<commit_before>{% set name = "fusioncatcher" %}
{% set version = "1.20" %}
{% set sha256 = "a13b4083e5e4544ec5482535341654c80fe641bd0be1dd722929b98ebcf78171" %}

package:
  name: {{ name }}
  version: {{ version }}

source:
  url: https://sourceforge.net/projects/{{ name }}/files/{{ name }}_v{{ version }}.zip
  sha256: {{ sha256 }}
  patches:
    - paths.patch

build:
  number: 1
  noarch: generic

requirements:
  run:
    - python <3
    - biopython >=1.50
    - bowtie=1.2.3
    - fusioncatcher-seqtk=1.2
    - star=2.7.2b
    - bowtie2=2.3.5
    - bbmap=38.44
    - blat=35
    - lzo
    - bwa=0.7.12
    - ucsc-faToTwoBit 
    - velvet=1.2.10
    - openpyxl=2.5.0a2
    - xlrd=1.0.0
    - pigz=2.3
    - samtools=0.1.19
    - picard=2.10.6
    - numpy=1.13.1
    - parallel=20171222
    - ucsc-liftover
    - oases
    - lzop
    - openjdk
    - sra-tools=2.9.6
    - zip

test:
  commands:
    - export FC_DB_PATH=${PREFIX}/share/${PKG_NAME}-${PKG_VERSION}/db && fusioncatcher.py -h<commit_msg>[ci skip] Merge PR 20338<commit_after>{% set name = "fusioncatcher" %}
{% set version = "1.20" %}
{% set sha256 = "a13b4083e5e4544ec5482535341654c80fe641bd0be1dd722929b98ebcf78171" %}

package:
  name: {{ name }}
  version: {{ version }}

source:
  url: https://sourceforge.net/projects/{{ name }}/files/{{ name }}_v{{ version }}.zip
  sha256: {{ sha256 }}
  patches:
    - paths.patch

build:
  number: 2
  noarch: generic

requirements:
  run:
    - python <3
    - biopython >=1.50
    - bowtie=1.2.3
    - fusioncatcher-seqtk=1.2
    - star=2.7.2b
    - bowtie2=2.3.5
    - bbmap=38.44
    - blat=35
    - lzo
    - bwa=0.7.12
    - ucsc-faToTwoBit 
    - velvet=1.2.10
    - openpyxl=2.5.0a2
    - xlrd=1.0.0
    - pigz=2.3
    - samtools=0.1.19
    - picard=2.10.6
    - numpy=1.13.1
    - parallel=20171222
    - ucsc-liftover
    - oases
    - lzop
    - openjdk
    - sra-tools=2.9.6
    - zip
    - coreutils
    - grep

test:
  commands:
    - export FC_DB_PATH=${PREFIX}/share/${PKG_NAME}-${PKG_VERSION}/db && fusioncatcher.py -h
{'fraction_non_alphanumeric': 0.16536203522504891, 'fraction_numerical': 0.11888454011741682, 'mean_word_length': 2.160741885625966, 'pattern_counts': {'":': 0, '<': 5, '<?xml version=': 0, '>': 5, 'https://': 2, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '7297044', 'n_tokens_mistral': 1023, 'n_tokens_neox': 902, 'n_words': 141}