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arundurvasula / angsd-wrapper

A project for extending ANGSD
MIT License
8 stars 12 forks source link

Configuration confusing and limiting #85

Closed mojaveazure closed 9 years ago

mojaveazure commented 9 years ago

Using angsd-wrapper is far to confusing to make it useful. I've had to edit three different configuration files to try and use ANGSD via angsd-wrapper while following the tutorial listed on this GitHub repository, but it's getting frustrating.

I would recommend condensing all options to one configuration file, and also not having defaults for directories and names. Please make this easily user-configurable.

arundurvasula commented 9 years ago

Hi,

Thanks! One of the things we're working on right now is streamlining this process and updating the tutorial/documentation. As soon as we finish up the features we will work on this.

I think we will be moving to one configuration file soon.

mojaveazure commented 9 years ago

Awesome, thank you!

mojaveazure commented 9 years ago

Hi Arun,

I've forked your version of angsd-wrapper and started reworking the configuration files and wrapper scripts to make it, in my opinion, easier to use. I've done this so far with the SFS and 2D SFS scripts. I have also updated the wrappers a little to work with the most recent version of ANGSD. You can see what I've done here; if you'd like, I'd be more than happy to help do this with the rest of ansd-wrapper.

rossibarra commented 9 years ago

Updating to work with most recent version of ANGSD would be good. Arun you should make a release based on your current wrapper; that's what will go with the paper. But no reason not to update to newest version and if we can get it done ASAP no reason not to include Paul on the paper?

-J

Jeffrey Ross-Ibarra

Dept. of Plant Sciences 262 Robbins Hall, Mail Stop 4 University of California One Shields Ave Davis, CA 95616

Tel: 530-752-1152 @jrossibarra www.rilab.org

On Mon, Jul 6, 2015 at 7:31 AM, Paul Hoffman notifications@github.com wrote:

Hi Arun,

I've forked your version of angsd-wrapper and started reworking the configuration files and wrapper scripts to make it, in my opinion, easier to use. I've done this so far with the SFS and 2D SFS scripts. I have also updated the wrappers a little to work with the most recent version of ANGSD. You can see what I've done here https://github.com/mojaveazure/angsd-wrapper; if you'd like, I'd be more than happy to help do this with the rest of ansd-wrapper.

— Reply to this email directly or view it on GitHub https://github.com/arundurvasula/angsd-wrapper/issues/85#issuecomment-118873325 .

tvkent commented 9 years ago

collaboration ongoing