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smangul1 / rop

The Read Origin Protocol (ROP) is a computational protocol that aims to discover the source of all reads, including those originating from repeat sequences, recombinant B and T cell receptors, and microbial communities.
https://github.com/smangul1/rop/wiki
GNU General Public License v3.0
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Enable ROP-mouse #133

Closed igordot closed 6 years ago

igordot commented 6 years ago

By default, the install.sh script installs the human database. I am trying to add a non-human database. I tried running:

./install.sh -o mouse

That gave an error:

----- Downloading databases ----------------------------------------------------
Downloading item: BWAindex for mouse
Error: Unknown ORGANISM.

I also checked the wiki where the instructions are:

python getDB.py --organism mouse ~/

However, it seems that file does not exist anymore.

smangul1 commented 6 years ago

Thanks for bringing this up! We will investigate this and will let you know. Thanks, Serghei

kahsieh commented 6 years ago

@smangul1 What is the status on the mouse database?

smangul1 commented 6 years ago

ROP-mouse is ready. Please give a try! Serghei and Kevin

igordot commented 6 years ago

Is there a way to install a database without reinstalling everything from scratch? If you run install.sh, it will do the full install.

kahsieh commented 6 years ago

Not currently, but we can change this! #137 changes the behavior so that ROP won't reinstall by default when downloading an additional database.