Commit 08452c07 authored by Blaise Li's avatar Blaise Li
Browse files

Made libhts a submodule.

parent 6e9f7831
......@@ -7,3 +7,6 @@
[submodule "libworkflows"]
path = libworkflows
url = git@gitlab.pasteur.fr:bli/libworkflows.git
[submodule "libhts"]
path = libhts
url = git@gitlab.pasteur.fr:bli/libhts.git
Subproject commit 7e25a230845896610a1a11a8ba91a51c824e9d0f
# Compiled python modules.
*.pyc
# Setuptools distribution folder.
/dist/
# Python egg metadata, regenerated from source files by setuptools.
/*.egg-info
# Backups
*~
#!/bin/sh
python3.6 setup.py build_ext
# .egg-link does not work with PYTHONPATH ?
python3.6 -m pip install -e .
python3.6 -m pip install --no-deps --ignore-installed .
from .libhts import (
aligner2min_mapq,
gtf_2_genes_exon_lengths,
id_list_gtf2bed,
make_empty_bigwig,
make_seeding_function,
median_ratio_to_pseudo_ref_size_factors,
plot_boxplots, plot_counts_distribution, plot_histo,
plot_lfc_distribution, plot_MA,
plot_norm_correlations, plot_paired_scatters, plot_scatter,
repeat_bed_2_lengths, size_factor_correlations,
spikein_gtf_2_lengths, status_setter)
This diff is collapsed.
from setuptools import setup, find_packages
#from Cython.Build import cythonize
name = "libhts"
# Adapted from Biopython
__version__ = "Undefined"
for line in open("%s/__init__.py" % name):
if (line.startswith('__version__')):
exec(line.strip())
setup(
name=name,
version=__version__,
description="Miscellaneous things to process high throughput sequencing data.",
author="Blaise Li",
author_email="blaise.li@normalesup.org",
license="MIT",
packages=find_packages(),
install_requires=[
# "libworkflows",
"matplotlib",
"networkx",
"numpy",
"pandas",
"pyBigWig",
"pybedtools",
"scipy",
"seaborn"])
#ext_modules = cythonize("libsmallrna/libsmallrna.pyx"),
#install_requires=["cytoolz"],
#zip_safe=False
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