diff options
Diffstat (limited to 'academic')
| -rw-r--r-- | academic/ugene/README | 54 | ||||
| -rw-r--r-- | academic/ugene/References | 5 | ||||
| -rw-r--r-- | academic/ugene/ugene.SlackBuild | 13 | ||||
| -rw-r--r-- | academic/ugene/ugene.info | 10 |
4 files changed, 51 insertions, 31 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 diff --git a/academic/ugene/References b/academic/ugene/References new file mode 100644 index 0000000000..4b68b81b25 --- /dev/null +++ b/academic/ugene/References @@ -0,0 +1,5 @@ +To cite UGENE use the following article: + +Unipro UGENE: a unified bioinformatics toolkit +Konstantin Okonechnikov; Olga Golosova; Mikhail Fursov; the UGENE team +Bioinformatics 2012 28: 1166-1167 diff --git a/academic/ugene/ugene.SlackBuild b/academic/ugene/ugene.SlackBuild index d8ce0658a4..29f1b8902e 100644 --- a/academic/ugene/ugene.SlackBuild +++ b/academic/ugene/ugene.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for ugene -# Copyright 2013 Petar Petrov, ppetrov@paju.oulu.fi +# Copyright 2013 Petar Petrov, petar.petrov@student.oulu.fi # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -23,7 +23,7 @@ # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. PRGNAM=ugene -VERSION=${VERSION:-1.11.5} +VERSION=${VERSION:-1.13.0} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} @@ -68,10 +68,10 @@ tar xvf $CWD/$PRGNAM-$VERSION.tar.gz cd $PRGNAM-$VERSION chown -R root:root . find -L . \ - \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 -o -perm 511 \) \ - -exec chmod 755 {} \; -o \ - \( -perm 666 -o -perm 664 -o -perm 600 -o -perm 444 -o -perm 440 -o -perm 400 \) \ - -exec chmod 644 {} \; + \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ + -o -perm 511 \) -exec chmod 755 {} \; -o \ + \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; # Fix libraries and man pages paths sed -i "s:/lib:/lib${LIBDIRSUFFIX}:g" src/ugene_globals.pri @@ -95,6 +95,7 @@ cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc cat $CWD/doinst.sh > $PKG/install/doinst.sh +cat $CWD/References > $PKG/usr/doc/$PRGNAM-$VERSION/References cd $PKG /sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} diff --git a/academic/ugene/ugene.info b/academic/ugene/ugene.info index a46806acf9..d16947120a 100644 --- a/academic/ugene/ugene.info +++ b/academic/ugene/ugene.info @@ -1,10 +1,10 @@ PRGNAM="ugene" -VERSION="1.11.5" +VERSION="1.13.0" HOMEPAGE="http://ugene.unipro.ru/" -DOWNLOAD="http://ugene.unipro.ru/downloads/ugene-1.11.5.tar.gz" -MD5SUM="ccd3acbd418215004523cdb16a9bb1d2" +DOWNLOAD="http://ugene.unipro.ru/downloads/ugene-1.13.0.tar.gz" +MD5SUM="0d77dfd494b0b6ee7545069e1eab8f1d" DOWNLOAD_x86_64="" MD5SUM_x86_64="" -REQUIRES="bowtie bwa cap3 clustalw mafft mrbayes ncbi-blast ncbi-blast-plus t_coffee" +REQUIRES="%README%" MAINTAINER="Petar Petrov" -EMAIL="ppetrov@paju.oulu.fi" +EMAIL="petar.petrov@student.oulu.fi" |