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authorPetar Petrov <slackalaxy@gmail.com>2020-09-19 01:01:15 +0700
committerWilly Sudiarto Raharjo <willysr@slackbuilds.org>2020-09-19 01:01:15 +0700
commit2f026a37f993ad3f58ba0a92d773b93f7dc33267 (patch)
tree21869fa765fe7969306381eb0c61a2f33cdca54e
parent64e6c76a4382e225c9ca28933594010509f25a53 (diff)
academic/lalnview: Update script.
Signed-off-by: Willy Sudiarto Raharjo <willysr@slackbuilds.org>
-rw-r--r--academic/lalnview/README7
-rw-r--r--academic/lalnview/lalnview.SlackBuild28
-rw-r--r--academic/lalnview/lalnview.pngbin977 -> 2394 bytes
3 files changed, 22 insertions, 13 deletions
diff --git a/academic/lalnview/README b/academic/lalnview/README
index e91c30683f43..364d8d037869 100644
--- a/academic/lalnview/README
+++ b/academic/lalnview/README
@@ -5,6 +5,13 @@ similarities between the two sequences. Blocks of similarity between
the two sequences are colored according to the degree of identity
between segments.
+A suitable alignment tool for protein sequences is SIM at ExPASy:
+https://web.expasy.org/sim/
+
+SIM finds a user-defined number of best non-intersecting alignments
+between two protein sequences or within a sequence. Once the alignment
+is computed, you can view it using LalnView.
+
For details and citation:
Duret, L., Gasteiger, E. and Perriere, G. (1996) LalnView: a
graphical viewer for pairwise sequence alignments. Comput. Applic.
diff --git a/academic/lalnview/lalnview.SlackBuild b/academic/lalnview/lalnview.SlackBuild
index cb92a3bcc3ad..3ba95c44d551 100644
--- a/academic/lalnview/lalnview.SlackBuild
+++ b/academic/lalnview/lalnview.SlackBuild
@@ -2,7 +2,7 @@
# Slackware build script for lalnview
-# Copyright 2011-2016 Petar Petrov slackalaxy@gmail.com
+# Copyright 2011-2020 Petar Petrov slackalaxy@gmail.com
# All rights reserved.
#
# Redistribution and use of this script, with or without modification, is
@@ -26,12 +26,14 @@
PRGNAM=lalnview
VERSION=${VERSION:-3.0}
-BUILD=${BUILD:-2}
+BUILD=${BUILD:-3}
TAG=${TAG:-_SBo}
+SRCTAR=sources20050615.tar
+
if [ -z "$ARCH" ]; then
case "$( uname -m )" in
- i?86) ARCH=i486 ;;
+ i?86) ARCH=i586 ;;
arm*) ARCH=arm ;;
*) ARCH=$( uname -m ) ;;
esac
@@ -42,8 +44,8 @@ TMP=${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"
@@ -64,24 +66,24 @@ cd $TMP
rm -rf $PRGNAM-$VERSION
mkdir $PRGNAM-$VERSION
cd $PRGNAM-$VERSION
-tar xvf $CWD/sources20050615.tar
+tar xvf $CWD/$SRCTAR
chown -R root:root .
find -L . \
- \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 -o -perm 511 \) \
- -exec chmod 755 {} \; -o \
- \( -perm 666 -o -perm 664 -o -perm 600 -o -perm 444 -o -perm 440 -o -perm 400 \) \
- -exec chmod 644 {} \;
+ \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \
+ -o -perm 511 \) -exec chmod 755 {} \; -o \
+ \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \
+ -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \;
# Point to the correct place of lalnview.help
-sed -i "s:lalnview.help:/usr/doc/$PRGNAM-$VERSION/lalnview.help:" MF_MainWindow.cxx
+sed -i "s:$PRGNAM.help:/usr/doc/$PRGNAM-$VERSION/$PRGNAM.help:" MF_MainWindow.cxx
OPT="$SLKCFLAGS" make
-install -D -m755 lalnview $PKG/usr/bin/$PRGNAM
+install -D -m755 $PRGNAM $PKG/usr/bin/$PRGNAM
find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \
| cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true
-# Couldn't find an icon, so i made one myself. I know it sucks.
+# Couldn't find an icon, so i made one myself.
mkdir -p $PKG/usr/share/{applications,pixmaps}
cp $CWD/$PRGNAM.desktop $PKG/usr/share/applications
cp $CWD/$PRGNAM.png $PKG/usr/share/pixmaps
diff --git a/academic/lalnview/lalnview.png b/academic/lalnview/lalnview.png
index f4cc77c61cd9..f528cc3d46f4 100644
--- a/academic/lalnview/lalnview.png
+++ b/academic/lalnview/lalnview.png
Binary files differ