-
Notifications
You must be signed in to change notification settings - Fork 1k
/
.k8s_ci.Dockerfile
196 lines (169 loc) · 6.72 KB
/
.k8s_ci.Dockerfile
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
# Stage 1:
# - base: ubuntu (default) OR prebuilt image0
# - install build tools
# - clone playbook
# Stage 2: build galaxy client and server in parallel
# Stage 2.1:
# - run playbook with server build steps only
# - remove build artifacts + files not needed in container
# Stage 2.2:
# - run playbook with client build steps only
# - remove build artifacts + files not needed in container
# Stage 3:
# - create galaxy user + group + directory
# - copy galaxy files from stage 2.1 and 2.2
# - finalize container (set path, user...)
# Init ARGs
ARG ROOT_DIR=/galaxy
ARG SERVER_DIR=$ROOT_DIR/server
ARG STAGE1_BASE=python:3.12-slim
ARG FINAL_STAGE_BASE=$STAGE1_BASE
ARG GALAXY_USER=galaxy
ARG GALAXY_PLAYBOOK_REPO=https://github.com/galaxyproject/galaxy-docker-k8s
ARG GALAXY_PLAYBOOK_BRANCH=v4.1.0
ARG GIT_COMMIT=unspecified
ARG BUILD_DATE=unspecified
ARG IMAGE_TAG=unspecified
#======================================================
# Stage 1 - Setup common requirements for build
#======================================================
FROM $STAGE1_BASE AS stage1
ARG DEBIAN_FRONTEND=noninteractive
ARG SERVER_DIR
ARG GALAXY_PLAYBOOK_REPO
ARG GALAXY_PLAYBOOK_BRANCH
# Init Env
ENV LC_ALL=en_US.UTF-8
ENV LANG=en_US.UTF-8
# Install build dependencies + ansible
RUN set -xe; \
echo "Acquire::http {No-Cache=True;};" > /etc/apt/apt.conf.d/no-cache \
&& apt-get -qq update && apt-get install -y --no-install-recommends \
locales locales-all \
git \
make \
libc-dev \
bzip2 \
gcc \
&& pip install --no-cache virtualenv ansible \
&& apt-get autoremove -y && apt-get clean \
&& rm -rf /var/lib/apt/lists/* /tmp/*
# Remove context from previous build; copy current context; run playbook
WORKDIR /tmp/ansible
RUN rm -rf *
ENV LC_ALL en_US.UTF-8
RUN git clone --depth 1 --branch $GALAXY_PLAYBOOK_BRANCH $GALAXY_PLAYBOOK_REPO galaxy-docker
WORKDIR /tmp/ansible/galaxy-docker
RUN ansible-galaxy install -r requirements.yml -p roles --force-with-deps
# Add Galaxy source code
COPY . $SERVER_DIR/
#======================================================
# Stage 2.1 - Build galaxy server
#======================================================
FROM stage1 AS server_build
ARG SERVER_DIR
RUN ansible-playbook -i localhost, playbook.yml -v -e "{galaxy_build_client: false}" -e galaxy_virtualenv_command=virtualenv
# Remove build artifacts + files not needed in container
WORKDIR $SERVER_DIR
# Save commit hash of HEAD before zapping git folder
RUN git rev-parse HEAD > GITREVISION
RUN rm -rf \
.ci \
.git \
.venv/include/node \
.venv/src/node* \
doc \
test \
test-data
# Clean up *all* node_modules, including plugins. Everything is already built+staged.
RUN find . -name "node_modules" -type d -prune -exec rm -rf '{}' +
#======================================================
# Stage 2.2 - Build galaxy client
#======================================================
FROM stage1 AS client_build
ARG SERVER_DIR
RUN ansible-playbook -i localhost, playbook.yml -v --tags "galaxy_build_client" -e galaxy_virtualenv_command=virtualenv
WORKDIR $SERVER_DIR
RUN rm -rf \
.ci \
.git \
.venv/include/node \
.venv/src/node* \
doc \
test \
test-data
# Clean up *all* node_modules, including plugins. Everything is already built+staged.
RUN find . -name "node_modules" -type d -prune -exec rm -rf '{}' +
#======================================================
# Stage 3 - Build final image based on previous stages
#======================================================
FROM $FINAL_STAGE_BASE
ARG DEBIAN_FRONTEND=noninteractive
ARG ROOT_DIR
ARG SERVER_DIR
ARG GALAXY_USER
ARG GIT_COMMIT
ARG BUILD_DATE
ARG IMAGE_TAG
LABEL org.opencontainers.image.title="Galaxy Minimal Image" \
org.opencontainers.image.description="A size optimized image for Galaxy targeting k8s and ci applications" \
org.opencontainers.image.authors="galaxyproject.org" \
org.opencontainers.image.vendor="Galaxy Project" \
org.opencontainers.image.documentation="https://github.com/galaxyproject/galaxy-docker-k8s" \
org.opencontainers.image.licenses="MIT" \
org.opencontainers.image.version="$IMAGE_TAG" \
org.opencontainers.image.url="https://github.com/galaxyproject/galaxy-docker-k8s" \
org.opencontainers.image.source="https://github.com/galaxyproject/galaxy.git" \
org.opencontainers.image.revision=$GIT_COMMIT \
org.opencontainers.image.created=$BUILD_DATE
# Init Env
ENV LC_ALL=en_US.UTF-8
ENV LANG=en_US.UTF-8
# Install procps (contains kill, ps etc.), less, curl, vim-tiny and nano-tiny
# for convenience and debugging purposes. Nano and vim commands are aliased
# to their tiny variants using the debian alternatives system.
# Bzip2 and virtualenv are installed for backwards compatibility with older
# versions of this image which was based on Ubuntu and contained these
# utilities.
RUN set -xe; \
echo "Acquire::http {No-Cache=True;};" > /etc/apt/apt.conf.d/no-cache \
&& apt-get -qq update && apt-get install -y --no-install-recommends \
locales \
vim-tiny \
nano-tiny \
curl \
procps \
less \
bzip2 \
tini \
nodejs \
&& update-alternatives --install /usr/bin/nano nano /bin/nano-tiny 0 \
&& update-alternatives --install /usr/bin/vim vim /usr/bin/vim.tiny 0 \
&& echo "set nocompatible\nset backspace=indent,eol,start" >> /usr/share/vim/vimrc.tiny \
&& echo "$LANG UTF-8" > /etc/locale.gen \
&& locale-gen $LANG && update-locale LANG=$LANG \
&& curl -L https://github.com/galaxyproject/gxadmin/releases/latest/download/gxadmin > /usr/bin/gxadmin \
&& chmod +x /usr/bin/gxadmin \
&& apt-get autoremove -y && apt-get clean \
&& rm -rf /var/lib/apt/lists/* /tmp/*
# Create Galaxy user, group, directory; chown
RUN set -xe; \
adduser --system --group --uid 101 $GALAXY_USER \
&& mkdir -p $SERVER_DIR \
&& chown $GALAXY_USER:$GALAXY_USER $ROOT_DIR -R
WORKDIR $ROOT_DIR
# Copy galaxy files to final image
# The chown value MUST be hardcoded (see https://github.com/moby/moby/issues/35018)
COPY --chown=$GALAXY_USER:$GALAXY_USER --from=server_build $ROOT_DIR .
COPY --chown=$GALAXY_USER:$GALAXY_USER --from=client_build $SERVER_DIR/static ./server/static
WORKDIR $SERVER_DIR
# The data in version.json will be displayed in Galaxy's /api/version endpoint
RUN printf "{\n \"git_commit\": \"$(cat GITREVISION)\",\n \"build_date\": \"$BUILD_DATE\",\n \"image_tag\": \"$IMAGE_TAG\"\n}\n" > version.json \
&& chown $GALAXY_USER:$GALAXY_USER version.json
EXPOSE 8080
USER $GALAXY_USER
ENV PATH="$SERVER_DIR/.venv/bin:${PATH}"
ENV GALAXY_CONFIG_CONDA_AUTO_INIT=False
ENTRYPOINT ["tini", "--"]
# [optional] to run:
CMD galaxy