diff options
Diffstat (limited to 'academic')
| -rw-r--r-- | academic/ugene/README | 14 | ||||
| -rw-r--r-- | academic/ugene/slack-desc | 2 | ||||
| -rw-r--r-- | academic/ugene/ugene.SlackBuild | 4 | ||||
| -rw-r--r-- | academic/ugene/ugene.info | 6 |
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" |