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-rw-r--r--academic/genpak/README3
-rw-r--r--academic/genpak/genpak.SlackBuild101
-rw-r--r--academic/genpak/genpak.info2
-rw-r--r--academic/genpak/slack-desc2
4 files changed, 43 insertions, 65 deletions
diff --git a/academic/genpak/README b/academic/genpak/README
index 583261ae98..6b257d0ebe 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 84509b7085..87c2f2c2df 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 4f0075bb34..061fbac137 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 f36088d51d..3a977f2c67 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/