bkleef / BacPipe

BacPipe

macOS with Docker

1. Install XQuartz by Homebrew:

   brew cask install xquartz

2. Start BacPipe in Docker:

   IP=$(ifconfig en0 | grep inet | awk '$1=="inet" {print $2}')
   xhost + $IP
   docker run -it -e DISPLAY=$IP:0 -v /tmp/.X11-unix:/tmp/.X11-unix -v $HOME/BaseSpace:/data mahmed/bacpipe python ./Pipeline.py unix

Dropdown Species

Not all species fit in the drop down, it is not scrollable, which means that the lower items cannot be selected.

The default value is ecoli and is set in configure.yaml:

mlst_typing:
  organism: ecolis

The order of items in the drop down is determined in: Pipeline.py:

app.addLabelOptionBox("Species", ["ecoli","ecoli_2","kpneumoniae","paeruginosa","pfluorescens","abaumannii","abaumannii_2","senterica","saureus","spneumoniae","spyogenes","efaecalis","efaecium","----------------------------","achromobacter","aeromonas","afumigatus","aphagocytophilum","arcobacter","bcc","bcereus","bhampsonii","bhenselae","bhyodysenteriae","bintermedia","blicheniformis","bordetella","borrelia","bpilosicoli","bpseudomallei","brachyspira","bsubtilis","calbicans","campylobacter","cbotulinum","cconcisus","cdifficile","cdiphtheriae","cfetus","cfreundii","cglabrata","chelveticus","chlamydiales","chyointestinalis","cinsulaenigrae","ckrusei","clanienae","clari","cmaltaromaticum","cronobacter","csepticum","csinensis","csputorum","ctropicalis","cupsaliensis","ecloacae","fpsychrophilum","hcinaedi","hinfluenzae","hparasuis","hpylori","hsuis","kkingae","koxytoca","kseptempunctata","leptospira","leptospira_2","leptospira_3","llactis","lmonocytogenes","lsalivarius","mabscessus","magalactiae","mbovis","mcatarrhalis","mhaemolytica","mhyopneumoniae","mhyorhinis","mmassiliense","mplutonius","mpneumoniae","neisseria","orhinotracheale","otsutsugamushi","pacnes","pgingivalis","plarvae","pmultocida_multihost","pmultocida_rirdc","ppentosaceus","ranatipestifer","sagalactiae","sbsec","scanis","sdysgalactiae","sepidermidis","sgallolyticus","shaemolyticus","shominis","sinorhizobium","slugdunensis","smaltophilia","soralis","spseudintermedius","ssuis","sthermophilus","sthermophilus_2","streptomyces","suberis","szooepidemicus","taylorella","tenacibaculum","tvaginalis","vcholerae","vibrio","vparahaemolyticus","vtapetis","vvulnificus","wolbachia","xfastidiosa","yersinia","ypseudotuberculosis","yruckeri"], raw,3,2)

To use a value that cannot be selected, I recommend defining it in configure.yaml before starting the program. For example:

mlst_typing:
  # organism: ecolis
  organism: szooepidemicus