academic/ugene: Updated for version 1.13.0.

Signed-off-by: Willy Sudiarto Raharjo <willysr@slackbuilds.org>

4 files changed, 51 insertions, 31 deletions

diff --git a/academic/ugene/README b/academic/ugene/README
index 713391c36c..4d1fc9662b 100644
--- a/academic/ugene/README
+++ b/academic/ugene/README
@@ -7,11 +7,11 @@ interface. The toolkit supports multiple biological data formats and
 allows the retrieval of data from remote data sources. It provides
 visualization modules for biological objects such as:
 
-- annotated genome sequences;
-- Next Generation Sequencing (NGS) assembly data;
-- multiple sequence alignments;
-- phylogenetic trees;
-- 3D structures.
+- annotated genome sequences
+- Next Generation Sequencing (NGS) assembly data
+- multiple sequence alignments
+- phylogenetic trees
+- 3D structures
 
 Most of the integrated algorithms are tuned for maximum performance by
 the usage of multithreading and special processor instructions. UGENE
@@ -21,20 +21,34 @@ be launched on local resources or in a High Performance Computing
 built-in plugin system and structured UGENE API make it possible to
 extend the toolkit with new functionality.
 
-CITING:
-If you use UGENE in your work, please quote this publication:
-Unipro UGENE: a unified bioinformatics toolkit
-Konstantin Okonechnikov, Olga Golosova, Mikhail Fursov, the UGENE team
-Bioinformatics 2012 28: 1166-1167 doi: 10.1093/bioinformatics/bts091
+IMPORTANT: External tools
+UGENE can use and drive a number of external tools, providing a nice
+and unified GUI. These are not needed at build time, but are highly
+recommended for the complete (and extended) functionality of the
+program. Almost all of them can be found at SlackBuilds.org:
+
+- cistrome-CEAS (CEAS: Cis-regulatory Element Annotation System)
+- cistrome-MACS (MACS: Model-based Analysis of ChIP-Seq)
+- cufflinks (A reference-guided assembler for RNA-Seq experiments)
+- bowtie (A short read aligner of DNA sequences)
+- bowtie2 (A tool for aligning sequencing reads)
+- bwa (Burrows-Wheeler Aligner)
+- cap3 (CAP3: A DNA sequence assembly program)
+- clustalo (Clustal Omega)
+- clustalw (Multiple Sequence Alignment)
+- ncbi-blast (BLAST: Basic Local Alignment Search Tool)
+- ncbi-blast-plus (BLAST+ Command Line Applications)
+- samtools (Sequence Alignment/Map Tools)
+- spidey (mRNA-to-genomic alignment)
+- t_coffee (A multiple sequence alignment program)
+- tabix (Generic indexer for TAB-delimited genome position files )
+- tophat (Splice junction mapper for RNA-Seq reads)
+- vcftools (A program package designed for working with VCF files)
 
-NOTE!
-While not needed for building of UGENE, the dependencies listed as
-"REQUIRED" are highly recommended for the complete functionality of
-the program. UGENE will also drive spidey if you have it installed,
-but keep in mind that it is available only as a 32-bit binary.
+Alternatively, check the program's website if you want to get them
+precompiled.
 
-NOTE ABOUT CUDA:
-UGENE is built without CUDA support and CUDA-BLAST is not included
-among the "REQUIRED", either. Simply, I do not have the hardware. If
-someone is interested in such functionality and can offer help with
-the script, please contact me.
+CITING:
+Unipro UGENE: a unified bioinformatics toolkit
+Konstantin Okonechnikov; Olga Golosova; Mikhail Fursov; the UGENE team
+Bioinformatics 2012 28: 1166-1167
diff --git a/academic/ugene/References b/academic/ugene/References
new file mode 100644
index 0000000000..4b68b81b25
--- /dev/null
+++ b/academic/ugene/References
@@ -0,0 +1,5 @@
+To cite UGENE use the following article:
+
+Unipro UGENE: a unified bioinformatics toolkit
+Konstantin Okonechnikov; Olga Golosova; Mikhail Fursov; the UGENE team
+Bioinformatics 2012 28: 1166-1167
diff --git a/academic/ugene/ugene.SlackBuild b/academic/ugene/ugene.SlackBuild
index d8ce0658a4..29f1b8902e 100644
--- a/academic/ugene/ugene.SlackBuild
+++ b/academic/ugene/ugene.SlackBuild
@@ -2,7 +2,7 @@
 
 # Slackware build script for ugene
 
-# Copyright 2013 Petar Petrov, ppetrov@paju.oulu.fi
+# Copyright 2013 Petar Petrov, petar.petrov@student.oulu.fi
 # All rights reserved.
 #
 # Redistribution and use of this script, with or without modification, is
@@ -23,7 +23,7 @@
 #  ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 
 PRGNAM=ugene
-VERSION=${VERSION:-1.11.5}
+VERSION=${VERSION:-1.13.0}
 BUILD=${BUILD:-1}
 TAG=${TAG:-_SBo}
 
@@ -68,10 +68,10 @@ tar xvf $CWD/$PRGNAM-$VERSION.tar.gz
 cd $PRGNAM-$VERSION
 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 {} \;
 
 # Fix libraries and man pages paths
 sed -i "s:/lib:/lib${LIBDIRSUFFIX}:g" src/ugene_globals.pri
@@ -95,6 +95,7 @@ cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild
 mkdir -p $PKG/install
 cat $CWD/slack-desc > $PKG/install/slack-desc
 cat $CWD/doinst.sh > $PKG/install/doinst.sh
+cat $CWD/References > $PKG/usr/doc/$PRGNAM-$VERSION/References
 
 cd $PKG
 /sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz}
diff --git a/academic/ugene/ugene.info b/academic/ugene/ugene.info
index a46806acf9..d16947120a 100644
--- a/academic/ugene/ugene.info
+++ b/academic/ugene/ugene.info
@@ -1,10 +1,10 @@
 PRGNAM="ugene"
-VERSION="1.11.5"
+VERSION="1.13.0"
 HOMEPAGE="http://ugene.unipro.ru/"
-DOWNLOAD="http://ugene.unipro.ru/downloads/ugene-1.11.5.tar.gz"
-MD5SUM="ccd3acbd418215004523cdb16a9bb1d2"
+DOWNLOAD="http://ugene.unipro.ru/downloads/ugene-1.13.0.tar.gz"
+MD5SUM="0d77dfd494b0b6ee7545069e1eab8f1d"
 DOWNLOAD_x86_64=""
 MD5SUM_x86_64=""
-REQUIRES="bowtie bwa cap3 clustalw mafft mrbayes ncbi-blast ncbi-blast-plus t_coffee"
+REQUIRES="%README%"
 MAINTAINER="Petar Petrov"
-EMAIL="ppetrov@paju.oulu.fi"
+EMAIL="petar.petrov@student.oulu.fi"