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Docker version of RiboGalaxy
08-Mar-2018, 04:31 PM
Post: #4
RE: Docker version of RiboGalaxy
(08-Mar-2018 03:56 PM)audrey Wrote:  Hi Katerina,

Firstly, thanks very much for you interest in the RiboGalaxy docker.

You are correct in that the bowtie indexes are not available in the docker version. The reason for this is that the genomic and rRNA indexes on the public RiboGalaxy GUI version are quite large and so for space reasons we do not provide them with the docker version.

If you are using the docker for your own personal use, we could provide you with the rRNA sequences you require which you can upload to your history and when running the 'Remove rRNA using Bowtie' tool, select ' Use one from the history' for the index drop-down selection. All the other parameters will remain the same.

If, on the other hand, you wish for the docker to be used by your group, then we could send you instructions which would involve some command line statements etc. If you can let us know if this is of interest?

Kind regards,
Audrey


Hi Audrey,
thank you very much!! We would like to have rRNA indexes and reference genomes (for alignment to genome) for human hg19 and hg38 and Drosophila melanogaster, of that's ok. My email is bsad@leeds.ac.uk. I will be looking forward to hearing back from you,

all the best,

Katerina
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Messages In This Thread
Docker version of RiboGalaxy - jamesp - 20-Sep-2017, 10:36 AM
RE: Docker version of RiboGalaxy - audrey - 08-Mar-2018, 03:56 PM
RE: Docker version of RiboGalaxy - Katerina-D - 08-Mar-2018 04:31 PM
RE: Docker version of RiboGalaxy - jamesp - 21-May-2018, 11:50 AM

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