academic/genpak: Added (Utilities to manipulate DNA sequences)

Signed-off-by: Niels Horn <niels.horn@slackbuilds.org>

4 files changed, 157 insertions, 0 deletions

diff --git a/academic/genpak/README b/academic/genpak/README
new file mode 100644
index 0000000000000..39ec806ab900c
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+++ 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 0000000000000..37a42407ace6d
--- /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 0000000000000..0a3511afad75b
--- /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 0000000000000..4df3bad49610b
--- /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/
\ No newline at end of file