academic/ugene: Updated for version 1.31.1.

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

academic/ugene/README

@@ -35,7 +35,7 @@ program. All of them are available at SlackBuilds.org:
 - bedGraphToBigWig (Convert bedGraph to bigWig file)
 - bedtools (A powerful toolset for genome arithmetic)
 - bowtie (A short read aligner of DNA sequences)
-- bowtie2 (A tool for aligning sequencing reads)
+- bowtie2-legacy (A tool for aligning sequencing reads)
 - bwa (Burrows-Wheeler Aligner)
 - cap3 (CAP3: A DNA sequence assembly program)
 - cistrome-CEAS (CEAS: Cis-regulatory Element Annotation System)
@@ -43,23 +43,27 @@ program. All of them are available at SlackBuilds.org:
 - cistrome-extra (Cistrome Applications Harvard extra apps)
 - cistrome-MACS (MACS: Model-based Analysis of ChIP-Seq)
 - cistrome-mdseqpos (Cistrome Applications Harvard mdseqpos)
+- clark-ugene (Ugene's forked CLAssifier based on Reduced K-mers)
 - clustalo (Clustal Omega)
 - clustalw (Multiple Sequence Alignment)
 - cufflinks (A reference-guided assembler for RNA-Seq experiments)
 - cutadapt (Trim adapters from high-throughput sequencing reads)
+- diamond (A sequence aligner for protein and translated DNA)
 - fastqc (A quality control tool for high throughput sequence data)
 - HMMER (Biosequence analysis using profile hidden Markov models)
+- kraken (Assign taxonomic labels to short DNA sequences)
 - ncbi-blast (BLAST: Basic Local Alignment Search Tool)
-- ncbi-blast-plus (BLAST+ Command Line Applications)
+- ncbi-blast+ (BLAST+ Command Line Applications)
 - PhyML (Phylogenetic estimation using Maximum Likelihood)
-- samtools (Sequence Alignment/Map Tools)
+- samtools-legacy (Sequence Alignment/Map Tools)
 - snpEff (Genetic variant annotation and effect prediction toolbox)
 - spades (SPAdes Genome Assembler)
 - spidey (mRNA-to-genomic alignment)
 - t_coffee (A multiple sequence alignment program)
-- tabix (Generic indexer for TAB-delimited genome position files )
+- tabix-legacy (Generic indexer for TAB-delimited genome position files )
 - tophat (Splice junction mapper for RNA-Seq reads)
+- trimmomatic (A flexible read trimming tool for Illumina NGS data)
 - vcftools (A program package designed for working with VCF files)
 
 Alternatively, check the program's website if you want to get them
-precompiled: http://ugene.net/external.html
+precompiled.

academic/ugene/slack-desc

@@ -16,4 +16,4 @@ ugene: user nterface. The toolkit supports multiple biological data formats
 ugene: and allows the retrieval of data from remote data sources.
 ugene:
 ugene: Home: http://ugene.net/
-ugene:
+ugene: GitHub: https://github.com/ugeneunipro

academic/ugene/ugene.SlackBuild

@@ -23,7 +23,7 @@
 #  ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 
 PRGNAM=ugene
-VERSION=${VERSION:-1.30.0}
+VERSION=${VERSION:-1.31.1}
 BUILD=${BUILD:-1}
 TAG=${TAG:-_SBo}
 
@@ -88,7 +88,7 @@ find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | gr
 
 mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION
 cp -a \
-  build.txt COPYRIGHT LICENSE.txt LICENSE.3rd_party.txt \
+  build.txt README.md LICENSE.txt LICENSE.3rd_party.txt \
   $PKG/usr/doc/$PRGNAM-$VERSION
 cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild
 

academic/ugene/ugene.info

@@ -1,8 +1,8 @@
 PRGNAM="ugene"
-VERSION="1.30.0"
+VERSION="1.31.1"
 HOMEPAGE="http://ugene.net/"
-DOWNLOAD="http://ugene.net/downloads/ugene-1.30.0.tar.gz"
-MD5SUM="cfdf3c93d0301d5eec6001301dfc4c0d"
+DOWNLOAD="https://github.com/ugeneunipro/ugene/archive/1.31.1/ugene-1.31.1.tar.gz"
+MD5SUM="ec32889089b7b9f6c6a9668aa56c198e"
 DOWNLOAD_x86_64=""
 MD5SUM_x86_64=""
 REQUIRES="qt5-webkit"