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authorPetar Petrov <slackalaxy@gmail.com>2018-06-17 22:44:42 +0100
committerDavid Spencer <idlemoor@slackbuilds.org>2018-06-17 22:44:42 +0100
commita43d2d2e5116cfefc6fc9af447841c7a6c7b410a (patch)
treeedd26e7c6a8297d6398fd006976b3e10292e78fe
parent1861748c093979a87b9916053d24921893af754d (diff)
downloadslackbuilds-a43d2d2e5116cfefc6fc9af447841c7a6c7b410a.tar.gz
academic/aliview: Updated for version 1.23.
Signed-off-by: David Spencer <idlemoor@slackbuilds.org>
-rw-r--r--academic/aliview/README42
-rw-r--r--academic/aliview/References3
-rw-r--r--academic/aliview/aliview.SlackBuild13
-rw-r--r--academic/aliview/aliview.info6
4 files changed, 31 insertions, 33 deletions
diff --git a/academic/aliview/README b/academic/aliview/README
index d9e65dc923..6d6a532cd1 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 0000000000..788ea92323
--- /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 12f023916d..dcd65c971b 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 f4241366de..2dc48d1e31 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"