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berkeley-dsep-infra / datahub

JupyterHubs for use by Berkeley enrolled students
https://docs.datahub.berkeley.edu
BSD 3-Clause "New" or "Revised" License
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Request NanoClust for Calgenomics on Biology hub #3382

Closed petersudmant closed 2 years ago

petersudmant commented 2 years ago

Package Name

https://github.com/genomicsITER/NanoCLUST

Hub details

Course Name

https://ib.berkeley.edu/cgsre

Semester Details

now

Installation Deadline

05/17/2022

balajialg commented 2 years ago

@petersudmant @felder will be on vacation during the next couple of days. Considering his nonavailability and the tight deadline for the installation, Will you be able to create a new PR to install this package (if in case you had added this package to the docker image prior?) Please let us know!

or else @yuvipanda Would you have some bandwidth to help with this package installation?

yuvipanda commented 2 years ago

@petersudmant I'm not entirely sure what needs to be installed here. Is it nextflow? The linked GitHub repo seems to indicate that it might require docker access at runtime, which we don't have. It also suggests ~32-36GB of RAM requirement, which the biology hub doesn't have either.

3383 adds java, and that should allow you to install nextflow (https://nf-co.re/usage/installation) and try this out. Wanna give it a go?

petersudmant commented 2 years ago

bah - this seems like a no go. the package is this https://github.com/genomicsITER/NanoCLUST - for which nextflow is required. Shall we abandon ship?

On Thu, May 12, 2022 at 5:57 AM Yuvi Panda @.***> wrote:

@petersudmant https://github.com/petersudmant I'm not entirely sure what needs to be installed here. Is it nextflow https://nf-co.re/usage/installation? The linked GitHub repo seems to indicate that it might require docker access at runtime, which we don't have. It also suggests ~32-36GB of RAM requirement, which the biology hub doesn't have either.

3383 https://github.com/berkeley-dsep-infra/datahub/pull/3383 adds

java, and that should allow you to install nextflow ( https://nf-co.re/usage/installation) and try this out. Wanna give it a go?

— Reply to this email directly, view it on GitHub https://github.com/berkeley-dsep-infra/datahub/issues/3382#issuecomment-1124960689, or unsubscribe https://github.com/notifications/unsubscribe-auth/AJTP6FXAWCSUJCZ3WNAXBKTVJT53XANCNFSM5VVXBOHA . You are receiving this because you were mentioned.Message ID: @.***>

-- Peter Sudmant Assistant Professor (he/him/his) Department of Integrative Biology University of California, Berkeley 510-664-4700

yuvipanda commented 2 years ago

@petersudmant yeah, I think docker is a no-go, and I'm not sure about 36GB of RAM - we can probably do that for a really short time for a really small subset of users, but a bit messy.

petersudmant commented 2 years ago

I’ll get the requestors to find an alternative option. Close out.

On Thu, May 12, 2022 at 6:45 AM Yuvi Panda @.***> wrote:

@petersudmant https://github.com/petersudmant yeah, I think docker is a no-go, and I'm not sure about 36GB of RAM - we can probably do that for a really short time for a really small subset of users, but a bit messy.

— Reply to this email directly, view it on GitHub https://github.com/berkeley-dsep-infra/datahub/issues/3382#issuecomment-1125015707, or unsubscribe https://github.com/notifications/unsubscribe-auth/AJTP6FSPMJBCDJB3GXATRALVJUDP7ANCNFSM5VVXBOHA . You are receiving this because you were mentioned.Message ID: @.***>

-- Peter Sudmant Assistant Professor (he/him/his) Department of Integrative Biology University of California, Berkeley 510-664-4700

yuvipanda commented 2 years ago

Thanks @petersudmant!

balajialg commented 2 years ago

@petersudmant If required can put the instructor in touch with peers at Research IT running Savio systems. Considering the large compute requirements, they may be able to help here. Amy Neeser (Amy Neeser aneeser@berkeley.edu) is their point of contact for any such inquiries.