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academic/aline: Add option to change row length.

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Signed-off-by: Willy Sudiarto Raharjo <willysr@slackbuilds.org>
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Petar Petrov 2015-04-11 18:20:35 +07:00 committed by Willy Sudiarto Raharjo
parent 448e1d0f2d
commit 3f5f2cea71
3 changed files with 21 additions and 10 deletions
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10
academic/aline/README
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@ -6,11 +6,15 @@ sequence alignment formats which the user can then alter, embellish,
markup etc to produce the kind of sequence figure commonly found in
biochemical articles.
Please cite:
Bond, C.S. and Schüttelkopf, A.W. (2009), Acta cryst. D65, 510-512
NOTE
The default row length is 100 residues. If you want to change that to
something else (e.g. 1000) pass ROW=1000 to the script.
NOTE:
OPTIONAL
Although not needed for running Aline, clustalw and mkDSSP are
desirable for its complete functionality. A third tool is CHAINSAW,
part of the CCP4 suite (http://www.ccp4.ac.uk/). Visit the web site
for more information and installation instructions if you want it.
CITING
Bond, C.S. and Schüttelkopf, A.W. (2009), Acta cryst. D65, 510-512

19
academic/aline/aline.SlackBuild
View file

@ -2,7 +2,7 @@
# Slackware build script for aline
# Copyright 2013 Petar Petrov, ppetrov@paju.oulu.fi
# Copyright 2013-2015 Petar Petrov, petar.petrov@student.oulu.fi
# All rights reserved.
#
# Redistribution and use of this script, with or without modification, is
@ -24,7 +24,7 @@
PRGNAM=aline
VERSION=${VERSION:-1.0.025}
BUILD=${BUILD:-1}
BUILD=${BUILD:-2}
TAG=${TAG:-_SBo}
SRCVER=011208
@ -35,6 +35,10 @@ TMP=${TMP:-/tmp/SBo}
PKG=$TMP/package-$PRGNAM
OUTPUT=${OUTPUT:-/tmp}
# Maximum row length. The default is 100 and will not be changed,
# unless you pass some other value to the script.
ROW=${ROW:-100}
set -e
rm -rf $PKG
@ -45,10 +49,10 @@ tar xvf $CWD/${PRGNAM}_${SRCVER}.tar.gz
cd ${PRGNAM}_${SRCVER}
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 aline to the correct paths of its colour schemes, examples,
# plugins and scripts.
@ -57,6 +61,9 @@ sed -i "s:%%SELFexample:/usr/share/$PRGNAM/example:g" bin/aline
sed -i "s:%%SELFplugins:/usr/share/$PRGNAM/plugins:g" bin/aline
sed -i "s:%%SELFscripts:/usr/share/$PRGNAM/scripts:g" bin/aline
# Change the maximum row length to a value you specify.
[ ! "$ROW" = "100" ] && sed -i "s:10,100,40:10,$ROW,40:g" bin/aline
install -D -m755 bin/$PRGNAM $PKG/usr/bin/$PRGNAM
install -D -m755 bin/convertdump $PKG/usr/bin/convertdump

2
academic/aline/aline.info
View file

@ -7,4 +7,4 @@ DOWNLOAD_x86_64=""
MD5SUM_x86_64=""
REQUIRES="perl-tk"
MAINTAINER="Petar Petrov"
EMAIL="ppetrov@paju.oulu.fi"
EMAIL="petar.petrov@student.oulu.fi"