Unipro UGENE User Manual v. 34
Page tree

Versions Compared

Old Version 1

changes.mady.by.user Dmitrii Sukhomlinov

Saved on

compared with

New Version Current

changes.mady.by.user Olga Golosova

Saved on

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.

...

See the list of the currently integrated external tools, information about their availability on different operating systems and version included into the corresponding External Tools Package in the table below.

 


External toolWindows (64-bit)
Windows (32-bit)
macOS (64-bit)Linux (64
-bit)Linux (32
-bit)
bedGraphToBigWig4
N/A
44
N/A
bedtools
2.20.1
2.20.12.20.12.20.1
2.20.1
BLAST
2.2.262.2.262.2.262.2.262.2.26BLAST
+
2.2.302.2.30
2.2.302.2.302.2.30
Bowtie
0.12.7
0.12.71.0.01.0.0
1.0.0
Bowtie22.3.4.32.
1.02.
3.4.32.3.4.3
2.1.0
BWA
0.7.120.7.12
0.7.120.7.120.7.12
CAP312/21/07

12/21/07

12/21/07
12/21/0712/21/07
CEAS
1.0.2
1.0.21.0.21.0.2
N/A

CLARK

N/A

N/A1.2.4 (UGENE-customized)1.2.4 (UGENE-customized)
N/A
ClustalO1.2.11.2.11.2.1
1.2.11.2.1
ClustalW
2.1
2.12.12.1
2.1
ConductGOVersion not specifiedVersion not specifiedVersion not specified
Version not specifiedN/A
conservation_plot
0.1.0
0.1.00.1.00.1.0
N/A
Cufflinks tools
N/A
N/A2.0.22.0.2
N/A
Cutadapt
1.7.1
1.7.11.7.11.7.1
1.7.1
DIAMONDN/A
N/A
0.9.220.9.22
N/A
FastQC
0.11.20.11.2
0.11.20.11.20.11.2
JRE (java)
1.8.0
1.8.0N/AN/A
N/A
HMMER3.1b23.1b23.1b2
3.1b23.1b2
Kraken
N/A
N/A1.01.0
N/A
MACS1.4.21.4.21.4.2
1.4.2N/A
MAFFT7.
212
4507.
212
4507.
2127.2127.212

MetaPhlAn2

N/A
450

MetaPhlAn2

N/A2.0.02.0.0
N/A
MrBayes
3.2.3
3.2.33.2.33.2.3
3.2.3
peak2gene
1.02
1.021.021.02
N/A
perl5.24.3
5.24.0N/A
N/AN/A
PhyML
2012041220120412
201204122012041220120412
python2.7.52.7.52.7.5
2.7.52.7.5
RscriptR is not included into the External Tools Packages. However, it may be installed using the UGENE Online Installer package.
samtools
0.1.190.1.19
0.1.190.1.190.1.19
SeqPos
1.01
1.011.011.01
N/A
SnpEff4.3i4.3i4.3i
4.3i4.3i
SPAdes
N/A
N/A3.12.03.12.0
N/A
SpideyVersion not specified
Version not specified
N/A
Version not specified
Version not specified
StringTieN/A
N/A
1.3.4d1.3.4d
N/A
T-Coffee8.99
8.99
11.0011.00
11.00
TopHat
N/A
N/A2.1.12.1.1
N/A
Trimmomatic0.380.380.38
0.380.38
vcftools
0.1.12b
0.1.12b0.1.12b0.1.12b
0.1.12b
WEVOTE
N/A
N/AVersion not specifiedVersion not specified
N/A