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author Petar Petrov <slackalaxy@gmail.com>2016-11-26 21:19:25 +0000
committer Willy Sudiarto Raharjo <willysr@slackbuilds.org>2016-12-03 07:17:45 +0700
commit8d79c453ce84a7b17a6c78f14cd474bb3b23d5eb (patch)
tree5bd0e686add7bcfef23ed52e373115e4b334a578 /academic
parente3ea54d6f0b05cf4c859d53cc2ab1e095672a20d (diff)
downloadslackbuilds-8d79c453ce84a7b17a6c78f14cd474bb3b23d5eb.tar.gz
slackbuilds-8d79c453ce84a7b17a6c78f14cd474bb3b23d5eb.tar.xz
academic/bwa: Updated for version 0.7.15.
Signed-off-by: David Spencer <idlemoor@slackbuilds.org>
Diffstat (limited to 'academic')
-rw-r--r--academic/bwa/README16
-rw-r--r--academic/bwa/bwa.SlackBuild8
-rw-r--r--academic/bwa/bwa.info6
-rw-r--r--academic/bwa/slack-desc2
4 files changed, 18 insertions, 14 deletions
diff --git a/academic/bwa/README b/academic/bwa/README
index fe07da7e2d..a77a28a8e4 100644
--- a/academic/bwa/README
+++ b/academic/bwa/README
@@ -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 $HOME. An example configuration file is available in
+/usr/share/archeopteryx.
If you use BWA-SW, please cite:
Li H. and Durbin R. (2010) Fast and accurate long-read alignment with
diff --git a/academic/bwa/bwa.SlackBuild b/academic/bwa/bwa.SlackBuild
index 94e53adc12..07c804c70b 100644
--- a/academic/bwa/bwa.SlackBuild
+++ b/academic/bwa/bwa.SlackBuild
@@ -23,13 +23,13 @@
# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
PRGNAM=bwa
-VERSION=${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"
diff --git a/academic/bwa/bwa.info b/academic/bwa/bwa.info
index b401afd98c..1e94df0cc0 100644
--- a/academic/bwa/bwa.info
+++ b/academic/bwa/bwa.info
@@ -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=""
diff --git a/academic/bwa/slack-desc b/academic/bwa/slack-desc
index 976bf7677e..361afb74c3 100644
--- a/academic/bwa/slack-desc
+++ b/academic/bwa/slack-desc
@@ -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: