diff options
| author | Petar Petrov <petar.petrov@student.oulu.fi> | 2015-04-11 18:20:35 +0700 |
|---|---|---|
| committer | Willy Sudiarto Raharjo <willysr@slackbuilds.org> | 2015-04-11 18:20:35 +0700 |
| commit | 3f5f2cea710c6b601e3f55f17856ac6191717a40 (patch) | |
| tree | 8994dba4226aa965b96e76e90e8605b530709345 | |
| parent | 448e1d0f2d1401a9dbee7cf0f52cdb4935ae3ae6 (diff) | |
academic/aline: Add option to change row length.
Signed-off-by: Willy Sudiarto Raharjo <willysr@slackbuilds.org>
| -rw-r--r-- | academic/aline/README | 10 | ||||
| -rw-r--r-- | academic/aline/aline.SlackBuild | 19 | ||||
| -rw-r--r-- | academic/aline/aline.info | 2 |
3 files changed, 21 insertions, 10 deletions
diff --git a/academic/aline/README b/academic/aline/README index 28549e30b4355..e0c0e9354c6dc 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 30f92ce9fdf98..469e0812b6674 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 ac75aa84831bc..8bc94a0236097 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" |