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academic/bwa: Updated for version 0.7.15.

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Signed-off-by: David Spencer <idlemoor@slackbuilds.org>
This commit is contained in:
Petar Petrov 2016-11-26 21:19:25 +00:00 committed by Willy Sudiarto Raharjo
parent e3ea54d6f0
commit 8d79c453ce
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GPG key ID: 887B8374D7333381
4 changed files with 18 additions and 14 deletions
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16
academic/bwa/README
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@ -1,10 +1,14 @@
Burrows-Wheeler Aligner (BWA) is an efficient program that aligns
relatively short nucleotide sequences against a long reference
sequence such as the human genome. It implements two algorithms, bwa-
short and BWA-SW. The former works for query sequences shorter than
200bp and the latter for longer sequences up to around 100kbp. Both
algorithms do gapped alignment. They are usually more accurate and
faster on queries with low error rates.
relatively short nucleotide sequences against a long reference sequence
such as the human genome. It implements two algorithms, bwa-short and
BWA-SW. The former works for query sequences shorter than 200bp and the
latter for longer sequences up to around 100kbp. Both algorithms do
gapped alignment. They are usually more accurate and faster on queries
with low error rates.
A configuration file ("_aptx_configuration_file") will be used if it is
in your $HOME. An example configuration file is available in
/usr/share/archeopteryx.
If you use BWA-SW, please cite:
Li H. and Durbin R. (2010) Fast and accurate long-read alignment with

8
academic/bwa/bwa.SlackBuild
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@ -23,13 +23,13 @@
# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
PRGNAM=bwa
VERSION=${VERSION:-0.7.13}
VERSION=${VERSION:-0.7.15}
BUILD=${BUILD:-1}
TAG=${TAG:-_SBo}
if [ -z "$ARCH" ]; then
case "$( uname -m )" in
i?86) ARCH=i486 ;;
i?86) ARCH=i586 ;;
arm*) ARCH=arm ;;
*) ARCH=$( uname -m ) ;;
esac
@ -40,8 +40,8 @@ TMP=${TMP:-/tmp/SBo}
PKG=$TMP/package-$PRGNAM
OUTPUT=${OUTPUT:-/tmp}
if [ "$ARCH" = "i486" ]; then
SLKCFLAGS="-O2 -march=i486 -mtune=i686"
if [ "$ARCH" = "i586" ]; then
SLKCFLAGS="-O2 -march=i586 -mtune=i686"
LIBDIRSUFFIX=""
elif [ "$ARCH" = "i686" ]; then
SLKCFLAGS="-O2 -march=i686 -mtune=i686"

6
academic/bwa/bwa.info
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@ -1,8 +1,8 @@
PRGNAM="bwa"
VERSION="0.7.13"
VERSION="0.7.15"
HOMEPAGE="http://bio-bwa.sourceforge.net/"
DOWNLOAD="http://sourceforge.net/projects/bio-bwa/files/bwa-0.7.13.tar.bz2"
MD5SUM="f094f609438511766c434178a3635ab4"
DOWNLOAD="https://sourceforge.net/projects/bio-bwa/files/bwa-0.7.15.tar.bz2"
MD5SUM="fcf470a46a1dbe2f96a1c5b87c530554"
DOWNLOAD_x86_64=""
MD5SUM_x86_64=""
REQUIRES=""

2
academic/bwa/slack-desc
View file

@ -15,5 +15,5 @@ bwa: bwa-short and BWA-SW. The former works for query sequences shorter
bwa: than 200bp and the latter for longer sequences up to around 100kbp.
bwa:
bwa: Home: http://bio-bwa.sourceforge.net/
bwa: References: /usr/doc/bwa-0.7.13/References
bwa: References: /usr/doc/bwa-0.7.15/References
bwa: