<commit_before>#!/usr/bin/env python
"""Setup file and install script for NextGen sequencing analysis scripts.
"""
from setuptools import setup, find_packages

setup(name = "bcbio-nextgen",
      version = "0.1",
      author = "<NAME>",
      author_email = "<EMAIL>",
      description = "Automated nextgen sequencing analysis coupled with Galaxy",
      license = "BSD",
      url = "http://bcbio.wordpress.com",
      namespace_packages = ["bcbio"],
      packages = find_packages(),
      scripts = ['scripts/align_summary_report.py',
                 'scripts/analyze_finished_sqn.py',
                 'scripts/analyze_quality_recal.py',
                 'scripts/automated_initial_analysis.py',
                 'scripts/bam_to_wiggle.py',
                 'scripts/barcode_sort_trim.py',
                 'scripts/gatk_genotyper.py',
                 'scripts/gatk_variant_eval.py',
                 'scripts/illumina_finished_msg.py',
                 'scripts/picard_gatk_recalibrate.py',
                 'scripts/picard_maq_recalibrate.py',
                 'scripts/picard_sam_to_bam.py',
                 'scripts/solexa_qseq_to_fastq.py',
                 'scripts/store_finished_sqn.py',
                 'scripts/upload_to_galaxy.py',
                 'scripts/variant_effects.py',
                 ],
      package_data = {
          'config' : ['*.yaml'],
          },
      install_requires = [
          "biopython >= 1.56",
          "Mako >= 0.3.6",
          "PyYAML >= 3.09",
          "amqplib >= 0.6.1",
          "Logbook >= 0.3",
          "pysam >= 0.3.1",
          "rpy2 >= 2.0.7"
      ])<commit_msg>Leave out rpy2 requirement since R not needed in all environments<commit_after>#!/usr/bin/env python
"""Setup file and install script for NextGen sequencing analysis scripts.
"""
from setuptools import setup, find_packages

setup(name = "bcbio-nextgen",
      version = "0.1",
      author = "<NAME>",
      author_email = "<EMAIL>",
      description = "Automated nextgen sequencing analysis coupled with Galaxy",
      license = "BSD",
      url = "http://bcbio.wordpress.com",
      namespace_packages = ["bcbio"],
      packages = find_packages(),
      scripts = ['scripts/align_summary_report.py',
                 'scripts/analyze_finished_sqn.py',
                 'scripts/analyze_quality_recal.py',
                 'scripts/automated_initial_analysis.py',
                 'scripts/bam_to_wiggle.py',
                 'scripts/barcode_sort_trim.py',
                 'scripts/gatk_genotyper.py',
                 'scripts/gatk_variant_eval.py',
                 'scripts/illumina_finished_msg.py',
                 'scripts/picard_gatk_recalibrate.py',
                 'scripts/picard_maq_recalibrate.py',
                 'scripts/picard_sam_to_bam.py',
                 'scripts/solexa_qseq_to_fastq.py',
                 'scripts/store_finished_sqn.py',
                 'scripts/upload_to_galaxy.py',
                 'scripts/variant_effects.py',
                 ],
      package_data = {
          'config' : ['*.yaml'],
          },
      install_requires = [
          "biopython >= 1.56",
          "Mako >= 0.3.6",
          "PyYAML >= 3.09",
          "amqplib >= 0.6.1",
          "Logbook >= 0.3",
          "Cython >= 0.14",
          "pysam >= 0.3.1",
          #"rpy2 >= 2.0.7"
      ])
{'fraction_non_alphanumeric': 0.12929232606748284, 'fraction_numerical': 0.014929829799940281, 'mean_word_length': 1.7800829875518671, 'pattern_counts': {'":': 0, '<': 7, '<?xml version=': 0, '>': 22, 'https://': 0, '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': '1704204', 'n_tokens_mistral': 1065, 'n_tokens_neox': 1055, 'n_words': 164}