERSION=${VERSION:-0.26} -BUILD=${BUILD:-3} +BUILD=${BUILD:-4} TAG=${TAG:-_SBo} if [ -z "$ARCH" ]; then @@ -55,57 +69,25 @@ find . \ \( -perm 666 -o -perm 664 -o -perm 600 -o -perm 444 -o -perm 440 -o -perm 400 \) \ -exec chmod 644 {} \; -# Use our CFLAGS -sed -i "/^CFLAGS/s/=/+=/" Makefile - -# Correct libdir -sed -i "s:/lib:/lib${LIBDIRSUFFIX}:" Makefile -sed -i "s:/lib:/lib${LIBDIRSUFFIX}:" src/genpak.c -sed -i "s:/lib:/lib${LIBDIRSUFFIX}:" src/genpak.h - -CFLAGS="$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_gc $PKG/usr/bin/gp_gc -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 $PKG/usr/lib${LIBDIRSUFFIX}/genpak/ecoli.mtx -install -D -m644 enzyme.enz $PKG/usr/lib${LIBDIRSUFFIX}/genpak/enzyme.enz -install -D -m644 myco.cdn $PKG/usr/lib${LIBDIRSUFFIX}/genpak/myco.cdn -install -D -m644 myco.mtx $PKG/usr/lib${LIBDIRSUFFIX}/genpak/myco.mtx -install -D -m644 myco0 $PKG/usr/lib${LIBDIRSUFFIX}/genpak/myco0 -install -D -m644 sample.seq $PKG/usr/lib${LIBDIRSUFFIX}/genpak/sample.seq -install -D -m644 standard.cdn $PKG/usr/lib${LIBDIRSUFFIX}/genpak/standard.cdn -install -D -m644 mporfs.seq $PKG/usr/lib${LIBDIRSUFFIX}/genpak/mporfs.seq - -# Put man pages to their proper place -mkdir -p $PKG/usr/man/man1 -cp ../man1/* $PKG/usr/man/man1 -cd .. +# arch-independent data files belong in /usr/share: +sed -i "s,usr/lib/,usr/share/,g" src/* man1/* html/* *.TXT + +make \ + CFLAGS="$SLKCFLAGS" \ + TREE=/usr \ + BINDIR=/usr/bin \ + DATADIR=/usr/share \ + MANDIR=/usr/man \ + DOCDIR=/usr/doc + +mkdir -p $PKG/usr/{bin,doc,man/man1,share} + +make install docs \ + TREE=$PKG/usr \ + BINDIR=$PKG/usr/bin \ + DATADIR=$PKG/usr/share \ + MANDIR=$PKG/usr/man \ + DOCDIR=$PKG/usr/doc 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 @@ -113,10 +95,7 @@ find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | gr 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 \ - html CHANGES.TXT INSTALL.TXT LICENSE.TXT README.TXT \ - $PKG/usr/doc/$PRGNAM-$VERSION/ +( cd $PKG/usr/doc ; mv gp $PRGNAM-$VERSION ; ln -s $PRGNAM-$VERSION gp ) cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild mkdir -p $PKG/install diff --git a/academic/genpak/genpak.info b/academic/genpak/genpak.info index 4f0075bb345ea..061fbac137afe 100644 --- a/academic/genpak/genpak.info +++ b/academic/genpak/genpak.info @@ -7,4 +7,4 @@ DOWNLOAD_x86_64="" MD5SUM_x86_64="" MAINTAINER="Petar Petrov" EMAIL="ppetrov@paju.oulu.fi" -APPROVED="Erik Hanson,Niels Horn" +APPROVED="rworkman" diff --git a/academic/genpak/slack-desc b/academic/genpak/slack-desc index f36088d51d350..3a977f2c67291 100644 --- a/academic/genpak/slack-desc +++ b/academic/genpak/slack-desc @@ -12,8 +12,8 @@ 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: Home: http://www.bioinformatics.org/genpak/ genpak: genpak: genpak: genpak: -genpak: Home: http://www.bioinformatics.org/genpak/ |