diff options
Diffstat (limited to 'academic/bwa')
| -rw-r--r-- | academic/bwa/README | 16 | ||||
| -rw-r--r-- | academic/bwa/bwa.SlackBuild | 8 | ||||
| -rw-r--r-- | academic/bwa/bwa.info | 6 | ||||
| -rw-r--r-- | academic/bwa/slack-desc | 2 |
4 files changed, 18 insertions, 14 deletions
diff --git a/academic/bwa/README b/academic/bwa/README index fe07da7e2dfa6..a77a28a8e410c 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 $HOME. An example configuration file is available in +/usr/share/archeopteryx. If you use BWA-SW, please cite: Li H. and Durbin R. (2010) Fast and accurate long-read alignment with diff --git a/academic/bwa/bwa.SlackBuild b/academic/bwa/bwa.SlackBuild index 94e53adc124df..07c804c70bccc 100644 --- a/academic/bwa/bwa.SlackBuild +++ b/academic/bwa/bwa.SlackBuild @@ -23,13 +23,13 @@ # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. PRGNAM=bwa -VERSION=${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 b401afd98ca3d..1e94df0cc06b2 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 976bf7677e03e..361afb74c3799 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: |