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cfcrane / SLAG

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Looks like a great tool, any chance to make it available via conda? #1

Open AntonioBaeza opened 2 years ago

AntonioBaeza commented 2 years ago

Looks like a great tool, any chance to make it available via conda?

cfcrane commented 2 years ago

Dear Antonio Baeza, Thanks for your interest. I will admit my ignorance here: is the advantage of conda that SLAG could be locally installed on a cluster where you don't have writing privileges? The containerized version is supposed to address that--does your system have Singularity? Also, the "free-living" executable works in one's home or scratch space without formal installation, if you have available modules or installed instances of blast and the assemblers that you want to use. Currently I have no idea how to put SLAG on conda, but if you can convince me to do so I could try. I am very busy for now with two other projects, though.

Charles Crane

From: AntonioBaeza @.> Sent: Thursday, January 27, 2022 1:05 PM To: cfcrane/SLAG @.> Cc: Subscribed @.***> Subject: [cfcrane/SLAG] Looks like a great tool, any chance to make it available via conda? (Issue #1)

Looks like a great tool, any chance to make it available via conda?

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AntonioBaeza commented 2 years ago

Hi Charles. You are correct. That is the main advantage. For instance, I do use a server and I do not have sudo privileges. We do not use singularity. Conda is widely used, especially useful for beginners, and makes package installation and updates pain-free. Thanks for considering my suggestion.

cfcrane commented 2 years ago

Dear Antonio Baeza, In the meantime, you can do this: Make your downloaded SLAG.pl executable if it isn't already, i.e., chmod 755 SLAG.pl. Then you can run SLAG.pl with a configuration file (download the templates for the Github repository to get started). If blast is not available on your server, you can get it for free directly from NCBI. You can get cap3 from the Internet (Iowa State or Github). What is your operating system? Are you trying to run SLAG on a personal computer? What kind of reads are you attempting to assemble, how many seeding (target) sequences are there, and how long are they? With this information, I might be able to give you some suggestions.

Charles Crane

From: AntonioBaeza @.> Sent: Sunday, February 13, 2022 10:25 AM To: cfcrane/SLAG @.> Cc: Crane, Charles F. @.>; Comment @.> Subject: Re: [cfcrane/SLAG] Looks like a great tool, any chance to make it available via conda? (Issue #1)

Hi Charles. You are correct. That is the main advantage. For instance, I do use a server and I do not have sudo privileges. We do not use singularity. Conda is widely used, especially useful for beginners, and makes package installation and updates pain-free. Thanks for considering my suggestion.

— Reply to this email directly, view it on GitHubhttps://github.com/cfcrane/SLAG/issues/1#issuecomment-1038192351, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AEEUMSRCIKUUWCAOLOTODHTU27EOJANCNFSM5M6VCD7A. Triage notifications on the go with GitHub Mobile for iOShttps://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Androidhttps://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub. You are receiving this because you commented.Message ID: @.***>

AntonioBaeza commented 2 years ago

Thank you! I will give it a try in short. Best, Antonio

On Sun, Feb 13, 2022 at 2:37 PM cfcrane @.***> wrote:

Dear Antonio Baeza, In the meantime, you can do this: Make your downloaded SLAG.pl executable if it isn't already, i.e., chmod 755 SLAG.pl. Then you can run SLAG.pl with a configuration file (download the templates for the Github repository to get started). If blast is not available on your server, you can get it for free directly from NCBI. You can get cap3 from the Internet (Iowa State or Github). What is your operating system? Are you trying to run SLAG on a personal computer? What kind of reads are you attempting to assemble, how many seeding (target) sequences are there, and how long are they? With this information, I might be able to give you some suggestions.

Charles Crane

From: AntonioBaeza @.> Sent: Sunday, February 13, 2022 10:25 AM To: cfcrane/SLAG @.> Cc: Crane, Charles F. @.>; Comment @.> Subject: Re: [cfcrane/SLAG] Looks like a great tool, any chance to make it available via conda? (Issue #1)

Hi Charles. You are correct. That is the main advantage. For instance, I do use a server and I do not have sudo privileges. We do not use singularity. Conda is widely used, especially useful for beginners, and makes package installation and updates pain-free. Thanks for considering my suggestion.

— Reply to this email directly, view it on GitHub< https://github.com/cfcrane/SLAG/issues/1#issuecomment-1038192351>, or unsubscribe< https://github.com/notifications/unsubscribe-auth/AEEUMSRCIKUUWCAOLOTODHTU27EOJANCNFSM5M6VCD7A

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-- 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: @. & @. 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 Website ScienceOpen: https://www.scienceopen.com/search#author/da87367c-ed52-40ed-93d4-ca81ebc8037d OSF Profile: https://osf.io/u9dea/