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guoyanzhao / VirusSeeker-Virome

VirusSeeker is a set of fully automated and modular software package designed for mining sequence data to identify sequences of microbial origin.
GNU General Public License v3.0
17 stars 5 forks source link

Configuration files / environment #10

Open emollier opened 4 years ago

emollier commented 4 years ago

Greetings,

I'm giving a hand to the Debian Med Team in packaging VirusSeeker-Virome. As is, I'm progressing slowly but surely, step by step, making sure each stage is able to run properly. I see a lot of parameters, and for the moment tuning them requires editing Perl scripts directly; it does the job, but does not marry very well with package distribution.

I've been suggested the use of environment variables, and I believe it should give a fair way of setting up tunable parameters. But I'm wondering, have you already thought about using some sort of configuration file, to store tunables parameters such as the location of NCBI databases, scratch directories and maybe Slurm resource requirements ?

Kind Regards.

guoyanzhao commented 4 years ago

Hi Étienne Mollier,

Thank you for your interest of doing this. I have left the virome field. So I'm not doing anything with it right now except answering people's question and help trouble shoot if anyone is trying to install it on their cluster. So please feel free to do whatever you think is easier for you. 

Best, Guoyan

On Wednesday, May 13, 2020, 01:59:55 PM CDT, Étienne Mollier notifications@github.com wrote:

Greetings,

I'm giving a hand to the Debian Med Team in packaging VirusSeeker-Virome. As is, I'm progressing slowly but surely, step by step, making sure each stage is able to run properly. I see a lot of parameters, and for the moment tuning them requires editing Perl scripts directly; it does the job, but does not marry very well with package distribution.

I've been suggested the use of environment variables, and I believe it should give a fair way of setting up tunable parameters. But I'm wondering, have you already thought about using some sort of configuration file, to store tunables parameters such as the location of NCBI databases, scratch directories and maybe Slurm resource requirements ?

Kind Regards.

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emollier commented 4 years ago

Hi Guoyan,

guoyanzhao, on 2020-05-14 20:41:11 -0700:

Thank you for your interest of doing this. I have left the virome field. So I'm not doing anything with it right now except answering people's question and help trouble shoot if anyone is trying to install it on their cluster. So please feel free to do whatever you think is easier for you. 

Thank you too for sharing your current status.

In that case, well, I guess I'll stick to the initial idea, and go for setting up a few environment variables. I might show up again with a pull request with the changes, if they prove to be a convenience and do not break the existing expected workflow.

Take care, Kind Regards, -- Étienne Mollier

guoyanzhao commented 4 years ago

sounds great. Thank you! Best wishes, Guoyan

On Friday, May 15, 2020, 02:43:10 PM CDT, Étienne Mollier notifications@github.com wrote:

Hi Guoyan,

guoyanzhao, on 2020-05-14 20:41:11 -0700:

Thank you for your interest of doing this. I have left the virome field. So I'm not doing anything with it right now except answering people's question and help trouble shoot if anyone is trying to install it on their cluster. So please feel free to do whatever you think is easier for you. 

Thank you too for sharing your current status.

In that case, well, I guess I'll stick to the initial idea, and go for setting up a few environment variables. I might show up again with a pull request with the changes, if they prove to be a convenience and do not break the existing expected workflow.

Take care, Kind Regards, -- Étienne Mollier

— You are receiving this because you commented.

Reply to this email directly, view it on GitHub, or unsubscribe .