academic/lalnview: Added (Visualize local alignments)

Signed-off-by: Niels Horn <niels.horn@slackbuilds.org>

8 files changed, 138 insertions, 0 deletions

diff --git a/academic/lalnview/README b/academic/lalnview/README
new file mode 100644
index 0000000000000..0592d2b7f8295
--- /dev/null
+++ b/academic/lalnview/README
@@ -0,0 +1,13 @@
+LalnView is a graphical program for visualizing local alignments 
+between two sequences (protein or nucleic acids). Sequences are 
+represented by colored rectangles to give an overall picture of the 
+similarities between the two sequences. Blocks of similarity between 
+the two sequences are colored according to the degree of identity 
+between segments.
+
+For details and citation:
+Duret, L., Gasteiger, E. and Perrière, G. (1996) LalnView: a 
+graphical viewer for pairwise sequence alignments. Comput. Applic. 
+Biosci., 12, 507-510
+
+This requires fltk and PDFlib-Lite.
diff --git a/academic/lalnview/References b/academic/lalnview/References
new file mode 100644
index 0000000000000..2ba7f071bbc41
--- /dev/null
+++ b/academic/lalnview/References
@@ -0,0 +1,5 @@
+References:
+
+Duret, L., Gasteiger, E. and Perrière, G. (1996) LalnView: a graphical
+viewer for pairwise sequence alignments. Comput. Applic. Biosci.,
+12, 507-510
diff --git a/academic/lalnview/doinst.sh b/academic/lalnview/doinst.sh
new file mode 100644
index 0000000000000..5fb28930db0b9
--- /dev/null
+++ b/academic/lalnview/doinst.sh
@@ -0,0 +1,3 @@
+if [ -x /usr/bin/update-desktop-database ]; then
+  /usr/bin/update-desktop-database -q usr/share/applications >/dev/null 2>&1
+fi
diff --git a/academic/lalnview/lalnview.SlackBuild b/academic/lalnview/lalnview.SlackBuild
new file mode 100644
index 0000000000000..7b2f004dd33f7
--- /dev/null
+++ b/academic/lalnview/lalnview.SlackBuild
@@ -0,0 +1,81 @@
+#!/bin/sh
+
+# Slackware build script for lalnview
+# Written by Petar Petrov, <ppetrov@paju.oulu.fi> and 
+# hereby submitted to the public domain
+
+# THIS SLACKBUILD IS DISTRIBUTETD IN THE HOPE OF BEING 
+# USEFUL BUT WITHOUT ANY WARRANTY. THE AUTHOR IS _NOT_ 
+# RESPONSIBLE FOR ANY DAMAGE OR DATA LOSS CAUSED BY IT.
+
+PRGNAM=lalnview		
+VERSION=${VERSION:-3.0}	
+BUILD=${BUILD:-1}
+TAG=${TAG:-_SBo}	
+
+if [ -z "$ARCH" ]; then
+  case "$( uname -m )" in
+    i?86) ARCH=i486 ;;
+    arm*) ARCH=arm ;;
+       *) ARCH=$( uname -m ) ;;
+  esac
+fi
+
+CWD=$(pwd)
+TMP=${TMP:-/tmp/SBo}
+PKG=$TMP/package-$PRGNAM
+OUTPUT=${OUTPUT:-/tmp}	
+
+if [ "$ARCH" = "i486" ]; then
+  SLKCFLAGS="-O2 -march=i486 -mtune=i686"
+  LIBDIRSUFFIX=""
+elif [ "$ARCH" = "i686" ]; then
+  SLKCFLAGS="-O2 -march=i686 -mtune=i686"
+  LIBDIRSUFFIX=""
+elif [ "$ARCH" = "x86_64" ]; then
+  SLKCFLAGS="-O2 -fPIC"
+  LIBDIRSUFFIX="64"
+else
+  SLKCFLAGS="-O2"
+  LIBDIRSUFFIX=""
+fi
+
+set -e
+
+rm -rf $PKG
+mkdir -p $TMP $PKG $OUTPUT
+cd $TMP
+rm -rf $PRGNAM-$VERSION
+mkdir $PRGNAM-$VERSION
+cd $PRGNAM-$VERSION
+tar xvf $CWD/sources20050615.tar
+chown -R root:root .
+find . \
+ \( -perm 777 -o -perm 775 -o -perm 711 -o -perm 555 -o -perm 511 \) \
+ -exec chmod 755 {} \; -o \
+ \( -perm 666 -o -perm 664 -o -perm 600 -o -perm 444 -o -perm 440 -o -perm 400 \) \
+ -exec chmod 644 {} \;
+
+OPT="$SLKCFLAGS" \
+  make
+install -D -m755 lalnview $PKG/usr/bin/lalnview
+
+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
+
+# Menu item and icon (couldn't find an icon, so i made one myself. I know it sucks.)
+mkdir -p $PKG/usr/share/{applications,pixmaps}
+cp $CWD/$PRGNAM.desktop $PKG/usr/share/applications
+cp $CWD/$PRGNAM.png $PKG/usr/share/pixmaps
+
+mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION
+cp lalnview.help $PKG/usr/doc/$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
+cat $CWD/doinst.sh > $PKG/install/doinst.sh
+
+cd $PKG
+/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz}
diff --git a/academic/lalnview/lalnview.desktop b/academic/lalnview/lalnview.desktop
new file mode 100644
index 0000000000000..5abde1062d0fd
--- /dev/null
+++ b/academic/lalnview/lalnview.desktop
@@ -0,0 +1,7 @@
+[Desktop Entry]
+Categories=Education;
+Exec=lalnview
+Icon=lalnview.png
+Name=Lalnview
+StartupNotify=false
+Type=Application
diff --git a/academic/lalnview/lalnview.info b/academic/lalnview/lalnview.info
new file mode 100644
index 0000000000000..9c544ebaef9cd
--- /dev/null
+++ b/academic/lalnview/lalnview.info
@@ -0,0 +1,10 @@
+PRGNAM="lalnview"
+VERSION="3.0"
+HOMEPAGE="http://pbil.univ-lyon1.fr/software/lalnview.html"
+DOWNLOAD="ftp://pbil.univ-lyon1.fr/pub/logiciel/lalnview/sources/sources20050615.tar"
+MD5SUM="127952631b17df843c9721d4da64f42e"
+DOWNLOAD_x86_64=""
+MD5SUM_x86_64=""
+MAINTAINER="Petar Petrov"
+EMAIL="ppetrov@paju.oulu.fi"
+APPROVED="Niels Horn"
diff --git a/academic/lalnview/lalnview.png b/academic/lalnview/lalnview.png
new file mode 100644
index 0000000000000..f4cc77c61cd9c
--- /dev/null
+++ b/academic/lalnview/lalnview.png
diff --git a/academic/lalnview/slack-desc b/academic/lalnview/slack-desc
new file mode 100644
index 0000000000000..53cc73d8e2080
--- /dev/null
+++ b/academic/lalnview/slack-desc
@@ -0,0 +1,19 @@
+# HOW TO EDIT THIS FILE:
+# The "handy ruler" below makes it easier to edit a package description.  Line
+# up the first '|' above the ':' following the base package name, and the '|'
+# on the right side marks the last column you can put a character in.  You must
+# make exactly 11 lines for the formatting to be correct.  It's also
+# customary to leave one space after the ':'.
+
+        |-----handy-ruler------------------------------------------------------|
+lalnview: lalnview (Visualize local alignments)
+lalnview:
+lalnview: LalnView is a graphical program for visualizing local alignments
+lalnview: between two sequences (protein or nucleic acids).
+lalnview:
+lalnview:
+lalnview:
+lalnview:
+lalnview:
+lalnview: References: /usr/doc/lalnview-$VERSION/References
+lalnview: Home: http://pbil.univ-lyon1.fr/software/lalnview.html