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academic/aliview: Updated for version 1.23.

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Signed-off-by: David Spencer <idlemoor@slackbuilds.org>
This commit is contained in:
Petar Petrov 2018-06-17 22:44:42 +01:00 committed by David Spencer
parent 1861748c09
commit a43d2d2e51
4 changed files with 31 additions and 33 deletions
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42
academic/aliview/README
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@ -1,36 +1,36 @@
AliView is yet another alignment viewer and editor, but this is
probably one of the fastest and most intuitive to use. Features:
- fast and light-weight
- fast and light-weight
- simple navigation, mouse-wheel zoom out and zoom in
- highlight consensus characters or characters deviating
- edit sequences/alignment (manually)
- align, add and align automatically with any aligner of your choice
- align new sequences to existing or realign all
- realign a selected block
- realign nucleotides as translated amino-acids
- delete vertical gaps
- undo/redo
- align, add and align automatically with any aligner of your choice
- align new sequences to existing or realign all
- realign a selected block
- realign nucleotides as translated amino-acids
- delete vertical gaps
- undo/redo
- find degenerate primers in conserved regions in an alignment
- open and save in FASTA, NEXUS, PHYLIP, CLUSTAL or MSF format
- print (current view)
- export whole alignment as an image file (png-format)
- copy selection (as fasta-sequences or just characters)
- paste sequences (as sequences or filenames)
- add more sequences from file
- print (current view)
- export whole alignment as an image file (png-format)
- copy selection (as fasta-sequences or just characters)
- paste sequences (as sequences or filenames)
- add more sequences from file
- merge two sequences - and calculate consensus
- translate (view) nucleotide sequences as amino-acid sequences
- save translated alignment
- read / preserve Codonpos, Charset and Excludes (Nexus-specification)
- change Codonpos for selected regions (Nexus-specification)
- drag-drop/remove of sequences/files
- move sequences to top/bottom with key-stroke
- translate (view) nucleotide sequences as amino-acid sequences
- save translated alignment
- read / preserve Codonpos, Charset and Excludes (Nexus-specification)
- change Codonpos for selected regions (Nexus-specification)
- drag-drop/remove of sequences/files
- move sequences to top/bottom with key-stroke
- a simple "external interface" that lets you invoke other programs
- search function that finds patterns across gaps and follows IUPAC
- search multiple sequence names at once (stored in clipboard)
- reverse complement/reverse/complement sequences or whole alignment
- search multiple sequence names at once (stored in clipboard)
- reverse complement/reverse/complement sequences or whole alignment
- different color schemes
- sort sequences by name
- sort sequences by name
- sort sequences by residue in selected column
Citation:

3
academic/aliview/References Normal file
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@ -0,0 +1,3 @@
Larsson, A. (2014). AliView: a fast and lightweight alignment viewer
and editor for large data sets. Bioinformatics30(22): 3276-3278.
http://dx.doi.org/10.1093/bioinformatics/btu531

13
academic/aliview/aliview.SlackBuild
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@ -23,18 +23,10 @@
# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
PRGNAM=aliview
VERSION=${VERSION:-1.21}
VERSION=${VERSION:-1.23}
BUILD=${BUILD:-1}
TAG=${TAG:-_SBo}
if [ -z "$ARCH" ]; then
case "$( uname -m )" in
i?86) ARCH=i586 ;;
arm*) ARCH=arm ;;
*) ARCH=$( uname -m ) ;;
esac
fi
CWD=$(pwd)
TMP=${TMP:-/tmp/SBo}
PKG=$TMP/package-$PRGNAM
@ -51,6 +43,8 @@ rm -rf $PRGNAM-$VERSION
mkdir $PRGNAM-$VERSION
cd $PRGNAM-$VERSION
tar xvf $CWD/$PRGNAM.tgz
cd $PRGNAM
chown -R root:root .
find -L . \
\( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \
@ -73,6 +67,7 @@ cp aliicon_128x128.png $PKG/usr/share/pixmaps/$PRGNAM.png
mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION
cp -a install.readme.txt README.txt $PKG/usr/doc/$PRGNAM-$VERSION
cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild
cat $CWD/References > $PKG/usr/doc/$PRGNAM-$VERSION/References
mkdir -p $PKG/install
cat $CWD/slack-desc > $PKG/install/slack-desc

6
academic/aliview/aliview.info
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@ -1,8 +1,8 @@
PRGNAM="aliview"
VERSION="1.21"
VERSION="1.23"
HOMEPAGE="http://www.ormbunkar.se/aliview/"
DOWNLOAD="http://www.ormbunkar.se/aliview/downloads/linux/linux-version-1.21/aliview.tgz"
MD5SUM="9b04979a88a5cae94d9b1580e9aa2f7a"
DOWNLOAD="http://www.ormbunkar.se/aliview/downloads/linux/linux-versions-all/linux-version-1.23/aliview.tgz"
MD5SUM="b05a65ad2a70332343ef9ce6a28a9dcb"
DOWNLOAD_x86_64=""
MD5SUM_x86_64=""
REQUIRES="jdk"