Looks like a great tool, any chance to make it available via conda? #1
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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
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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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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. |
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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
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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.
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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<
#1 (comment)>, or
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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
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Looks like a great tool, any chance to make it available via conda?
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