Page tree

Versions Compared

Key

  • This line was added.
  • This line was removed.
  • Formatting was changed.

...

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:

  1.  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.

  2. Configure the tools in UGENE: open the UGENE Application Settings dialog, select the "External Tools" page and specify the external tools executables.

...

External toolWindows (64-bit)macOS (64-bit)Linux (64-bit)
bedGraphToBigWig444
bedtools2.20.12.20.12.20.1
BLAST+2.2.302.2.302.2.30
Bowtie0.12.71.0.01.0.0
Bowtie22.3.4.32.3.4.32.3.4.3
BWA0.7.120.7.120.7.12
CAP312/21/07

12/21/07

12/21/07
CEAS1.0.21.0.21.0.2

CLARK

N/A1.2.4 (UGENE-customized)1.2.4 (UGENE-customized)
ClustalO1.2.11.2.11.2.1
ClustalW2.12.12.1
ConductGOVersion not specifiedVersion not specifiedVersion not specified
conservation_plot0.1.00.1.00.1.0
Cufflinks toolsN/A2.0.22.0.2
Cutadapt1.7.11.7.11.7.1
DIAMONDN/A0.9.220.9.22
FastQC0.11.20.11.20.11.2
JRE (java)1.8.0N/AN/A
HMMER3.1b23.1b23.1b2
KrakenN/A1.01.0
MACS1.4.21.4.21.4.2
MAFFT7.2124507.2124507.212450

MetaPhlAn2

N/A2.0.02.0.0
MrBayes3.2.33.2.33.2.3
peak2gene1.021.021.02
perl5.24.3N/AN/A
PhyML201204122012041220120412
python2.7.52.7.52.7.5
RscriptR is not included into the External Tools Packages. However, it may be installed using the UGENE Online Installer package.
samtools0.1.190.1.190.1.19
SeqPos1.011.011.01
SnpEff4.3i4.3i4.3i
SPAdesN/A3.12.03.12.0
SpideyVersion not specifiedN/AVersion not specified
StringTieN/A1.3.4d1.3.4d
T-Coffee8.9911.0011.00
TopHatN/A2.1.12.1.1
Trimmomatic0.380.380.38
vcftools0.1.12b0.1.12b0.1.12b
WEVOTEN/AVersion not specifiedVersion not specified