The REPET package is a package integrating bioinformatics programs in order to tackle biological issues at the genomic scale. REPET consists in two main pipelines, TEdenovo and TEannot, which are dedicated to the detection, annotation and analysis of repeats in genomic sequences. These pipelines are specifically designed for transposable elements (TEs) detection and annotation.
- TEdenovo - this pipeline starts by comparing the genome with itself using BLASTER. Then it clusters matches with GROUPER, RECON and PILER, programs specific for interspersed repeats. For each cluster, it builds a multiple alignment from which a consensus sequence is derived. Finally these consensus are classified according to TE features and redundant consensus are removed. At the end we obtain a library of classified, non-redundant consensus sequences.
- TEannot - this pipeline mines a genome with a library of TE sequences, for instance the one produced by the TEdenovo pipeline, using BLASTER, RepeatMasker and CENSOR. An empirical statistical filter is applied to discard false-positive matches. Short simple repeats (SSRs) are annotated along the way with TRF, RepeatMasker and MREPS. Then, MATCHER, via dynamic programming, chains TE fragments belonging to the same, disrupted copy. A "long join" procedure is subsequently applied to connect distant fragments. Finally, annotations are exported into GFF3 or gameXML files.
Versions and Availability
Softenv Keys for repet on supermike2
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The information here is applicable to LSU HPC and LONI systems.
A user may choose between using /bin/bash and /bin/tcsh. Details about each shell follows.
System resource file: /etc/profile
When one access the shell, the following user files are read in if they exist (in order):
- ~/.bash_profile (anything sent to STDOUT or STDERR will cause things like rsync to break)
- ~/.bashrc (interactive login only)
When a user logs out of an interactive session, the file ~/.bash_logout is executed if it exists.
The default value of the environmental variable, PATH, is set automatically using SoftEnv. See below for more information.
The file ~/.cshrc is used to customize the user's environment if his login shell is /bin/tcsh.
SoftEnv is a utility that is supposed to help users manage complex user environments with potentially conflicting application versions and libraries.
System Default Path
When a user logs in, the system /etc/profile or /etc/csh.cshrc (depending on login shell, and mirrored from csm:/cfmroot/etc/profile) calls /usr/local/packages/softenv-1.6.2/bin/use.softenv.sh to set up the default path via the SoftEnv database.
SoftEnv looks for a user's ~/.soft file and updates the variables and paths accordingly.
Viewing Available Packages
The command softenv will provide a list of available packages. The listing will look something like:
$ softenv These are the macros available: * @default These are the keywords explicitly available: +amber-8 Applications: 'Amber', version: 8 Amber is a +apache-ant-1.6.5 Ant, Java based XML make system version: 1.6. +charm-5.9 Applications: 'Charm++', version: 5.9 Charm++ +default this is the default environment...nukes /etc/ +essl-4.2 Libraries: 'ESSL', version: 4.2 ESSL is a sta +gaussian-03 Applications: 'Gaussian', version: 03 Gaussia ... some stuff deleted ...
The file ~/.soft in the user's home directory is where the different packages are managed. Add the +keyword into your .soft file. For instance, ff one wants to add the Amber Molecular Dynamics package into their environment, the end of the .soft file should look like this:
To update the environment after modifying this file, one simply uses the resoft command:
The command soft can be used to manipulate the environment from the command line. It takes the form:
$ soft add/delete +keyword
Using this method of adding or removing keywords requires the user to pay attention to possible order dependencies. That is, best results require the user to remove keywords in the reverse order in which they were added. It is handy to test out individual keys, but can lead to trouble if changing multiple keys. Changing the .soft file and issuing the resoft is the recommended way of dealing with multiple changes.
- For additional information, see the text files in: /usr/local/packages/bioinformatics/REPET/2.0/doc (as of the time this was written).
Last modified: August 22 2017 15:10:53.