Yarden Katz

It's a pain partly because of the GFF specification. GFFs only encode trees, so full graph support is not needed, but the format is bad at supporting them. To somewhat...

I've been thinking about two related GFF functionalities, which I believe reflect very common pattern usages for other users too, but unfortunately no tool that I know of has these...

One related question for you with respect to using `gffutils`: ), I wrote above that a key issue for me was finding an indexed representation of GFF where distinct cluster...

Hi Brad and Ryan, I think it'll be great to work on this together, and as Brad said, I'm happy to contribute code/tests/examples etc. I'll respond to some of Ryan's...

Python 3 is not supported by MISO at the moment. > On Aug 2, 2017, at 11:54 PM, Alistair Chalk wrote: > > Hi Guys, > > An installation bug...

There's a simpler way to do this. All you'd need is a wrapper script like `send_job` that takes a shell script as input and submits it to the cluster, passing...

Thank you for your input. I'm sorry that I have not had a chance to fix this yet. We're looking for another developer to take over MISO. I will update...

See: ``` $ miso_zip --help Usage: miso_zip [options] Options: -h, --help show this help message and exit --compress=COMPRESS Compress a directory containing MISO output. Takes as arguments: (1) the output...

I tried making one a very long time ago. The issue, as I recall, was having a platform-independent way to install certain dependencies like samtools. MISO requires samtools in order...

This is an indication that the package was not installed correctly; settings.txt should be available as data from the installed package directory. Did you install with a package manager like...