<commit_before>package:
  name: viral-ngs
  version: 1.6.1

about:
  home: https://github.com/broadinstitute/viral-ngs
  license: https://raw.githubusercontent.com/broadinstitute/viral-ngs/master/LICENSE
  summary: A set of scripts and tools for the analysis of viral NGS data

source:
  fn: viral-ngs-v1.6.1.zip
  url: https://github.com/broadinstitute/viral-ngs/archive/v1.6.1.zip
  md5: e8be4d718e04bdb4a774f0d153c2db90

build:
    number: 0
    rpaths:
        - lib/
        - lib//

requirements:
  build:
    - python
    - java-jdk >=7
    - biopython 
    - future >=0.15.2
    - futures ==3.0.5 # [py2k]
    - pytest 
    - pysam ==0.8.4
    - pyyaml >=3.11
    - boto ==2.38.0 
    - snakemake # [py3k]
    - blast ==2.2.31
    - bmtagger ==3.101
    - last ==719
    - gatk
    #- krona ==2.6.1
    - kraken-all # [linux]
    - mafft ==7.221
    - mummer ==3.23
    - muscle ==3.8.1551
    - mvicuna ==1.0
    - novoalign ==3.03.02
    - perl-threaded
    - picard ==1.126
    - prinseq ==0.20.4
    - samtools ==1.2
    - snpeff ==4.1l
    - trimmomatic ==0.36
    - trinity ==date.2011_11_26
    - vphaser2 ==2.0
    
    - gcc
    - boost ==1.60 # needed for diamond, among other packages

  run:
    - python
    - java-jdk >=7
    - biopython 
    - future >=0.15.2
    - futures ==3.0.5 # [py2k]
    - pytest 
    - pysam ==0.8.4
    - pyyaml >=3.11
    - boto ==2.38.0 
    - snakemake # [py3k]
    - blast ==2.2.31
    - bmtagger ==3.101
    - last ==719
    - gatk
    #- krona ==2.6.1
    - kraken-all # [linux]
    - mafft ==7.221
    - mummer ==3.23
    - muscle ==3.8.1551
    - mvicuna ==1.0
    - novoalign ==3.03.02
    - perl-threaded
    - picard ==1.126
    - prinseq ==0.20.4
    - samtools ==1.2
    - snpeff ==4.1l
    - trimmomatic ==0.36
    - trinity ==date.2011_11_26
    - vphaser2 ==2.0

    - gcc # used for compiling any tools that are installed by viral-ngs itself (rather than conda)
    - libgcc
    - boost ==1.60 # needed for diamond, among other packages

    - perl-threaded

    - libgcc

    # testing-related
    - flake8 <=3
    - mock >=2.0.0
    - six <2
    - pytest-cov
    - pytest-xdist

    - sphinx >=1.4.1
    - sphinx_rtd_theme >=0.1.9
    - sphinx-argparse >=0.1.15

test:
  commands:
    # preserve CONDA_DEFAULT_ENV to restore later
    - "export CONDA_DEFAULT_ENV_BAK=$CONDA_DEFAULT_ENV"
    # hack so _test env has the correct CONDA_DEFAULT_ENV (inspected by viral-ngs to determine tool install location)
    - "export CONDA_DEFAULT_ENV=$(echo $CONDA_DEFAULT_ENV | perl -lape 's/_build$/_test/g')"<commit_msg>update viral-ngs to 1.7.0<commit_after>package:
  name: viral-ngs
  version: 1.7.0

about:
  home: https://github.com/broadinstitute/viral-ngs
  license: https://raw.githubusercontent.com/broadinstitute/viral-ngs/master/LICENSE
  summary: A set of scripts and tools for the analysis of viral NGS data

source:
  fn: viral-ngs-v1.7.0.zip
  url: https://github.com/broadinstitute/viral-ngs/archive/v1.7.0.zip
  md5: 4c0bd15dcfc028e666ff03272e91376f

build:
    number: 0
    rpaths:
        - lib/
        - lib//

requirements:
  build:
    - python
    - java-jdk >=7
    - biopython 
    - future >=0.15.2
    - futures ==3.0.5 # [py2k]
    - pytest 
    - pysam ==0.8.4
    - pyyaml >=3.11
    - boto ==2.38.0 
    - snakemake # [py3k]
    - blast ==2.2.31
    - bmtagger ==3.101
    - last ==719
    - gatk
    #- krona ==2.6.1
    - kraken-all # [linux]
    - mafft ==7.221
    - mummer ==3.23
    - muscle ==3.8.1551
    - mvicuna ==1.0
    - novoalign ==3.03.02
    - perl-threaded
    - picard ==1.126
    - prinseq ==0.20.4
    - samtools ==1.3.1
    - snpeff ==4.1l
    - trimmomatic ==0.36
    - trinity ==date.2011_11_26
    - vphaser2 ==2.0
    - bwa ==0.7.15
    
    - gcc
    - boost ==1.60 # needed for diamond, among other packages

  run:
    - python
    - java-jdk >=7
    - biopython 
    - future >=0.15.2
    - futures ==3.0.5 # [py2k]
    - pytest 
    - pysam ==0.8.4
    - pyyaml >=3.11
    - boto ==2.38.0 
    - snakemake # [py3k]
    - blast ==2.2.31
    - bmtagger ==3.101
    - last ==719
    - gatk
    #- krona ==2.6.1
    - kraken-all # [linux]
    - mafft ==7.221
    - mummer ==3.23
    - muscle ==3.8.1551
    - mvicuna ==1.0
    - novoalign ==3.03.02
    - perl-threaded
    - picard ==1.126
    - prinseq ==0.20.4
    - samtools ==1.3.1
    - snpeff ==4.1l
    - trimmomatic ==0.36
    - trinity ==date.2011_11_26
    - vphaser2 ==2.0
    - bwa ==0.7.15

    - gcc # used for compiling any tools that are installed by viral-ngs itself (rather than conda)
    - libgcc
    - boost ==1.60 # needed for diamond, among other packages

    - perl-threaded

    - libgcc

    # testing-related
    - flake8 <=3
    - mock >=2.0.0
    - six <2
    - pytest-cov
    - pytest-xdist

    - sphinx >=1.4.1
    - sphinx_rtd_theme >=0.1.9
    - sphinx-argparse >=0.1.15

test:
  commands:
    # preserve CONDA_DEFAULT_ENV to restore later
    - "export CONDA_DEFAULT_ENV_BAK=$CONDA_DEFAULT_ENV"
    # hack so _test env has the correct CONDA_DEFAULT_ENV (inspected by viral-ngs to determine tool install location)
    - "export CONDA_DEFAULT_ENV=$(echo $CONDA_DEFAULT_ENV | perl -lape 's/_build$/_test/g')"
{'fraction_non_alphanumeric': 0.14650537634408603, 'fraction_numerical': 0.08390937019969279, 'mean_word_length': 1.8573779484366428, 'pattern_counts': {'":': 0, '<': 7, '<?xml version=': 0, '>': 23, 'https://': 6, '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': '6583857', 'n_tokens_mistral': 2341, 'n_tokens_neox': 2158, 'n_words': 464}