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/config/python-libs.yaml

https://github.com/pjotrp/cloudbiolinux
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  1. ---
    2. 

  2. # Configuration file defining python specific libraries on pypi to install
    3. 

  3. # using easy install
    4. 

  4. pypi:
    5. 

  5.   # infrastructure
    6. 

  6.   - setuptools
    7. 

  7.   - amqplib
    8. 

  8.   - BeautifulSoup
    9. 

  9.   - fabric
    10. 

  10.   - Logbook
    11. 

  11.   - lxml
    12. 

  12.   - mako
    13. 

  13.   - paste
    14. 

  14.   - pastescript
    15. 

  15.   - pycrypto
    16. 

  16.   - python-cjson
    17. 

  17.   - pyOpenSSL
    18. 

  18.   - routes
    19. 

  19.   - simplejson
    20. 

  20.   - sphinx
    21. 

  21.   - StarCluster 
    22. 

  22.   - webhelpers
    23. 

  23.   - webob
    24. 

  24.   - xlrd
    25. 

  25.   # build
    26. 

  26.   - Pyrex-real
    27. 

  27.   - cython  # needed for installing pybedtools
    28. 

  28. # concurrency/web
    29. 

  29.   - Twisted
    30. 

  30.   # science
    31. 

  31.   - cutadapt
    32. 

  32.   - ruffus
    33. 

  33.   - DendroPy
    34. 

  34.   - HTSeq
    35. 

  35.   - pybedtools
    36. 

  36.   - pygr
    37. 

  37.   - PyVCF
    38. 

  38.   - rpy2
    39. 

  39.   - ramp
    40. 

  40.   # databases
    41. 

  41.   - CouchDB
    42. 

  42.   - MySQL-python
    43. 

  43.   - pymongo
    44. 

  44.   - pysqlite
    45. 

  45.   - psycopg2
    46. 

  46.   # visualization
    47. 

  47.   - gnuplot-py
    48. 

  48.   - PIL
    49. 

  49.   - pypdf
    50. 

  50.   - reportlab
    51. 

  51.   # cloudman
    52. 

  52.   - oca
    53. 

  53.   - hoover
    54. 

  54.   - Mako
    55. 

  55. conda:
    56. 

  56.   - boto
    57. 

  57.   - biopython
    58. 

  58.   - cython
    59. 

  59.   - h5py
    60. 

  60.   - ipython
    61. 

  61.   - matplotlib
    62. 

  62.   - networkx
    63. 

  63.   - nose
    64. 

  64.   - numpy
    65. 

  65.   - pandas
    66. 

  66.   - pysam
    67. 

  67.   - pyyaml
    68. 

  68.   - pyzmq
    69. 

  69.   - scikit-learn
    70. 

  70.   - scipy
    71. 

  71.   - SQLAlchemy
    72. 

  72.   - statsmodels
    73. 

  73.   - tornado
    74. 

  74.   
    75. 

  75. ## compile problems
    76. 

  76.   #- cogent
    77. 

  77.   #- tables
    78. 

  78.   #- pygraphviz
    79. 

  79.   #- pysparse
    80. 

  80.   #- sympy
    81. 

  81.   #- pydot # references python 3-only pyparsing
    82. 

  82.   #- pygooglechart
    83. 

  83.   #- rpy2-bioconductor-extensions
    84. 

  84.