mirror of
https://github.com/Ponce/slackbuilds
synced 2024-11-22 19:44:21 +01:00
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
|
|
@ -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.
|
||||
|
|
|
|||
|
|
@ -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${LIBDIRSUFFIX}:" src/genpak.h
|
||||
# arch-independent data files belong in /usr/share:
|
||||
sed -i "s,usr/lib/,usr/share/,g" src/* man1/* html/* *.TXT
|
||||
|
||||
make \
|
||||
CFLAGS="$SLKCFLAGS" \
|
||||
CXXFLAGS="$SLKCFLAGS" \
|
||||
make
|
||||
TREE=/usr \
|
||||
BINDIR=/usr/bin \
|
||||
DATADIR=/usr/share \
|
||||
MANDIR=/usr/man \
|
||||
DOCDIR=/usr/doc
|
||||
|
||||
# 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
|
||||
mkdir -p $PKG/usr/{bin,doc,man/man1,share}
|
||||
|
||||
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/* $PKG/usr/man/man1
|
||||
cd ..
|
||||
make install docs \
|
||||
TREE=$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
|
||||
|
|
|
|||
|
|
@ -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"
|
||||
|
|
|
|||
|
|
@ -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:
|
||||
genpak:
|
||||
genpak:
|
||||
genpak:
|
||||
genpak: Home: http://www.bioinformatics.org/genpak/
|
||||
genpak:
|
||||
genpak:
|
||||
genpak:
|
||||
genpak:
|
||||
|
|
|
|||
Loading…
Reference in a new issue