1. mirnylab
  2. hiclib

Source

hiclib /

Filename Size Date modified Message
binarySearch
doc
examples
src/hiclib
tests
120 B
don't track .o and .so
1.5 KB
Dummy commit
250 B
download_bowtie.sh - download the latest version of bowtie (edited online with Bitbucket)
204 B
Update the documentation and the tutorial
269 B
sra update
2.6 KB
install_linux.py: bugfix in numpy version check
2.3 KB
! Add scripts to download bowtie, hg19 and sacCer3
2.0 KB
download_bowtie.sh: install bowtie2 into a folder with a standard name
1.2 KB
make_sacCer3_gap.py: fix a bug introduced by the recent changes in the syntax of mirnylab.genome.createGapFile()
855 B
More python3 fixes

hiclib

Read the documentation.

Installation

The easiest way is to use pip, but see notes below:

First, install mirnylib:

$ pip install https://bitbucket.org/mirnylab/mirnylib/get/tip.tar.gz

Then install hiclib:

$ pip install https://bitbucket.org/mirnylab/hiclib/get/tip.tar.gz

Alternatively, there is a linux install script that doesn't use pip.

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 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. 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

Optional:

  • Sphinx (to generate documentation)