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academic/genpak: Various packaging fixes
Signed-off-by: Robby Workman <rworkman@slackbuilds.org>
This commit is contained in:
Robby Workman
Niels Horn
parent
f125550a7f
commit
66716e78f6
4 changed files with 43 additions and 65 deletions
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@ -6,5 +6,4 @@ 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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You most likely want to install Arka, which provides a GUI for GenPak.
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@ -1,16 +1,30 @@
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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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# Copyright 2011 Petar Petrov, ppetrov@paju.oulu.fi
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# All rights reserved.
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#
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# Redistribution and use of this script, with or without modification, is
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# permitted provided that the following conditions are met:
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#
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# 1. Redistributions of this script must retain the above copyright
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# notice, this list of conditions and the following disclaimer.
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#
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# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED
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# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF
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# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO
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# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
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# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
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# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
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# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
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# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
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# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
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# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
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PRGNAM=genpak
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VERSION=${VERSION:-0.26}
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BUILD=${BUILD:-3}
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BUILD=${BUILD:-4}
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TAG=${TAG:-_SBo}
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if [ -z "$ARCH" ]; then
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@ -55,57 +69,25 @@ find . \
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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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# arch-independent data files belong in /usr/share:
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sed -i "s,usr/lib/,usr/share/,g" src/* man1/* html/* *.TXT
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# Correct libdir
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sed -i "s:/lib:/lib${LIBDIRSUFFIX}:" Makefile
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sed -i "s:/lib:/lib${LIBDIRSUFFIX}:" src/genpak.c
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sed -i "s:/lib:/lib${LIBDIRSUFFIX}:" src/genpak.h
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make \
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CFLAGS="$SLKCFLAGS" \
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TREE=/usr \
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BINDIR=/usr/bin \
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DATADIR=/usr/share \
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MANDIR=/usr/man \
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DOCDIR=/usr/doc
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CFLAGS="$SLKCFLAGS" \
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CXXFLAGS="$SLKCFLAGS" \
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make
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mkdir -p $PKG/usr/{bin,doc,man/man1,share}
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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_gc $PKG/usr/bin/gp_gc
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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 $PKG/usr/lib${LIBDIRSUFFIX}/genpak/ecoli.mtx
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install -D -m644 enzyme.enz $PKG/usr/lib${LIBDIRSUFFIX}/genpak/enzyme.enz
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install -D -m644 myco.cdn $PKG/usr/lib${LIBDIRSUFFIX}/genpak/myco.cdn
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install -D -m644 myco.mtx $PKG/usr/lib${LIBDIRSUFFIX}/genpak/myco.mtx
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install -D -m644 myco0 $PKG/usr/lib${LIBDIRSUFFIX}/genpak/myco0
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install -D -m644 sample.seq $PKG/usr/lib${LIBDIRSUFFIX}/genpak/sample.seq
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install -D -m644 standard.cdn $PKG/usr/lib${LIBDIRSUFFIX}/genpak/standard.cdn
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install -D -m644 mporfs.seq $PKG/usr/lib${LIBDIRSUFFIX}/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/* $PKG/usr/man/man1
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cd ..
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make install docs \
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TREE=$PKG/usr \
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BINDIR=$PKG/usr/bin \
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DATADIR=$PKG/usr/share \
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MANDIR=$PKG/usr/man \
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DOCDIR=$PKG/usr/doc
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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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@ -113,10 +95,7 @@ find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | gr
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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-$VERSION
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cp -a \
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html CHANGES.TXT INSTALL.TXT LICENSE.TXT README.TXT \
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$PKG/usr/doc/$PRGNAM-$VERSION/
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( cd $PKG/usr/doc ; mv gp $PRGNAM-$VERSION ; ln -s $PRGNAM-$VERSION gp )
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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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@ -7,4 +7,4 @@ 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="Erik Hanson,Niels Horn"
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APPROVED="rworkman"
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@ -12,8 +12,8 @@ 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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genpak:
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genpak:
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genpak:
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genpak:
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