snapcraft.yaml

name: pathogenie
version: '0.4.0'
summary: microbial gene finder and annotation
description: |
  pathogenie This is a desktop and command line program for annotating draft bacterial
  and viral genomes. It may also be used for quickly detecting arbitrary sequences such
  as antibiotic resistance genes (AMR) proteins in nucleotide sequences. It uses Blast
  to find hits to known gene sequences from sequence databases. The inputs are fasta files.
  Annotation is performed in a similar manner to Prokka and first requires an assembled
  genome if you have sequenced reads.

base: core18
grade: stable
confinement: strict
icon: snap/gui/icon.png

apps:
  pathogenie:
    command: desktop-launch $SNAP/bin/pathogenie-gui
    extensions:
      - kde-neon
    plugs:
      - home
      - opengl
      - network
      - network-bind
      - network-control
      - mount-observe
      - removable-media
    environment:
      LD_LIBRARY_PATH: $SNAP/usr/lib/ncbi-blast+
parts:
  pathogenie:
    plugin: python
    source: .
    stage-packages:
      - ncbi-blast+
      - clustalw
      - prodigal
      - hmmer
      - aragorn
      - xsel
      - python3-pyqt5