search

mozack / abra

Assembly Based ReAligner
MIT License
71 stars 12 forks source link

hidden dependency on bwa mem #34

Closed covingto closed 7 years ago

covingto commented 7 years ago

When I run I see that there is a hidden dependency on BWA mem. Would be nice to be able to specify the path to bwa mem since I might be using different versions.

mozack commented 7 years ago

The BWA dependency is clearly documented in the Running section of the README. Not sure that I would consider it hidden.

We are now focused on developing ABRA2 (https://github.com/mozack/abra2). The dependency on BWA has been removed in this new version. You might consider using the newer implementation.

If you wish to continue with the original ABRA, I suggest updating your PATH to use the desired BWA version.

covingto commented 7 years ago

So it does. I was looking in the building section. Will check out abra2.

Thanks