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MICS_Biomathematics
bioinfo
VariantAnnotator
Commits
9a55f932
Commit
9a55f932
authored
Feb 14, 2021
by
Pradat Yoann
Browse files
update ensembl-vep to release 102 and Makefile
parent
9e5f8892
Changes
4
Show whitespace changes
Inline
Side-by-side
.coveragerc
View file @
9a55f932
[run]
[run]
omit = */__init__.py, *tests*
omit = */__init__.py, *tests*
, setup.py
.gitignore
View file @
9a55f932
...
@@ -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~
...
...
Makefile
View file @
9a55f932
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
ensembl-vep
@
ef2b5865
Compare
bf8fce94
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ef2b5865
Subproject commit
bf8fce94cfe1889c92771695bb57931b43b7248
4
Subproject commit
ef2b5865f0c4c5fb8f8be31dafcb478c151e921
4
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