Installation of external software

TRAL is dependend on different external software which need to be installed before TRAL can be used.

Here, we explain how to install external software packages, such as de novo tandem repeat detectors. _Important_: Once a software is installed, the path to either the binary or the executable shell script needs to be indicated in the TRAL configuration file config.ini.

For each of the software an installation script can be found for :ref: easy setup <easy_setup>.

Sequence profile model generation

At current, only support for HMMER is integrated published in Bioinformatics (2008) (Installation instructions). TRAL searches for HMMER’s hmmbuild in the system path by default (modify in config.ini):

[hmm]
    hmmbuild = hmmbuild

If hmmbuild is not in your system path, set the absolute path:

[hmm]
    hmmbuild = path/to/hmmbuild

Alignment of tandem repeat units

Currently, MAFFT is the default tool for (re-)alignment of the tandem repeat units to each other (Installation instructions). TRAL searches for MAFFT’s ginsi in the system path by default (modify in config.ini):

[repeat]
    ginsi = ginsi

If ginsi is not in your system path, set the absolute path:

[repeat]
    ginsi = path/to/ginsi

Realignment of tandem repeat units with indel aware proPIP algorithm

The alignment module of (Castor) can be used to realign tandem repeat units with the indel aware algorithm proPIP (Installation instructions). TRAL searches for Castor in the system path by default (modify in config.ini):

[repeat]
    Castor = Castor

If Castor is not in your system path, set the absolute path:

[repeat]
    Castor = path/to/Castor

Currently integrated detectors

Software	License
HHrepID	CC-BY-NC-2.0
PHOBOS	Non-commercial
TRED	Non-commercial
T-REKS	Non-commercial?
TRF	Unlimited use
TRUST	?
XSTREAM	Non-commercial

HHrepID

HHrepID is a profile self alignment de novo amino acid tandem repeat detection software published e.g. in PLOS Computational Biology (2011) (Installation instructions). TRAL searches for the executable binary hhrepid64 in the system path by default (modify in config.ini):

[sequence]
    [[repeat_detector_path]]
        HHrepID = hhrepid_64

If the executable hhrepid is not in your system path, set the absolute path:

[sequence]
    [[repeat_detector_path]]
        HHrepID = path/to/hhrepid

Also, you need to supply a null hmm file for using HHrepID. A dummy file is located in your home/.tral. Supply the path to your null hmm file of choice:

[sequence]
    [[repeat_detector_path]]
        HHrepID_dummyhmm = /path/to/home/.tral/data/dummyHMM.hmm

PHOBOS

PHOBOS is an unpublished k-mer based de novo DNA tandem repeat detection software. TRAL searches for the executable phobos in the system path by default (modify in config.ini):

[sequence]
    [[repeat_detector_path]]
        PHOBOS = phobos

If phobos is not in your system path, set the absolute path:

[sequence]
    [[repeat_detector_path]]
        PHOBOS = path/to/phobos

TRED

TRED is a sequence self alignment de novo amino acid tandem repeat detection software published in Bioinformatics (2007) (The software is available on request). TRAL searches for the executable tred in the system path by default (modify in config.ini):

[sequence]
    [[repeat_detector_path]]
        TRED = tred

If phobos is not in your system path, set the absolute path:

[sequence]
    [[repeat_detector_path]]
        TRED = path/to/tred

T-REKS

T-REKS is a k-mer based de novo DNA/AA tandem repeat detection software published in Bioinformatics (2009) (Installation instructions). Create an executable text file T-REKS with the following content:

#!/bin/sh
java -jar /my/path/to/T-Reks.jar "$@"

If you place this text file in your systems path, TRAL finds it by default (modify in config.ini):

[sequence]
    [[repeat_detector_path]]
        T-REKS = T-REKS

If you did not place T-REKS in your system path or named it differently, set the absolute path:

[sequence]
    [[repeat_detector_path]]
        T-REKS = path/to/T-REKS

TRF

TRF is a k-mer based self alignment de novo DNA tandem repeat detection software published in Nucleic Acids Research (1999) (Installation instructions). TRAL searches for the executable trf in the system path by default (modify in config.ini):

[sequence]
    [[repeat_detector_path]]
        TRF = trf

If trf is not in your system path, set the absolute path:

[sequence]
    [[repeat_detector_path]]
        TRF = path/to/trf

TRUST

TRUST is a sequence self alignment de novo amino acid tandem repeat detection software published in Bioinformatics (2004) (Installation instructions).

Create an executable text file TRUST with the following content (you can amend the java memory consumption restrictions):

#!/bin/sh
java -Xmx30G -cp /my/path/to/TRUST/1.0.0/Align nl.vu.cs.align.SelfSimilarity "$@"

If you place this text file in your systems path, TRAL finds it by default (modify in config.ini):

[sequence]
    [[repeat_detector_path]]
        TRUST = TRUST

If you did not place TRUST in your system path or named it differently, set the absolute path:

[sequence]
    [[repeat_detector_path]]
        TRUST = path/to/TRUST

Also, you need to supply a substitution matrix for using TRUST (it ships with several substitution matrices). Supply the path of your favourite substitution matrix:

[sequence]
    [[repeat_detector_path]]
        TRUST_substitutionmatrix = /path/to/TRUST/Align/BLOSUM50

XSTREAM

XSTREAM is a k-mer based de novo DNA/AA tandem repeat detection software published in BMC Bioinformatics (2007) (Installation instructions).

Create an executable text file XSTREAM with the following content:

#!/bin/sh
java -jar /my/path/to/xstream.jar "$@"

If you place this text file in your systems path, TRAL finds it by default (modify in config.ini):

[sequence]
    [[repeat_detector_path]]
        XSTREAM = XSTREAM

If you did not place XSTREAM in your system path or named it differently, set the absolute path:

[sequence]
    [[repeat_detector_path]]
        XSTREAM = path/to/XSTREAM

Simulation of evolution in tandem repeats

For simulating evolved sequences ALF can be used which simulates a root genome into a number of related genomes. It was published in Molecular Biology and Evolution (2012) and can be downloaded on alfsim.org. TRAL searches for ALFs executable alfsim in the system path by default (modify in config.ini):

[repeat]
    alfsim = alfsim

If alfsim is not in your system path, set the absolute path:

[repeat]
    alfsim = path/to/alfsim

Not yet integrated software

There is a large number of tandem repeat detection software for which TRAL does not provide parsers. However, theses parsers are easily manually added to sequence.repeat_detection_io. Please file an issue on the tracker.