Add helen to bioconda.

[xiekunwhy]

Hi,

Can you add helen to bioconda? It is so difficult To install helen on a centos machine.

Best
Kun

[kishwarshafin]

I am sorry to hear that @xiekunwhy . We have some deadlines to meet otherwise I'd make this a priority. I will try my best to have this included in bioconda before the next release, which is hopefully next month, before or after London Calling.

[AntonioBaeza]

Hi, I work in a centos and have the same problem than xiekunwhy. Any news about bioconda? thanks

[kishwarshafin]

Hi @xiekunwhy and @AntonioBaeza ,

Our new polishing tool PEPPER (https://github.com/kishwarshafin/pepper), gives significantly better results than MarginPolish-HELEN with newer data, guppy 3.6.0 +. We are planning to support PEPPER for newer versions of basecallers. Would you mind trying PEPPER out? I am using PEPPER on centOS 7, so I can help you with errors if you face any.

[AntonioBaeza]

Hi Kishwarshafin/Helen! I will take a look at this tool soon! Thanks for letting me know. Best, Antonio

…

On Thu, Sep 10, 2020 at 12:34 PM Kishwar Shafin ***@***.***> wrote: Hi @xiekunwhy <https://github.com/xiekunwhy> and @AntonioBaeza <https://github.com/AntonioBaeza> , Our new polishing tool PEPPER (https://github.com/kishwarshafin/pepper), gives significantly better results than MarginPolish-HELEN with newer data, guppy 3.6.0 +. We are planning to support PEPPER for newer versions of basecallers. Would you mind trying PEPPER out? I am using PEPPER on centOS 7, so I can help you with errors if you face any. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#25 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ALIJRA7ARG4FKROJSIH4IMTSFD5YDANCNFSM4NFB2YEQ> .

-- J. Antonio Baeza Associate Professor Department of Biological Sciences, Clemson University South Carolina, USA & Research Associate Smithsonian Marine Station at Fort Pierce, Florida, USA & Adjunct Faculty Universidad Catolica del Norte, Coquimbo, Chile Email: baeza.antonio@google.com & jbaezam@clemson.edu Website: http://baezaantonio.wix.com/baezalabclemson Website (CI-team): https://baezaantonio.wixsite.com/clemsonmitogenomics Website ResearchGate: https://www.researchgate.net/profile/J_Baeza/ Website SemanticScholar: https://www.semanticscholar.org/author/Juan-Antonio-Baeza/144723920

[kishwarshafin]

@AntonioBaeza , we have replaced MarginPolish-HELEN with PEPPER:

https://github.com/kishwarshafin/pepper/releases/tag/v0.1

You can install it via pip. Please let me know if that works for you. I'm closing this issue.