Commit 9a55f932 authored by Pradat Yoann's avatar Pradat Yoann
Browse files

update ensembl-vep to release 102 and Makefile

parent 9e5f8892
[run] [run]
omit = */__init__.py, *tests* omit = */__init__.py, *tests*, setup.py
...@@ -22,6 +22,7 @@ __pycache__/ ...@@ -22,6 +22,7 @@ __pycache__/
*.coverage *.coverage
*.egg-info/ *.egg-info/
*htmlcov/ *htmlcov/
*.coveragerc
# Open cached files # Open cached files
*.m~ *.m~
......
PYTHON ?= python PYTHON ?= python
PYTEST ?= pytest PYTEST ?= pytest
CTAGS ?= ctags CTAGS ?= ctags
PIP ?= pip
ifeq (,$(CONDA_PREFIX)) # .PHONY defines parts of the makefile that are not dependant on any specific file
CONDA_ACTIVATED=True # This is most often used to store functions
else .PHONY = help test tags clean
CONDA_ACTIVATED=False
endif
#environment: # Defines the default target that `make` will to try to make, or in the case of a phony target, execute the specified commands
#ifeq (True, $(CONDA_ACTIVATED)) # This target is executed whenever we just type `make`
# @echo ">>> Found $(CONDA_PREFIX) environment activated. Install the requirements in this environment." .DEFAULT_GOAL = help
# conda env update --file reqs/requirements.yml
#else
# pip install -r requirements.txt
#endif
clean: # The @ makes sure that the command itself isn't echoed in the terminal
$(PYTHON) setup.py clean help:
@echo "---------------HELP-----------------"
# installation instructions are not clear to me: @echo "make setup to setup the project"
# setup.py install -> the package cannot be imported from outside the repository even though he is @echo "make test to run the tests"
# visible in the conda list as <develop> in the same way as when @echo "make clean to remove build/dev files"
# setup.py develop -> everything is ok @echo "make install to install"
#install: clean-ctags @echo "------------------------------------"
# $(PYTHON) setup.py install
install: ctags
$(PYTHON) setup.py develop
develop: ctags
$(PYTHON) setup.py develop
test: test:
$(PYTEST) --cov-config=.coveragerc --cov-report term-missing --cov variant_annotator variant_annotator $(PIP) install --upgrade pytest pytest-cov
$(PYTEST) --cov-config=.coveragerc --cov-report term-missing --cov . .
build:
@echo "---------------Build variant_annotator-----------------"
$(PYTHON) -m pip install --user --upgrade setuptools wheel
$(PYTHON) setup.py sdist bdist_wheel
install:
@echo "---------------Install variant_annotator-----------------"
$(PIP) install --upgrade pip setuptools wheel
$(PIP) install -r reqs/requirements.txt
$(PIP) install .
update:
@echo "---------------Update vcf2maf-----------------"
cd tools/vcf2maf
git pull
cd ../..
@echo "---------------Update ensembl-vep-----------------"
cd tools/ensembl-vep
git pull
cd ../..
tags:
$(CTAGS) --python-kinds=-i --exclude=*/tests/* -R .
ctags: clean:
$(CTAGS) --python-kinds=-i --exclude=*/tests/* -R variant_annotator
clean-ctags:
rm -f tags rm -f tags
rm -rf build
rm -rf dist
rm -rf *.egg-info
Subproject commit bf8fce94cfe1889c92771695bb57931b43b72484 Subproject commit ef2b5865f0c4c5fb8f8be31dafcb478c151e9214
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