Source Code to Run locally

[yzakir51]

Hello,

Our team wants to run the WGS pipeline locally on the HPC cluster. Please can you guide us how to do it?

Regards,
Yusuf.

[stephansanders]

Hi Yusuf, There are two components to this pipeline: 1) Docker containers with the individuals tools 2) A list of steps for the containers 3) The pipeline infrastructure on AWS The first of these should be portable to the HPC. The second could also be used on a local HPC, but might need some modifications. The third of these makes use of many AWS specific tools which will not have on the HPC. I hope that helps S

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On Fri, Feb 21, 2020 at 11:08 AM yzakir51 ***@***.***> wrote: Hello, Our team wants to run the WGS pipeline locally on the HPC cluster. Please can you guide us how to do it? Regards, Yusuf. — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#3?email_source=notifications&email_token=ABV4BAPVDDBWHFKDUMVCO63REAREBA5CNFSM4KZIZCP2YY3PNVWWK3TUL52HS4DFUVEXG43VMWVGG33NNVSW45C7NFSM4IPMIUXA>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABV4BAIJHWZHNU4TAEBHFT3REAREBANCNFSM4KZIZCPQ> .

-- Stephan Sanders, BMBS, PhD Associate Professor, UCSF Sanders Lab <http://sanderslab.ucsf.edu> To schedule a meeting please click here <http://doodle.com/stephansanders>

[gilsonm]

Greetings, Yusuf I can help answer your questions. Do let me know what you need! All the best, Michael On Fri, Feb 21, 2020 at 1:06 PM Stephan Sanders <notifications@github.com> wrote:

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Hi Yusuf, There are two components to this pipeline: 1) Docker containers with the individuals tools 2) A list of steps for the containers 3) The pipeline infrastructure on AWS The first of these should be portable to the HPC. The second could also be used on a local HPC, but might need some modifications. The third of these makes use of many AWS specific tools which will not have on the HPC. I hope that helps S On Fri, Feb 21, 2020 at 11:08 AM yzakir51 ***@***.***> wrote: > Hello, > > Our team wants to run the WGS pipeline locally on the HPC cluster. Please > can you guide us how to do it? > > Regards, > Yusuf. > > — > You are receiving this because you are subscribed to this thread. > Reply to this email directly, view it on GitHub > < #3?email_source=notifications&email_token=ABV4BAPVDDBWHFKDUMVCO63REAREBA5CNFSM4KZIZCP2YY3PNVWWK3TUL52HS4DFUVEXG43VMWVGG33NNVSW45C7NFSM4IPMIUXA >, > or unsubscribe > < https://github.com/notifications/unsubscribe-auth/ABV4BAIJHWZHNU4TAEBHFT3REAREBANCNFSM4KZIZCPQ > > . > -- Stephan Sanders, BMBS, PhD Associate Professor, UCSF Sanders Lab <http://sanderslab.ucsf.edu> To schedule a meeting please click here <http://doodle.com/stephansanders> — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#3?email_source=notifications&email_token=ADAIU5UYSJKA5XIAAXCD2V3REA64TA5CNFSM4KZIZCP2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEMUCVIY#issuecomment-589834915>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ADAIU5TODCIPD2UT5GKQJITREA64TANCNFSM4KZIZCPQ> .

-- Michael C Gilson Bioinformatics Programmer III UCSF Dept. of Psychiatry