From bb2dfa6f86fe328a54249df007ab1eb2f2d7852f Mon Sep 17 00:00:00 2001 From: Petar Petrov Date: Sat, 3 Sep 2011 11:02:20 -0300 Subject: academic/lalnview: Added (Visualize local alignments) Signed-off-by: Niels Horn --- academic/lalnview/README | 13 ++++++ academic/lalnview/References | 5 +++ academic/lalnview/doinst.sh | 3 ++ academic/lalnview/lalnview.SlackBuild | 81 ++++++++++++++++++++++++++++++++++ academic/lalnview/lalnview.desktop | 7 +++ academic/lalnview/lalnview.info | 10 +++++ academic/lalnview/lalnview.png | Bin 0 -> 977 bytes academic/lalnview/slack-desc | 19 ++++++++ 8 files changed, 138 insertions(+) create mode 100644 academic/lalnview/README create mode 100644 academic/lalnview/References create mode 100644 academic/lalnview/doinst.sh create mode 100644 academic/lalnview/lalnview.SlackBuild create mode 100644 academic/lalnview/lalnview.desktop create mode 100644 academic/lalnview/lalnview.info create mode 100644 academic/lalnview/lalnview.png create mode 100644 academic/lalnview/slack-desc (limited to 'academic/lalnview') diff --git a/academic/lalnview/README b/academic/lalnview/README new file mode 100644 index 0000000000..0592d2b7f8 --- /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 0000000000..2ba7f071bb --- /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 0000000000..5fb28930db --- /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 0000000000..7b2f004dd3 --- /dev/null +++ b/academic/lalnview/lalnview.SlackBuild @@ -0,0 +1,81 @@ +#!/bin/sh + +# Slackware build script for lalnview +# Written by Petar Petrov, 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 0000000000..5abde1062d --- /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 0000000000..9c544ebaef --- /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 0000000000..f4cc77c61c Binary files /dev/null and b/academic/lalnview/lalnview.png differ diff --git a/academic/lalnview/slack-desc b/academic/lalnview/slack-desc new file mode 100644 index 0000000000..53cc73d8e2 --- /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 -- cgit v1.2.3