David C Danko
David C Danko
# Bug Report ## Issue name gc: fails when attempting to remove cache shared by multiple projects ## Description When attempting to garbage collect files shared by multiple projects dvc...
Maybe an issue with numpy version. I have `v1.11.3` ``` $ PlasFlow.py --input scaff1k.fa --output scaff.plasflow.csv --threshold 0.7 ... Traceback (most recent call last): File "/home/dcdanko/miniconda3/envs/plasflow/bin/PlasFlow.py", line 346, in vote_proba...
Hello, I'm having some issues with BWA running on one the prebuilt databases and the error message is not particularly helpful. Any idea what's going wrong? ``` $ /home/dcd3001/bin/gottcha -t...
I'm getting the following error while using MICA ``` Error processing queries: Could not decompress coarse sequence 16859848 (16, 43): Could not read compressed sequence: Could not scan coarse sequence...
The database available on gems.csail.mit.edu at the time of writing is improperly formatted and will cause MICA to fail. The headers in the coarse.fasta file are formatted as '> seqname'...
Currently just samples from first chunk of reads, could be biased due to flowcells
Make a standalone rule that writes the number of reads to a file. This will free any normalizing rules from dependence on read_stats
CRASS Finds CRISPR spacers and inserts https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3664793/ https://github.com/ctskennerton/Crass
Add/Evaluate GOTTCHA. Formerly part of v.1.0.0 but GOTTCHA seems to have some software bugs that require more time and care to address. See #12
Add/Evaluate MelonnPan for the CAP https://bitbucket.org/biobakery/biobakery/wiki/melonnpan