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Specify integrated external tools in the installed package
The Most of the external tools (if available on the target operating system) are provided installed by default in the Online Installer, Full and NGS UGENE packages.
One can specify the tools manually:
- Download the tools executables, see links on the "Download UGENE and components" pagethe web page http://ugene.net/download-all.html:
- External Tools Package: the package contains all external tools except JRE (i.e. "java") and RScript.
- Java Runtime Environment (JRE): although UGENE is not a Java application, a few tools (e.g. FastQC, Trimmomatic) require JRE. Make sure JRE 8 or higher is installed.
RScript: R is currently used in UGENE for ChIP-Seq data analysis only.
- Configure the tools in UGENE: open the UGENE Application Settings dialog, select the "External Tools" page and specify the external tools executables.
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External tool | Windows (64-bit) | Windows (32-bit) | macOS (64-bit) | Linux (64-bit) | Linux (32-bit) |
---|---|---|---|---|---|
bedGraphToBigWig | 4 | N/A4 | 4 | N/A | |
bedtools | 2.20.12.20.1 | 2.20.1 | 2.20.1 | 2.20.1 | |
BLAST+ | 2.2.30 | 2.2.30 | 2.2.30 | 2.2.30 | 2.2.30 |
Bowtie | 0.12.7 | 0.12.7 | 1.0.0 | 1.0.0 | 1.0.0 |
Bowtie2 | 2.3.4.3 | 2.1.02.3.4.3 | 2.3.4.3 | 2.1.0 | |
BWA | 0.7.12 | 0.7.12 | 0.7.12 | 0.7.12 | 0.7.12 |
CAP3 | 12/21/07 | 12/21/07 | 12/21/07 | 12/21/07 | 12/21/07 |
CEAS | 1.0.2 | 1.0.2 | 1.0.2 | 1.0.2 | N/A |
CLARK | N/A | N/A | 1.2.4 (UGENE-customized) | 1.2.4 (UGENE-customized) | N/A|
ClustalO | 1.2.1 | 1.2.11.2.1 | 1.2.1 | 1.2.1 | |
ClustalW | 2.1 | 2.12.1 | 2.1 | 2.1 | |
ConductGO | Version not specified | Version not specified | Version not specified | Version not specified | N/A |
conservation_plot | 0.1.0 | 0.1.0 | 0.1.0 | 0.1.0 | N/A |
Cufflinks tools | N/A | N/A | 2.0.2 | 2.0.2 | N/A |
Cutadapt | 1.7.11.7.1 | 1.7.1 | 1.7.1 | 1.7.1 | |
DIAMOND | N/A | N/A | 0.9.22 | 0.9.22 | N/A|
FastQC | 0.11.20.11.2 | 0.11.2 | 0.11.2 | 0.11.2 | |
JRE (java) | 1.8.0 | 1.8.0 | N/A | N/A | N/A |
HMMER | 3.1b2 | 3.1b23.1b2 | 3.1b2 | 3.1b2 | |
Kraken | N/AN/A | 1.0 | 1.0 | N/A | |
MACS | 1.4.2 | 1.4.2 | 1.4.2 | 1.4.2 | N/A |
MAFFT | 7.212450 | 7.212450 | 7.212 | 7.212 | 7.212450 |
MetaPhlAn2 | N/A | N/A | 2.0.0 | 2.0.0 | N/A |
MrBayes | 3.2.3 | 3.2.3 | 3.2.3 | 3.2.3 | 3.2.3 |
peak2gene | 1.02 | 1.02 | 1.02 | 1.02 | N/A |
perl | 5.24.35.24.0 | N/A | N/A | N/A | |
PhyML | 20120412 | 20120412 | 20120412 | 20120412 | 20120412 |
python | 2.7.5 | 2.7.5 | 2.7.5 | 2.7.5 | 2.7.5 |
Rscript | R is not included into the External Tools Packages. However, it may be installed using the UGENE Online Installer package. | ||||
samtools | 0.1.19 | 0.1.19 | 0.1.19 | 0.1.19 | 0.1.19 |
SeqPos | 1.011.01 | 1.01 | 1.01 | N/A | |
SnpEff | 4.3i | 4.3i | 4.3i | 4.3i | 4.3i |
SPAdes | N/AN/A | 3.12.0 | 3.12.0 | N/A | |
Spidey | Version not specified | Version not specified | N/A | Version not specifiedVersion not specified | |
StringTie | N/A | N/A | 1.3.4d | 1.3.4d | N/A|
T-Coffee | 8.99 | 8.99 | 11.00 | 11.00 | 11.00 |
TopHat | N/A | N/A | 2.1.1 | 2.1.1 | N/A |
Trimmomatic | 0.38 | 0.38 | 0.38 | 0.38 | 0.38 |
vcftools | 0.1.12b | 0.1.12b0.1.12b | 0.1.12b | 0.1.12b | |
WEVOTE | N/A | N/A | Version not specified | Version not specified | N/A