academic/ugene: Updated for version 1.13.0.

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

1 files changed, 34 insertions, 20 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