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academic/ugene: Updated for version 1.22.0

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Signed-off-by: Willy Sudiarto Raharjo <willysr@slackbuilds.org>
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Petar Petrov 2016-06-05 15:52:22 +03:00 committed by Willy Sudiarto Raharjo
parent b6456152b1
commit a2d9c58b50
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4 changed files with 17 additions and 13 deletions
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18
academic/ugene/README
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@ -21,19 +21,28 @@ 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:
Unipro UGENE: a unified bioinformatics toolkit
Konstantin Okonechnikov; Olga Golosova; Mikhail Fursov; the UGENE team
Bioinformatics 2012 28: 1166-1167
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:
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)
- bwa (Burrows-Wheeler Aligner)
- cap3 (CAP3: A DNA sequence assembly program)
- cistrome-CEAS (CEAS: Cis-regulatory Element Annotation System)
- cistrome-conductGO (Find the top-n highest expressed TFs)
- cistrome-extra (Cistrome Applications Harvard extra apps)
- cistrome-MACS (MACS: Model-based Analysis of ChIP-Seq)
- cistrome-mdseqpos (Cistrome Applications Harvard mdseqpos)
- clustalo (Clustal Omega)
- clustalw (Multiple Sequence Alignment)
- cufflinks (A reference-guided assembler for RNA-Seq experiments)
@ -52,9 +61,4 @@ program. Almost all of them can be found at SlackBuilds.org:
- vcftools (A program package designed for working with VCF files)
Alternatively, check the program's website if you want to get them
precompiled.
CITING:
Unipro UGENE: a unified bioinformatics toolkit
Konstantin Okonechnikov; Olga Golosova; Mikhail Fursov; the UGENE team
Bioinformatics 2012 28: 1166-1167
precompiled: http://ugene.net/external.html

2
academic/ugene/slack-desc
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@ -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: References: /usr/doc/ugene-1.21.0/References
ugene: References: /usr/doc/ugene-1.22.0/References

2
academic/ugene/ugene.SlackBuild
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@ -23,7 +23,7 @@
# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
PRGNAM=ugene
VERSION=${VERSION:-1.21.0}
VERSION=${VERSION:-1.22.0}
BUILD=${BUILD:-1}
TAG=${TAG:-_SBo}

8
academic/ugene/ugene.info
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@ -1,10 +1,10 @@
PRGNAM="ugene"
VERSION="1.21.0"
VERSION="1.22.0"
HOMEPAGE="http://ugene.net/"
DOWNLOAD="http://sourceforge.net/projects/sboppetrov/files/ugene/ugene-1.21.0.tar.gz"
MD5SUM="d9745720a28e448b3c92bf7d03d510db"
DOWNLOAD="http://sourceforge.net/projects/sboppetrov/files/ugene/ugene-1.22.0.tar.gz"
MD5SUM="c876d46c75628a96ee1be5ae86b33b9c"
DOWNLOAD_x86_64=""
MD5SUM_x86_64=""
REQUIRES="qt5"
REQUIRES="qt5 libxkbcommon"
MAINTAINER="Petar Petrov"
EMAIL="slackalaxy@gmail.com"