RepeatModeler | De-Novo Repeat Discovery Tool

by Dfam-consortium Perl Version: 2.0.4 License: Non-SPDX

X-Ray Key Features Code Snippets Community Discussions(1)Vulnerabilities Install Support

kandi X-RAY | RepeatModeler Summary

RepeatModeler is a Perl library. RepeatModeler has no bugs, it has no vulnerabilities and it has low support. However RepeatModeler has a Non-SPDX License. You can download it from GitHub.

RepeatModeler is a de novo transposable element (TE) family identification and modeling package. At the heart of RepeatModeler are three de-novo repeat finding programs ( RECON, RepeatScout and LtrHarvest/Ltr_retriever ) which employ complementary computational methods for identifying repeat element boundaries and family relationships from sequence data. RepeatModeler assists in automating the runs of the various algorithms given a genomic database, clustering redundant results, refining and classifying the families and producing a high quality library of TE families suitable for use with RepeatMasker and ultimately for submission to the Dfam database ( ).

Support

Quality

Security

License

Reuse

Support

RepeatModeler has a low active ecosystem.

It has 142 star(s) with 20 fork(s). There are 7 watchers for this library.

It had no major release in the last 12 months.

There are 95 open issues and 92 have been closed. On average issues are closed in 65 days. There are 1 open pull requests and 0 closed requests.

It has a neutral sentiment in the developer community.

The latest version of RepeatModeler is 2.0.4

Quality

RepeatModeler has no bugs reported.

Security

RepeatModeler has no vulnerabilities reported, and its dependent libraries have no vulnerabilities reported.

License

RepeatModeler has a Non-SPDX License.

Non-SPDX licenses can be open source with a non SPDX compliant license, or non open source licenses, and you need to review them closely before use.

Reuse

RepeatModeler releases are available to install and integrate.

Installation instructions, examples and code snippets are available.

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RepeatModeler Key Features

No Key Features are available at this moment for RepeatModeler.

RepeatModeler Examples and Code Snippets

No Code Snippets are available at this moment for RepeatModeler.

Community Discussions

Trending Discussions on RepeatModeler

Run singularity docker in cluster

QUESTION

Run singularity docker in cluster

Asked 2020-Dec-02 at 12:51

for a sientific projet I need to use the singularity project here : https://github.com/Dfam-consortium/TETools

I manage to run it by running the Wrapper script : bash dfam-tetools.sh

then I get a new environment :

...

ANSWER

Answered 2020-Dec-02 at 12:51

Edit

Since it is necessary to have access to another directory not in the current one, the singularity command should be run instead of the dfam-tetools.sh script:

Source https://stackoverflow.com/questions/65105545

Community Discussions, Code Snippets contain sources that include Stack Exchange Network

Vulnerabilities

No vulnerabilities reported

Install RepeatModeler

Obtain the source distribution Github : https://github.com/Dfam-consortium/RepeatModeler Available by cloning the master branch of the RepeatModeler repository ( latest released version ) or by downloading a release from the repository "releases" tab. or RepeatMasker Website : http://www.repeatmasker.org/RepeatModeler
Uncompress and expand the distribution archive: ``` tar -zxvf RepeatModeler-#.#.tar.gz ```
Configure for your site: Automatic: + Run the "configure" script interactively with prompts for each setting: perl ./configure + Run the "configure" script with supplied paramters: perl ./configure -rscout_dir .. -recon_dir .. By Hand: + Edit the configuration file "RepModelConfig.pm" Dynamically: + Use the "configuration overrides" command line options with the RepeatModeler programs. e.g: ./RepeatModeler -rscout_dir .. -recon_dir ..

Support

For any new features, suggestions and bugs create an issue on GitHub. If you have any questions check and ask questions on community page Stack Overflow .

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