summaryrefslogtreecommitdiff
path: root/academic/sequence-analysis
diff options
context:
space:
mode:
authorPetar Petrov <petar.petrov@student.oulu.fi>2015-11-11 23:09:52 +0700
committerWilly Sudiarto Raharjo <willysr@slackbuilds.org>2015-11-11 23:09:52 +0700
commit9177640ee4b01bfb4413673abba9efad2f396e18 (patch)
tree40120d0b9ee466edd32376c435cb446ca835a117 /academic/sequence-analysis
parent49c8bb6b8f5963a6d4637a520dfb202eeac79b1a (diff)
downloadslackbuilds-9177640ee4b01bfb4413673abba9efad2f396e18.tar.gz
academic/sequence-analysis: Updated for version 1.7.2.
Signed-off-by: Willy Sudiarto Raharjo <willysr@slackbuilds.org>
Diffstat (limited to 'academic/sequence-analysis')
-rw-r--r--academic/sequence-analysis/README19
-rw-r--r--academic/sequence-analysis/sequence-analysis.SlackBuild31
-rw-r--r--academic/sequence-analysis/sequence-analysis.info8
3 files changed, 46 insertions, 12 deletions
diff --git a/academic/sequence-analysis/README b/academic/sequence-analysis/README
index 82dab2ac4c..87646b3052 100644
--- a/academic/sequence-analysis/README
+++ b/academic/sequence-analysis/README
@@ -1 +1,20 @@
A collage of coding projects for biologic sequences analysis.
+
+The upper window panel can hold several sequences, which are both
+editable and selectable. The tabs in the lower analysis panel try to
+keep up with the current sequence selection to provide immediate
+feedback. The selection is used in some modules as only the portion
+being analyzed for other modules i.e. Digest is used to determine if
+enzymes cut in the in or outside of the selection.
+
+Most commonly available sequence formats have been reverse engineered.
+You can also access a sequences from the NCBI via its GID or UID. This
+currently cannot be done from behind a firewall.
+
+Most of the analyses are simple enough that they are obvious to use,
+Composition, pI. Others could stand some documenation i.e. Pairwise
+and Primer Design. The Publish tab uses a string to control the
+layout. Click on the Legend button for some help.
+
+NOTE:
+The 'source' is hosted at SourceForge by the SlackBuild maintainer.
diff --git a/academic/sequence-analysis/sequence-analysis.SlackBuild b/academic/sequence-analysis/sequence-analysis.SlackBuild
index f7419ac791..03a62d71d7 100644
--- a/academic/sequence-analysis/sequence-analysis.SlackBuild
+++ b/academic/sequence-analysis/sequence-analysis.SlackBuild
@@ -1,19 +1,34 @@
#!/bin/sh
# Slackware build script for sequence-analysis
-# 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.
+# Copyright 2011-2015 Petar Petrov, petar.petrov@student.oulu.fi
+# All rights reserved.
+#
+# Redistribution and use of this script, with or without modification, is
+# permitted provided that the following conditions are met:
+#
+# 1. Redistributions of this script must retain the above copyright
+# notice, this list of conditions and the following disclaimer.
+#
+# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED
+# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF
+# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO
+# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
PRGNAM=sequence-analysis
-VERSION=${VERSION:-1.6.0}
-ARCH=noarch
-BUILD=${BUILD:-2}
+VERSION=${VERSION:-1.7.2}
+BUILD=${BUILD:-1}
TAG=${TAG:-_SBo}
+ARCH=noarch
+
CWD=$(pwd)
TMP=${TMP:-/tmp/SBo}
PKG=$TMP/package-$PRGNAM
diff --git a/academic/sequence-analysis/sequence-analysis.info b/academic/sequence-analysis/sequence-analysis.info
index ab8951183f..fe94933976 100644
--- a/academic/sequence-analysis/sequence-analysis.info
+++ b/academic/sequence-analysis/sequence-analysis.info
@@ -1,10 +1,10 @@
PRGNAM="sequence-analysis"
-VERSION="1.6.0"
+VERSION="1.7.2"
HOMEPAGE="http://informagen.com/SA/"
-DOWNLOAD="http://urchlay.naptime.net/~urchlay/src/sa.jar"
-MD5SUM="48609bfdd0d689cc62467159a0308886"
+DOWNLOAD="http://sourceforge.net/projects/sboppetrov/files/sequence-analysis/1.7.2/sa.jar"
+MD5SUM="815c7e6a8717a9e2a7fedc9ed94fbd0e"
DOWNLOAD_x86_64=""
MD5SUM_x86_64=""
REQUIRES="jdk"
MAINTAINER="Petar Petrov"
-EMAIL="ppetrov@paju.oulu.fi"
+EMAIL="petar.petrov@student.oulu.fi"