academic/aliview: Updated for version 1.23.

Signed-off-by: David Spencer <idlemoor@slackbuilds.org>

4 files changed, 31 insertions, 33 deletions

diff --git a/academic/aliview/README b/academic/aliview/README
index d9e65dc923e6..6d6a532cd14a 100644
--- a/academic/aliview/README
+++ b/academic/aliview/README
@@ -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:
diff --git a/academic/aliview/References b/academic/aliview/References
new file mode 100644
index 000000000000..788ea9232377
--- /dev/null
+++ b/academic/aliview/References
@@ -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
diff --git a/academic/aliview/aliview.SlackBuild b/academic/aliview/aliview.SlackBuild
index 12f023916dee..dcd65c971bf7 100644
--- a/academic/aliview/aliview.SlackBuild
+++ b/academic/aliview/aliview.SlackBuild
@@ -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
diff --git a/academic/aliview/aliview.info b/academic/aliview/aliview.info
index f4241366de6a..2dc48d1e3186 100644
--- a/academic/aliview/aliview.info
+++ b/academic/aliview/aliview.info
@@ -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"