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authorPetar Petrov <petar.petrov@student.oulu.fi>2015-04-11 18:20:35 +0700
committerWilly Sudiarto Raharjo <willysr@slackbuilds.org>2015-04-11 18:20:35 +0700
commit3f5f2cea710c6b601e3f55f17856ac6191717a40 (patch)
tree8994dba4226aa965b96e76e90e8605b530709345 /academic
parent448e1d0f2d1401a9dbee7cf0f52cdb4935ae3ae6 (diff)
downloadslackbuilds-3f5f2cea710c6b601e3f55f17856ac6191717a40.tar.gz
academic/aline: Add option to change row length.
Signed-off-by: Willy Sudiarto Raharjo <willysr@slackbuilds.org>
Diffstat (limited to 'academic')
-rw-r--r--academic/aline/README10
-rw-r--r--academic/aline/aline.SlackBuild19
-rw-r--r--academic/aline/aline.info2
3 files changed, 21 insertions, 10 deletions
diff --git a/academic/aline/README b/academic/aline/README
index 28549e30b4..e0c0e9354c 100644
--- a/academic/aline/README
+++ b/academic/aline/README
@@ -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
diff --git a/academic/aline/aline.SlackBuild b/academic/aline/aline.SlackBuild
index 30f92ce9fd..469e0812b6 100644
--- a/academic/aline/aline.SlackBuild
+++ b/academic/aline/aline.SlackBuild
@@ -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
diff --git a/academic/aline/aline.info b/academic/aline/aline.info
index ac75aa8483..8bc94a0236 100644
--- a/academic/aline/aline.info
+++ b/academic/aline/aline.info
@@ -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"