C. Titus Brown
C. Titus Brown
https://github.com/maxplanck-ie/snakepipes
check for broken yaml config (no 'samples' entry) and badly formatted 'samples.tsv' (#41 is relevant). These are common errors happening in GGG 201(b).
right now, the databases for dammit are put in `databases/` within the run directory, and (if you trash the eelpond repo, as Travis does) they need to be re-downloaded and...
students are getting really big nasty tracebacks from common errors, and it's really hard to decipher. I wonder if it's possible to make eelpond/elvers more friendly to newcomers by trapping...
see https://github.com/dib-lab/eelpond/issues/103#issuecomment-471185817 for initial motivation -- I think we need a modular way to do high-level correctness checking. e.g., * if `quantify` is run, *either* some assembly thingy needs to...
See commit - 3f753a1 - we could/should have a check that the number of lines in samples.tsv is matched by the number of rows in the loaded table, or something....
http://twitter.com/markrobinsonca/status/1104733337644457984 https://t.co/43sdCfGt7U looks like they do a nice job of downstream viz, but aren't interested in de novo assembly.
turns out the environment.yml in there already is almost good enough to get #108 running on mybinder.org! We just need to run `conda update -n base conda`. one issue right...
I think nema example is good for assembly/annotation, and assembly/annotation/diffexp; while yeast is good for diffexp. For the yeast tutorial, we could use the example files and then finish with,...
```-------- checking for required files: -------- while parsing a block mapping in "examples/yeast.yaml", line 36, column 3 expected , but found '' in "examples/yeast.yaml", line 37, column 5 Traceback (most...