Is BBMap really a hard dependency?

[anderspitman]

It's a pain to install (especially for continuous integration) and it appears we're only using one small script (rename.sh) from it.

[rachelss]

Ask @BobLiterman

[BobLiterman]

Long story short, what BBMap is doing now, a bash or Python script could do. I planned on integrating more down the line, but I'm open. As for installation, there isn't any. It just unzips. Do you mean Java is a pain?

[anderspitman]

Technically you have to unzip + add it to your path. It wasn't too bad but significantly less desirable than apt-get. Currently the java isn't a problem, since it's apparently not using any of that functionality. That might be a bigger issue later but probably not too bad.

[BobLiterman]

I see. I work out of an HPC system, so I can't apt-get anything. All dependencies must be compiled from source onto the cluster.

[BobLiterman]

I can definitely write a quick Python or Bash script for the scaffold renaming if it's less hassle. BBMap is just very versatile with NGS data, like samtools, bowtie, and so many other programs wrapped into one. Added bonus, best user support of any program I've ever used.