Commit 8dc9bb3d authored by Pradat Yoann's avatar Pradat Yoann

v1.1 change setup.py and update ensembl-vep

parent 4f4c4bae
PYTHON ?= python
PYTEST ?= pytest
CTAGS ?= ctags
PIP ?= pip
# .PHONY defines parts of the makefile that are not dependant on any specific file
# This is most often used to store functions
.PHONY = help test tags clean
.PHONY = clean develop install tags test
# Defines the default target that `make` will to try to make, or in the case of a phony target, execute the specified commands
# This target is executed whenever we just type `make`
.DEFAULT_GOAL = help
develop:
@echo "---------------Install varannot in develop mode-----------------"
$(PYTHON) -m pip install -e .
# The @ makes sure that the command itself isn't echoed in the terminal
help:
@echo "---------------HELP-----------------"
@echo "make setup to setup the project"
@echo "make test to run the tests"
@echo "make clean to remove build/dev files"
@echo "make install to install"
@echo "------------------------------------"
install:
@echo "---------------Install varannot-----------------"
$(PYTHON) setup.py install
tags:
$(CTAGS) --python-kinds=-i --exclude=*/tests/* -R .
test:
$(PIP) install --upgrade pytest pytest-cov
@echo "---------------Run varannot tests-----------------"
$(PYTHON) -m pip install pytest pytest-cov
$(PYTEST) --cov-config=.coveragerc --cov-report term-missing --cov . .
codecov:
bash <(curl -s https://codecov.io/bash) -t c8bcf054-f0cb-4bf1-8866-1b862905ef89
build:
@echo "---------------Build variant_annotator-----------------"
$(PYTHON) -m pip install --user --upgrade setuptools wheel
$(PYTHON) setup.py sdist bdist_wheel
install:
@echo "---------------Install variant_annotator-----------------"
git submodule update --init
$(PIP) install --upgrade pip setuptools wheel
$(PIP) install -r reqs/requirements.txt
$(PIP) install .
update:
@echo "---------------Update vcf2maf-----------------"
cd tools/vcf2maf
......@@ -56,3 +42,6 @@ clean:
rm -rf build
rm -rf dist
rm -rf *.egg-info
rm -rf ./*.pyc
rm -rf ./*.tgz
......@@ -27,7 +27,7 @@ import sys
if "." not in sys.path:
sys.path.append(".")
from variant_annotator import run_annotator, Vcf2mafConfig, VepConfig
from varannot import run_annotator, Vcf2mafConfig, VepConfig
#### # SCRIPT PARAMETERS
#### #####################################################################################################
......
......@@ -27,7 +27,7 @@ import sys
if "." not in sys.path:
sys.path.append(".")
from variant_annotator import run_annotator, Vcf2mafConfig, VepConfig
from varannot import run_annotator, Vcf2mafConfig, VepConfig
#### # SCRIPT PARAMETERS
#### #####################################################################################################
......
[build-system]
requires = ["setuptools", "wheel"]
build-backend = "setuptools.build_meta"
numpy>=1.14.0
pandas>=0.23.0
channels:
- defaults
dependencies:
- numpy
- pandas
- pytest
- pytest-cov
- ipython
[metadata]
name = varannot
description = "Variant annotation with VEP and vcf2maf"
license = BSD 2-Clause License
version = 1.1
classifiers =
Topic :: Scientific/Engineering :: Bio-Informatics
Development Status :: 4 - Beta
License :: OSI Approved :: BSD License
Programming Language :: Python :: 3
[options]
packages =
varannot
install_requires =
numpy >= 1.14.0
pandas >= 0.23.0
import os
from setuptools import setup, Command
class CleanCommand(Command):
user_options = []
def initialize_options(self):
self.cwd = None
def finalize_options(self):
self.cwd = os.getcwd()
def run(self):
assert os.getcwd() == self.cwd, 'Must be in package root: %s' % self.cwd
os.system ('rm -rf ./build ./dist ./*.pyc ./*.tgz ./*.egg-info')
setup(
name = "variant_annotator",
version = "1.0.0",
author = "Yoann Pradat",
author_email = "yoann.pradat@centralesupelec.fr",
install_requires = [
"numpy",
"pandas",
],
cmdclass={
'clean': CleanCommand
}
)
import setuptools
setuptools.setup()
"""
The :mod:`variant_annotator` module defines functions for annotating variants using a combination of manual, vep and
The :mod:`varannot` module defines functions for annotating variants using a combination of manual, vep and
vcf2maf annotations.
"""
......
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