Gus Dunn

as of now: ``` blacktie --prog all config.yaml --mode qsub_script ``` writes your individual qsub scripts but you have to submit them all by hand. `blacktie` should be able to...

``` blacktie --prog all ../../config_files/tophat_cufflinks_Cq_0-4-6-8-10.gtf_strict.hpc.yaml --mode qsub_script [Note] Starting tophat step. [Note] Starting cufflinks step. [Note] Starting cuffmerge step. [Note] Starting cuffdiff step. sh: R: command not found Traceback (most...

Is is possible for me to generate my own singularity images by changing install.smk?

1

I need a newer guppy install. I also want/need GPU. It SEEMS that I can alter the install.smk script to update these things. What I dont know how to do...

why lock so many pkgs to OLD versions in requirements.txt?

4

For example: - flask-admin==1.1.0 (Current: 1.4.2) - wtforms==1.0.5 (Current: 2.1) I understand locking these in your own dev environments perhaps, but does your code REALLY not work with libraries as...

I have created a conda package for pyrad that pulls in ALL deps (muscle and vsearch too)

3

Because I generally work on multiple clusters, I have to replicate my scientific software stack not infrequently and I generally hate my life for a few days each time I...

[serious] why? I can't figure out the use case based on the readme

4

Perhaps make this clearer in the readme? Also a quick answer here would be appreciated. I can't figure this things propose.

Ability to correctly display ipython notebooks in posts

3

I know that you can dump notebooks to rst, but that displays poorly. It WORKS, but it would be better if they actually looked like the output from a notebook....

respect the user's signature placement

2

First, you rock. I think that this approach has a much higher likelihood o f making a difference than trying to get everyone to use strong encryption by default. Second,...