1. mirnylab
  2. hiclib

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mimakaev  committed 2210932 Merge

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File .hgignore

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 *~
 *.pyc
+.DS_Store
 doc/build
 tests/mapping/tmp
 bin/
+build/
+sdist/
 data/
 fasta/

File README.md

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+hiclib
+======
+
+Read the [documentation](http://mirnylab.bitbucket.org/hiclib/index.html).
+
+Installation requirements
+-------------------------
+
+### Non-python dependencies
+
+- Mirnylib provides a HDF5 dictionary type based on the Python h5py package. For the h5py package to install properly, you need to have the shared library and development headers for HDF5 1.8.4 or newer installed (`libhdf5-dev` or similar). See the [h5py docs](http://docs.h5py.org/en/latest/build.html) for more information.
+
+- You will also need the `bowtie2` mapping software which can be downloaded manually or installed via the download_bowtie.sh script in the hiclib folder.
+
+### Python dependencies
+
+Required:
+
+Getting the basic Scientific Python stack (numpy/scipy/matplotlib) can be trickier on some platforms than others. For more details, see the [instructions on scipy.org](http://www.scipy.org/install.html). You should already have these dependencies installed and running correctly before attempting to install this package.
+
+- numpy (1.6+)
+- scipy
+- matplotlib
+
+Installed by setuptools if missing:
+
+- biopython
+- pysam
+- [mirnylib](https://bitbucket.org/mirnylab/mirnylib)
+
+Optional:
+
+- Sphinx (to generate documentation)

File setup.py

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+from setuptools import setup
+
+setup(
+    name='hiclib',
+    url='http://mirnylab.bitbucket.org/hiclib/index.html',
+    description=('Hi-C data analysis library.'),
+    package_dir={'': 'src'},
+    packages=['hiclib'],
+    install_requires=[
+        'biopython',
+        'mirnylib',
+        'pysam',
+    ],
+    dependency_links=[
+        'https://bitbucket.org/mirnylab/mirnylib/get/tip.tar.bz2'
+    ],
+)

File src/hiclib/__init__.py

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File src/hiclib/binnedData.py

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File src/hiclib/domainSearch.py

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File src/hiclib/fragmentHiC.py

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File src/hiclib/highResBinnedData.py

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File src/hiclib/mapping.py

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