The species-properties.json file generated by atlas_species.sh is not right

[alfonsomunozpomer]

Error introduced in 8f0da81

The following println statement in src/Directories.sc:

println("Using the following paths for sources of experiments:")

Makes that running the script to generate the species file, ./sh/atlas_species.sh, produces the following (badly-formatted) JSON file:

Using the following paths for sources of experiments:
[{
  "name":"Aegilops_tauschii",
  "defaultQueryFactorType":"ORGANISM_PART",
  "kingdom":"plants",
  "resources":[{
    "type":"genome_browser",
...

[pcm32]

Thanks for flagging up, probably safest thing would be to set:

atlas-annotations/src/atlas/AtlasSpecies.sc

Line 98 in 5abd229

case Right(res) => System.out.print(res)

to write to a file instead of stdout.