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Docker version of RiboGalaxy
20-Sep-2017, 10:36 AM
Post: #1
Docker version of RiboGalaxy
Dear user,
I just want to bring your attention to our release of RiboGalaxy on docker. This docker release of RiboGalaxy can be pulled from https://hub.docker.com/r/riboseq/ribogalaxy/ once you have installed and configured docker https://www.docker.io/gettingstarted/#h_installation.
For complete documentation and getting started with docker refer https://docs.docker.com/get-started/
Any queries related to this docker version of RiboGalaxy can be posted here.

Kind Regards
jamesp
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08-Mar-2018, 11:44 AM
Post: #2
RE: Docker version of RiboGalaxy
Hi,
we've set ribogalaxy docker up and it works fine in terms of uploading files and preliminary analysis but when I get to the point of rRNA removal using Bowtie it doesn't give the options of built-in index as the ribogalaxy normally does, even though I've clicked at the correct gemome assembly when I first uploaded my dataset. Could that have to do with the docker version?

Thanks for any replies,

Katerina
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08-Mar-2018, 03:56 PM
Post: #3
RE: Docker version of RiboGalaxy
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
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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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15-May-2018, 12:06 PM
Post: #5
RE: Docker version of RiboGalaxy
Hi,
I've been using the ribogalaxy docker and it was all running ok until today when I ran a Triplet periodicity and a Metagene analysis which appeared to have worked (green) but had the message "Fontconfig error: Cannot load default config file". When I try the next steps (plot ribosome profile and differential translation analysis) they start running but fail -differential translation analysis was running for ~2h before failing). The error message says
"Error in .local(.Object, ...) :
All vectors in '@groups' slot must equal number of columns of '@data' slot.
Fatal error: Exit code 1 (Error)
Traceback (most recent call last):
File "/shed_tools/toolshed.ribogalaxy.ucc.ie/repos/ribogalaxy/riboseqr_wr"

Anyone having an idea of why that happens or had the same issue?

Thanks for any advice,

Katerina
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