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marcelauliano / MitoHiFi

Find, circularise and annotate mitogenome from PacBio assemblies
MIT License
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where to download the Singularity image file mitohifi-v2.sif #8

Closed yizhouc closed 2 years ago

yizhouc commented 3 years ago

I am trying to use the singularity image and could not find the depot of mitohifi-v2.sif. Yizhou

ksenia-krasheninnikova commented 3 years ago

hi Yizhou, in order to build a singularity image you would need to build a docker container first (see https://github.com/marcelauliano/MitoHiFi#running-mitohifiv2-from-a-singularity-image) then save it to a tar archive and further convert it to a singularity container using the following commands: docker save ${HASH} -o mitohifi-v2.tar singularity build mitohifi-v2.sif docker-archive://mitohifi-v2.tar

yizhouc commented 3 years ago

Hi Ksenina, thanks for your quick reply. The singularity image works now. I was worried when I was building the docker image as there were a number of error messages displayed on the screen. thanks a lot. Yizhou

bishopia commented 2 years ago

Hi Yizhou, Is there any chance this docker file will be hosted in an online repo at some point, so we can pull and build the singularity image directly from a HPC cluster?

ksenia-krasheninnikova commented 2 years ago

We are working on it now.

claumer commented 2 years ago

Hi there - has this been followed up on? Would love to be able to download a singularity image from a repo.

yizhouc commented 2 years ago

Hi Christopher, Thanks for the following up. I should have informed you earlier that the image works fine. You can close this issue. I used it to assembly five spider mite genomes, it worked well.

With best wishes

Yizhou

Dr Yizhou Chen | Senior Research Scientist - Animal Genomics NSW Department of Primary Industries Elizabeth Macarthur Agricultural Institute | Woodbridge Road Menangle 2568 | PMB 4008 Narellan 2567 Australia Phone 61 2 4640 6453 Fax 61 2 46406300 @.**@.>

From: Christopher E. Laumer @.> Sent: Tuesday, 12 April 2022 7:10 AM To: marcelauliano/MitoHiFi @.> Cc: Yizhou Chen @.>; Author @.> Subject: Re: [marcelauliano/MitoHiFi] where to download the Singularity image file mitohifi-v2.sif (#8)

Hi there - has this been followed up on? Would love to be able to download a singularity image from a repo.

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yizhouc commented 2 years ago

Thanks. It works now. we can close this issue now.

marcelauliano commented 2 years ago

Hi all, new docker image for new version on github today v2.2 Let us know if anything breaks!

https://github.com/marcelauliano/MitoHiFi

Em seg., 11 de abr. de 2022 às 22:44, yizhouc @.***> escreveu:

Closed #8 https://github.com/marcelauliano/MitoHiFi/issues/8.

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-- Marcela Uliano da Silva, PhD

Senior Bioinformatician - Wellcome Sanger Institute Darwin Tree of Life Project

Churchill College Cambridge By-Fellow

Cambridge, UK