{% set name = "MSFragger" %}
{% set version = "4.2" %}

# This key was generated ONLY for the testing of this bioconda package.
# Users must generate their own key by agreeing to the terms at https://msfragger.arsci.com/upgrader/MSFragger-LICENSE.pdf.
{% set academic_use_only_key = "318e8e92-3844b3cd-42249910-37913a4d" %}

package:
  name: {{ name|lower }}
  version: {{ version }}

# This URL was generated building of this bioconda package.
# Users must generate their own download URL by agreeing to the terms at https://msfragger.arsci.com/upgrader/MSFragger-LICENSE.pdf.
source:
  url: https://msfragger-upgrader.nesvilab.org/upgrader/download.php?token=0000000&download=Release%204.2%24zip
  sha256: 55aa45f2d0c65dbb06cc1bbba32497d40cd65f28dda6a58b50bcb7caa71b2c86

build:
  number: 0
  noarch: generic
  run_exports:
    - {{ pin_subpackage(name|lower, max_pin="x") }}

requirements:
  host:
    - python =3.11
    - unzip
  run:
    - openjdk >=11
    - python =3.11
    - mono >=5, <6
    - zlib >=1.2.13

test:
  commands:
    - which msfragger

about:
  home: https://github.com/Nesvilab/MSFragger
  license: Academic License
  license_file:
    - licenses/LICENSE-ACADEMIC.pdf
  summary: Ultrafast, comprehensive peptide identification for mass spectrometry–based proteomics
  description: |
    MSFragger is an ultrafast database search tool for peptide identification in mass spectrometry-based proteomics.
    It has demonstrated excellent performance across a wide range of datasets and applications.
    MSFragger is suitable for standard shotgun proteomics analyses as well as large datasets (including timsTOF PASEF data),
    enzyme unconstrained searches (e.g., peptidome),
    open database searches (e.g., precursor mass tolerance set to hundreds of Daltons) for identification
    of modified peptides, and glycopeptide identification (N-linked and O-linked).

    MSFragger is available freely for academic research and educational purposes only, in accordance with the terms at https://msfragger.arsci.com/upgrader/MSFragger-LICENSE.pdf.

extra:
  notes: |
    The "msfragger" command runs the MSFragger java program.
  identifiers:
    - doi:10.1038/nmeth.4256
    - doi:10.1038/s41467-020-17921-y
    - doi:10.1038/s41592-020-0967-9
