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author Petar Petrov2018-12-24 16:15:39 +0100
committer Willy Sudiarto Raharjo2018-12-24 16:17:00 +0100
commit67694412807941c06eb65193ea0eb428dab4c4a4 (patch)
treee81dcb0e9ebcb605aa9f8ee8dcfce02ba4377dd3 /academic
parenta19766c3d8ff347b2ea61ecbe4c40f5f8dd40146 (diff)
downloadslackbuilds-67694412807941c06eb65193ea0eb428dab4c4a4.tar.gz
academic/ugene: Updated for version 1.31.1.
Signed-off-by: Willy Sudiarto Raharjo <willysr@slackbuilds.org>
Diffstat (limited to 'academic')
-rw-r--r--academic/ugene/README14
-rw-r--r--academic/ugene/slack-desc2
-rw-r--r--academic/ugene/ugene.SlackBuild4
-rw-r--r--academic/ugene/ugene.info6
4 files changed, 15 insertions, 11 deletions
diff --git a/academic/ugene/README b/academic/ugene/README
index ef532fe350..515ecec210 100644
--- a/academic/ugene/README
+++ b/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.
diff --git a/academic/ugene/slack-desc b/academic/ugene/slack-desc
index 14c4624e86..8ecef36a72 100644
--- a/academic/ugene/slack-desc
+++ b/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
diff --git a/academic/ugene/ugene.SlackBuild b/academic/ugene/ugene.SlackBuild
index 058e03b6b8..c93a523b65 100644
--- a/academic/ugene/ugene.SlackBuild
+++ b/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
diff --git a/academic/ugene/ugene.info b/academic/ugene/ugene.info
index 1c8b1f46bf..7f2ad37c91 100644
--- a/academic/ugene/ugene.info
+++ b/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"