Torsten Seemann
Torsten Seemann
@fluhus Amit, sorry for the slow reply, inundated with hCoV work right now my quick scan indicates it all looks very good! you did well to get through my very...
Maybe that bacteria is in your `banana` database (as contamination!) ?
Users sharing conda environments is a tricky situation. One way to handle it is to alter tb-profiler to use a user-local version of the database first, and if that does...
Any progress updates besides the repo renaming? :)
I discovered the problem was that I needed to install Cython as well (h5py doesn't have it as a dependency). These steps will install it fully: ``` % virtualenv /bio/sw/kPAL...
Thanks for looking into it. I'm not sure I'll ever fully understand Python packaging either!
From Fredrik Boulund: ``` #!/bin/bash # Download pre-made Kraken2 database based on GTDB r89 # https://github.com/rrwick/Metagenomics-Index-Correction # https://monash.figshare.com/articles/GTDB_r89_54k/8956970 # https://www.biorxiv.org/content/10.1101/712166v1 set -eou pipefail outdir="gtdb_r89_54k" base_filename="gtdb_r89_54k_kraken2_" mkdir -pv $outdir cd $outdir...
Linuxbrew is a fork of Brew started by @sjackman here: https://github.com/Homebrew/linuxbrew I use it for all my Linux servers and VMs. I will eventually write a formula for TreeToReads when...
`plugins/correct_vcf_filter.py`
@GonzaloYebra Normally a match is +1 and a mismatch is 0. How do you want the ambiguous IUPAC codes measured? A vs R = 0 C vs R = 0...