-
Notifications
You must be signed in to change notification settings - Fork 1
/
Copy pathMakefile
297 lines (259 loc) · 11 KB
/
Makefile
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
#
# - # **********************************************************************
# - # Copyright (C) 2020 Johns Hopkins University Applied Physics Laboratory
# - #
# - # All Rights Reserved.
# - # For any other permission, please contact the Legal Office at JHU/APL.
# - # **********************************************************************
#
# Define directory variables
SHELL=/bin/bash
BASE_DIR := $(dir $(CURDIR)/$(word $(words $(MAKEFILE_LIST)),$(MAKEFILE_LIST)))
ROOT_DIR := $(patsubst %/,%,$(BASE_DIR))
THIS_FILE := $(ROOT_DIR)/Makefile
THIS_DIR := $(notdir $(patsubst %/,%,$(ROOT_DIR)))
TEST_DATA := $(ROOT_DIR)/test-data
PYTHON_EXECUTABLE := $(shell which python)
CLIENT_DIR := $(ROOT_DIR)/client
DATA_DIR := ${CLIENT_DIR}/data
UID := $(shell id -u)
GID := $(shell id -g)
UNAME := $(shell uname -s)
ARCH := $(shell uname -m)
HOME := $(shell echo $${HOME})
CONDA_ACTIVATE=source $$(conda info --base)/etc/profile.d/conda.sh ; conda activate ; conda activate
WHOAMI := $(shell whoami)
#Indictate whete or not dependencies are present in the makefile as assigned variables
PYTHON := $(shell command -v python 2> /dev/null)
WGET := $(shell command -v wget 2> /dev/null)
CONDA := $(shell command -v conda 2> /dev/null)
DOCKER := $(shell command -v docker 2> /dev/null)
BREW := $(shell command -v brew 2> /dev/null)
ARTIC := $(shell command docker images -q artic:latest 2> /dev/null)
# Build entire app from scratch, including dev mode
build-win: variables install-modules clone build-app
build-unix: variables install-modules clone build-app
# Use pre-compiled binaries and install docker images from scratch (requires internet)
install-unix: variables build-docker-images-unix
install-win: variables build-docker-images-win
#Use pre-compile binaries and install docker images from pre-compressed .tar.gz files (requires internet for initial install)
load-unix: variables check-images-installed
load-win: variables check-images-installed
load-unix-fresh: rm-docker-local load-unix
load-win-fresh: rm-docker-local load-win
build-base-deps: install-deps source-miniconda create-basestack activate-basestack
test-source: source-miniconda create-basestack
install-deps: check-python check-wget check-docker check-conda
#Check if binaries/commands exist. IF not, install them
check-python:
@echo "Checking if python is installed..."
ifndef PYTHON
@echo "Please install python for your OS. Exiting"
exit 1
endif
@echo "\t...python is installed, continuing"
check-wget:
@echo "Checking if wget installed..."
ifndef WGET
$(MAKE) install-wget
endif
@echo "\t...wget installed, continuing"
check-docker:
@echo "Checking if docker is installed..."
ifndef DOCKER
$(MAKE) install-docker
endif
@echo "\t...docker installed, continuing"
check-conda:
@echo "Checking if conda is installed..."
ifndef CONDA
@if [ ! -d "${HOME}/miniconda3" ]; then\
$(MAKE) install-miniconda;\
exit 0;\
else\
echo "conda is not findable in your env but is available in ${HOME} directory (assuming it went through the default install process into your Home (${HOME}) directory)";\
echo -e "\n\nPlease source your conda environment and rerun your installation option: 'source ${HOME}/miniconda3/etc/profile.d/conda.sh'";\
echo -e "\n\n\n. Ignore the following files";\
exit 1;\
fi
endif
@echo "\t...conda installed, continuing"
check-images-installed:
@echo "Checking if docker is installed on your machine, installing if not."
$(MAKE) check-docker
@echo "Checking if the docker image (Artic) is already available to the user"
$(MAKE) check-artic-installed
# https://drive.google.com/open?id=1M39vc0uTMsNJE3sS9X7zW_rCXUdyLk3j - location of artic.tar.gz dockerfile
check-artic-installed:
ifndef ARTIC
@echo "Not defined: artic docker image, using local image to install."
$(MAKE) download-load-docker-images
else
@echo "Artic already defined. If you want to reinstall locally, please rm the image first and try again."
endif
@echo "Artic (consensus and rampart) completed"
rm-docker-local:
rm -rf 'client/data/dockerbuild/artic/images/artic.tar.gz'
download-load-docker-images:
mkdir -p 'client/data/dockerbuild/artic/images'
ifeq (,$(wildcard 'client/data/dockerbuild/artic/images/artic.tar.gz'))
@echo "Downloading docker images from gdrive"
$(shell gdown 'https://drive.google.com/uc?id=1M39vc0uTMsNJE3sS9X7zW_rCXUdyLk3j' -O 'client/data/dockerbuild/artic/images/artic.tar.gz')
endif
@echo "installing artic docker"
$(shell docker load < 'client/data/dockerbuild/artic/images/artic.tar.gz')
@echo "installed artic docker"
#Install 3rd parety dependencies
install-brew:
@echo "Checking if brew installed"
ifndef BREW
@echo "Installing brew"
curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install | /bin/bash
else
echo "Brew already installed, continuing"
endif
install-wget:
@echo "installing wget"
@if [ ${UNAME} = "Linux" ]; then\
sudo apt-get install wget;\
else\
$(MAKE) install-brew;\
brew install wget;\
fi
install-docker:
# $(MAKE) install-brew;\
# brew install caskroom/cask/brew-cask;\
# brew cask install docker-toolbox;\
@echo "installing docker"
@if [ ${UNAME} = "Linux" ]; then\
wget -O docker.sh https://get.docker.com && mv docker.sh /tmp/ ;\
bash /tmp/docker.sh;\
rm /tmp/docker.sh;\
sudo usermod -aG docker ${WHOAMI};\
else\
echo "Please install Docker manually at: https://docs.docker.com/get-docker/";\
exit 1;\
fi
install-miniconda:
@echo "installing miniconda. This will error out if you already have miniconda3 installed in ${HOME}"
@if [ ${UNAME} = "Linux" ]; then\
echo "Installing Conda on Linux";\
wget "https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh";\
bash Miniconda3-latest-Linux-x86_64.sh -b -p "${HOME}/miniconda3";\
rm Miniconda3-latest-Linux-x86_64.sh ;\
source ${HOME}/.bashrc && which conda;\
else\
echo "Installing Conda on Mac";\
wget https://repo.anaconda.com/miniconda/Miniconda3-latest-MacOSX-x86_64.sh -O ${HOME}/miniconda.sh;\
bash ${HOME}/miniconda.sh -b -p ${HOME}/miniconda;\
source ${HOME}/.bashrc && which conda;\
fi
#Not used at the moment due to makefile limitations
source-miniconda:
ifndef CONDA
@if [ ! -d "${HOME}/miniconda3" ]; then\
echo "Conda not currently available in your environment and not present in ${HOME}. Exiting. Please follow the necessary steps to install anaconda/miniconda on your own environment or rerun this installation process";\
exit 1;\
else\
echo "conda is not findable in your env but is available in ${HOME} directory (assuming it went through the default install process into your Home (${HOME}) directory)";\
echo -e "\n\nPlease source your conda environment and rerun your installation option: 'source ${HOME}/miniconda3/etc/profile.d/conda.sh'";\
echo -e "\n\n\n. Ignore the following files";\
exit 1;\
fi
else
echo "Conda already available in your env, skipping..."
endif
create-basestack:
bash -c "conda env create -f ${ROOT_DIR}/environment.yml"; exit 0;
activate-basestack:
@echo "Now, be sure to activate basestack with 'conda activate basestack'"
($(CONDA_ACTIVATE) basestack ; which python )
#Run the development process for basestack
dev:
@echo "running development app"
@if [[ ${UNAME} = "Linux" || ${UNAME} = "Darwin" ]]; then\
cd ${ROOT_DIR}/client && ($(CONDA_ACTIVATE) basestack ; npm run dev );\
else\
cd ${ROOT_DIR}/client && npm run dev ;\
fi
#Build images depending on the HOST OS
build-docker-images-win:
@echo "building docker images for windows env"
@if [[ ${UNAME} = "Linux" || ${UNAME} = "Darwin" ]]; then\
cd ${ROOT_DIR}/client/data/dockerbuild && ($(CONDA_ACTIVATE) basestack ; docker-compose build --build-arg ENVIRONMENT="WIN" );\
else\
cd ${ROOT_DIR}/client/data/dockerbuild/ && docker-compose build --build-arg ENVIRONMENT="WIN";\
fi
build-docker-images-unix:
@echo "building docker images for unix env"
@if [[ ${UNAME} = "Linux" || ${UNAME} = "Darwin" ]]; then\
cd ${ROOT_DIR}/client/data/dockerbuild/ && \
($(CONDA_ACTIVATE) basestack ; \
docker-compose build --build-arg USER_ID=${UID} --build-arg GROUP_ID=${GID} --build-arg ENVIRONMENT="UNIX");\
else\
"Can't build unix package from this OS: ${UNAME}";\
fi
#Build the app (both production and dev)
install-modules:
@echo "Installing Dependencies in: "${ROOT_DIR}/client/node_modules
@if [[ ${UNAME} = "Linux" || ${UNAME} = "Darwin" ]]; then\
cd ${ROOT_DIR}/client && ($(CONDA_ACTIVATE) basestack ; npm install );\
else\
cd ${ROOT_DIR}/client && npm install;\
fi
#Just build the production
build-app:
@echo "\nBuilding app..."
@if [[ ${UNAME} = "Linux" || ${UNAME} = "Darwin" ]]; then\
cd ${ROOT_DIR}/client && ($(CONDA_ACTIVATE) basestack ; npm run build );\
else\
cd ${ROOT_DIR}/client && npm run build;\
fi ;\
echo "Executable file is located in "${ROOT_DIR}/client/build/
#Clone test-data and artic primer schemes and protocols
clone:
@echo "Cloning repos from artic network"
rm -rf ${DATA_DIR}/protocols/artic-ncov2019 ${DATA_DIR}/protocols/rampart-iva
mkdir -p ${DATA_DIR}/protocols
mkdir -p ${DATA_DIR}/primer_schemes
$(MAKE) clone-shell
cp -fr ${DATA_DIR}/protocols/artic-ncov2019/primer-schemes/* ${DATA_DIR}/primer_schemes/
mv ${DATA_DIR}/primer_schemes/SARS-CoV-2 ${DATA_DIR}/primer_schemes/nCoV-2019
cp -fr ${DATA_DIR}/protocols/artic-ncov2019/rampart ${DATA_DIR}/protocols/rampart-ncov2019
cp -fr ${DATA_DIR}/protocols/rampart-iva/protocol ${DATA_DIR}/protocols/rampart-iva19
rm -rf ${DATA_DIR}/protocols/artic-ncov2019
rm -rf ${DATA_DIR}/protocols/rampart-iva
clone-shell:
# There is an issue with syntax for makefile and using shell git clone. consider refactor in the future
ifneq ($(UNAME), Linux)
ifneq ($(UNAME), Darwin)
$(shell git clone --recurse-submodules https://github.com/artic-network/artic-ncov2019.git ${DATA_DIR}/protocols/artic-ncov2019)
$(shell git clone https://github.com/artic-network/rampart-iva.git ${DATA_DIR}/protocols/rampart-iva)
else
($(CONDA_ACTIVATE) basestack ; git clone --recurse-submodules https://github.com/artic-network/artic-ncov2019.git ${DATA_DIR}/protocols/artic-ncov2019)
($(CONDA_ACTIVATE) basestack ; git clone https://github.com/artic-network/rampart-iva.git ${DATA_DIR}/protocols/rampart-iva)
endif
else
($(CONDA_ACTIVATE) basestack ; git clone --recurse-submodules https://github.com/artic-network/artic-ncov2019.git ${DATA_DIR}/protocols/artic-ncov2019)
($(CONDA_ACTIVATE) basestack ; git clone https://github.com/artic-network/rampart-iva.git ${DATA_DIR}/protocols/rampart-iva)
endif
#Print out variables in use
variables:
@echo "-------------------------------------"
@echo "BASE_DIR = ${BASE_DIR}"
@echo "ROOT_DIR = ${ROOT_DIR}"
@echo "THIS_FILE = ${THIS_FILE}"
@echo "THIS_DIR = ${THIS_DIR}"
@echo "TEST_DIR = ${TEST_DATA}"
@echo "UID = ${UID}"
@echo "GID = ${GID}"
@echo "UNAME = ${UNAME}"
@echo "architecture = ${ARCH}"
@echo "home = ${HOME}"
@echo "whoami = ${WHOAMI}"
@echo "data dir = ${DATA_DIR}"
@echo "client dir = ${CLIENT_DIR}"
@echo "conda activate = ${CONDA_ACTIVATE}"
@echo "python = ${PYTHON_EXECUTABLE}"
@echo "artic = ${ARTIC}"
@echo "-------------------------------------"