[ensembl-dev] Ensembl annotation pipeline software available?

[Thibaut Hourlier]

Hi David,
Yes all the code used by Ensembl is free to use and can be found on github.com/Ensembl <http://github.com/Ensembl>. Unfortunately we do not have a proper documentation on how to install the pipelines and how to use them but we are working on it.

If by locally you mean on your laptop, it might take some time, probably more than a month but it is hard to predict. Our pipeline is made to be run on a cluster with hundreds of job running in parallel.

All our pipelines are made to use MySQL databases which are created when the pipeline needs them. You need to have a database with the Ensembl schema containing your dna. If the assembly is available at NCBI the pipeline will do the right thing. Otherwise you will need to manually load your assembly into the database.

We are using linuxbrew to install all the software we need:
https://github.com/Ensembl/homebrew-ensembl <https://github.com/Ensembl/homebrew-ensembl>
https://github.com/Ensembl/homebrew-cask <https://github.com/Ensembl/homebrew-cask>
https://github.com/Ensembl/homebrew-external <https://github.com/Ensembl/homebrew-external>
https://github.com/Ensembl/homebrew-moonshine <https://github.com/Ensembl/homebrew-moonshine> (you will need to get the license and archive for software like genscan)
brew tap ensembl/ensembl
brew tap ensembl/cask
brew tap ensembl/external
brew tap ensembl/moonshine
brew install genebuild-annotation
brew install rnaseq-pipeline

Once all the softwares are installed, you will need these repositories to run the pipeline:
https://github.com/Ensembl/ensembl <https://github.com/Ensembl/ensembl>
https://github.com/Ensembl/ensembl-analysis <https://github.com/Ensembl/ensembl-analysis> dev/hive_master (branch)
https://github.com/Ensembl/ensembl-hive <https://github.com/Ensembl/ensembl-hive>
https://github.com/Ensembl/ensembl-compara <https://github.com/Ensembl/ensembl-compara>
https://github.com/Ensembl/ensembl-io <https://github.com/Ensembl/ensembl-io>
https://github.com/Ensembl/ensembl-killlist <https://github.com/Ensembl/ensembl-killlist>
https://github.com/Ensembl/ensembl-production <https://github.com/Ensembl/ensembl-production>
https://github.com/bioperl/bioperl-live <https://github.com/bioperl/bioperl-live> release-1-6-924 (tag)

ensembl-hive is our job manager which we use with LSF, SGE is supported and some others job scheduler too. If you want to run jobs locally a bit more tuning might be required.

The configuration of the pipeline will need some tweaking but we will be happy to help.

Thanks
Thibaut


> On 9 Apr 2018, at 17:46, David Mathog <mathog at caltech.edu> wrote:
> 
> On 06-Apr-2018 14:12, David Mathog wrote:
>> Greetings all,
>> Is the software used for this
>>   http://uswest.ensembl.org/info/genome/genebuild/automatic_coding.html
>> publicly available?  That is, can it be downloaded and run locally?
> 
> Found these:
> 
> https://github.com/Ensembl/ensembl-analysis
>  Modules to interface with tools used in Ensembl Gene Annotation
>  Process and scripts to run pipelines
> 
> https://github.com/Ensembl/ensembl
>  The Ensembl Core Perl API and SQL schema
> 
> https://github.com/Ensembl/ensembl-annotation
>  The Ensembl gene annotation pipeline (a work in progress)
> 
> and dozens of others.  Have not located any documentation about how to install and run the pipeline though.  Anybody know where that might be, or who to ask???
> 
> I only need the parts to work from data in (genome, proteins, RNA) to gff output.  Anything having to do with checking data into or out of EMBL databases is not required.
> 
> Thanks,
> 
> David Mathog
> mathog at caltech.edu
> Manager, Sequence Analysis Facility, Biology Division, Caltech
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