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| -rw-r--r-- | academic/cap3/LICENSE | 9 | ||||
| -rw-r--r-- | academic/cap3/README | 14 | ||||
| -rw-r--r-- | academic/cap3/References | 3 | ||||
| -rw-r--r-- | academic/cap3/cap3.SlackBuild | 92 | ||||
| -rw-r--r-- | academic/cap3/cap3.info | 10 | ||||
| -rw-r--r-- | academic/cap3/slack-desc | 19 |
6 files changed, 147 insertions, 0 deletions
diff --git a/academic/cap3/LICENSE b/academic/cap3/LICENSE new file mode 100644 index 0000000000..06e153b3fa --- /dev/null +++ b/academic/cap3/LICENSE @@ -0,0 +1,9 @@ +CAP3 and PCAP are freely available for use at non-profit +organizations. + +CAP3 and PCAP are available for use at company under a +licensing agreement from Michigan Tech. +For information on a licensing agreement, please contact +Robin Kolehmainen by email at rakolehm@mtu.edu or by +phone at 906-487-2228. Michigan Tech handles licensing +agreements on PCAP for Iowa State. diff --git a/academic/cap3/README b/academic/cap3/README new file mode 100644 index 0000000000..62792bb4c7 --- /dev/null +++ b/academic/cap3/README @@ -0,0 +1,14 @@ +CAP3: A DNA sequence assembly program. + +CAP3 if the third generation of the CAP sequence assembly program. The +program has a capability to clip 5' and 3' low-quality regions of reads. +It uses base quality values in computation of overlaps between reads, +construction of multiple sequence alignments of reads, and generation +of consensus sequences. The program also uses forward-reverse constraints +to correct assembly errors and link contigs. + +This just repackages the binaries provided from upstream. + +If you use CAP3 in any published work, please cite: +Huang, X. and Madan, A. (1999) CAP3: A DNA sequence assembly program. +Genome Res., 9, 868-877. diff --git a/academic/cap3/References b/academic/cap3/References new file mode 100644 index 0000000000..cdcda85dd0 --- /dev/null +++ b/academic/cap3/References @@ -0,0 +1,3 @@ +If you use CAP3 in any published work, please cite: +Huang, X. and Madan, A. (1999) CAP3: A DNA sequence assembly program. +Genome Res., 9, 868-877. diff --git a/academic/cap3/cap3.SlackBuild b/academic/cap3/cap3.SlackBuild new file mode 100644 index 0000000000..0a18de25cf --- /dev/null +++ b/academic/cap3/cap3.SlackBuild @@ -0,0 +1,92 @@ +#!/bin/sh + +# Slackware build script for cap3 + +# Copyright 2013 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=cap3 +VERSION=${VERSION:-20091029} # Use the last modification date as version +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i386 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +CWD=$(pwd) +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +set -e + +if [ "$ARCH" != "i386" ] && [ "$ARCH" != "x86_64" ]; then + printf "\n\n$ARCH is not supported... \n" + exit 1 +fi + +# Determine the tarball arch +if [ "$ARCH" = "x86_64" ]; then + SRCARCH=".opteron64" +else + SRCARCH="" +fi + +# Construct tarball name +TARNAME=${PRGNAM}.linux${SRCARCH} +DIRNAM=CAP3 + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP +rm -fr $DIRNAM +tar xvf $CWD/$TARNAME.tar +cd $DIRNAM +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 {} \; + +install -D -m755 $PRGNAM $PKG/usr/bin/$PRGNAM +install -D -m755 formcon $PKG/usr/bin/formcon + +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 + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp -a \ + aceform doc README \ + $PKG/usr/doc/$PRGNAM-$VERSION +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild +cat $CWD/References > $PKG/usr/doc/$PRGNAM-$VERSION/References +cat $CWD/LICENSE > $PKG/usr/doc/$PRGNAM-$VERSION/LICENSE + +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.${PKGTYPE:-tgz} diff --git a/academic/cap3/cap3.info b/academic/cap3/cap3.info new file mode 100644 index 0000000000..c0186331d1 --- /dev/null +++ b/academic/cap3/cap3.info @@ -0,0 +1,10 @@ +PRGNAM="cap3" +VERSION="20091029" +HOMEPAGE="http://seq.cs.iastate.edu/" +DOWNLOAD="http://seq.cs.iastate.edu/CAP3/cap3.linux.tar" +MD5SUM="55f57f61e588d4de06c0506cf2696c29" +DOWNLOAD_x86_64="http://seq.cs.iastate.edu/CAP3/cap3.linux.opteron64.tar" +MD5SUM_x86_64="2d924766f6e8b5cf03bd2db81016d821" +REQUIRES="" +MAINTAINER="Petar Petrov" +EMAIL="ppetrov@paju.oulu.fi" diff --git a/academic/cap3/slack-desc b/academic/cap3/slack-desc new file mode 100644 index 0000000000..8940c92865 --- /dev/null +++ b/academic/cap3/slack-desc @@ -0,0 +1,19 @@ +# HOW TO EDIT THIS FILE: +# The "handy ruler" below makes it easier to edit a package description. +# Line up the first '|' above the ':' following the base package name, and +# the '|' on the right side marks the last column you can put a character in. +# You must make exactly 11 lines for the formatting to be correct. It's also +# customary to leave one space after the ':' except on otherwise blank lines. + + |-----handy-ruler------------------------------------------------------| +cap3: cap3 (CAP3: A DNA sequence assembly program) +cap3: +cap3: CAP3 if the third generation of the CAP sequence assembly program. +cap3: The program has a capability to clip 5' and 3' low-quality regions +cap3: of reads. It uses base quality values in computation of overlaps +cap3: between reads, construction of multiple sequence alignments of reads, +cap3: and generation of consensus sequences. +cap3: +cap3: Home: http://seq.cs.iastate.edu/ +cap3: References: /usr/doc/cap3-$VERSION/References +cap3: |