forked from mkadlof/nf_nanopore_sars
-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathDockerfile
395 lines (357 loc) · 16.5 KB
/
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
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
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
# Package versions
ARG SAMTOOLS_VERSION="1.17"
ARG BCFTOOLS_VERSION="1.17"
ARG HTSLIB_VERSION="1.17"
ARG BEDTOOLS_VERSION="2.31.0"
ARG VARSCAN_VERSION="2.4.6"
ARG PANGOLIN_VERSION="4.3.1"
ARG NEXTCLADE_VERSION="3.3.1"
ARG PICARD_VERSION="2.27.5"
ARG GOFASTA_VERSION="1.2.1"
ARG USHER_VERSION="0.6.3"
ARG ISA_VERSION="2.30.0"
ARG TBB_VERSION="2019_U9"
ARG TBB_VERSION2="v2021.10.0"
ARG KRAKEN2_VERSION="v2.1.3"
# This is multistage, parallel build. We first build a base image.
# Then, in parallel, we build all the tools we need.
# And then in the end we copy only necessary files to production image.
# builder-base
FROM python:3.11.8-bookworm AS builder-base
ENV LANG en_US.UTF-8
ENV VIRTUAL_ENV=/opt/venv
ENV PATH=/$VIRTUAL_ENV/bin:$PATH:usr/local/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
# We install some basic tools, build tools and libraries
RUN apt update && \
apt install --yes --no-install-recommends curl \
ca-certificates \
git \
lbzip2 \
build-essential \
autoconf \
automake \
cmake \
pkg-config \
libtool \
zlib1g-dev \
libbz2-dev \
liblzma-dev
# Here we create a new python virtual environment. We can later just copy it to production container
# It is "activated" by adding it to PATH
RUN python3 -m venv $VIRTUAL_ENV
# builder-samtools
FROM builder-base AS builder-samtools
ARG SAMTOOLS_VERSION
WORKDIR /downloads
RUN curl -fsSL "https://github.com/samtools/samtools/releases/download/${SAMTOOLS_VERSION}/samtools-${SAMTOOLS_VERSION}.tar.bz2" \
-o "samtools-${SAMTOOLS_VERSION}.tar.bz2" && \
tar -xf samtools-${SAMTOOLS_VERSION}.tar.bz2 && \
rm samtools-${SAMTOOLS_VERSION}.tar.bz2
WORKDIR /downloads/samtools-${SAMTOOLS_VERSION}
RUN ./configure --prefix=/opt/samtools --without-curses --disable-bz2 --disable-lzma && \
make -j `nproc` && \
make -j `nproc` install
ENV PATH=/opt/samtools/bin:${PATH}
# builder-bcftools
FROM builder-base as builder-bcftools
ARG BCFTOOLS_VERSION
WORKDIR /downloads
RUN curl -fsSL "https://github.com/samtools/bcftools/releases/download/${BCFTOOLS_VERSION}/bcftools-${BCFTOOLS_VERSION}.tar.bz2" -o "bcftools-${BCFTOOLS_VERSION}.tar.bz2" && \
tar -xf "bcftools-${BCFTOOLS_VERSION}.tar.bz2" && \
rm "bcftools-${BCFTOOLS_VERSION}.tar.bz2"
WORKDIR /downloads/bcftools-${BCFTOOLS_VERSION}
RUN ./configure --prefix=/opt/bcftools --disable-bz2 --disable-lzma && \
make -j `nproc` && \
make -j `nproc` install
ENV PATH=/opt/bcftools/bin:${PATH}
# builder-htslib
FROM builder-base as builder-htslib
ARG HTSLIB_VERSION
WORKDIR /downloads
RUN curl -fsSL "https://github.com/samtools/htslib/releases/download/${HTSLIB_VERSION}/htslib-${HTSLIB_VERSION}.tar.bz2" -o "htslib-${HTSLIB_VERSION}.tar.bz2" && \
tar -xf htslib-${HTSLIB_VERSION}.tar.bz2 && \
rm htslib-${HTSLIB_VERSION}.tar.bz2
WORKDIR /downloads/htslib-${HTSLIB_VERSION}
RUN ./configure --prefix="/opt/htslib" --disable-bz2 --disable-lzma && \
make -j `nproc` && \
make -j `nproc` install
ENV PATH=/opt/htslib/bin:${PATH}
# builder-bedtools
FROM builder-base as builder-bedtools
ARG BEDTOOLS_VERSION
WORKDIR /downloads
RUN curl -fsSL "https://github.com/arq5x/bedtools2/releases/download/v${BEDTOOLS_VERSION}/bedtools-${BEDTOOLS_VERSION}.tar.gz" -o "bedtools-${BEDTOOLS_VERSION}.tar.gz" && \
tar -zxf bedtools-${BEDTOOLS_VERSION}.tar.gz && \
rm bedtools-${BEDTOOLS_VERSION}.tar.gz
WORKDIR /downloads/bedtools2
RUN make -j `nproc`
# builder-varscan
FROM builder-base as builder-varscan
ARG VARSCAN_VERSION
WORKDIR /opt/varscan
RUN curl -fsSL "https://github.com/dkoboldt/varscan/releases/download/v${VARSCAN_VERSION}/VarScan.v${VARSCAN_VERSION}.jar" -o "VarScan.v${VARSCAN_VERSION}.jar" && \
ln -s VarScan.v${VARSCAN_VERSION}.jar varscan.jar
# builder-vcftools
FROM builder-base as builder-vcftools
# TODO: git is always downloading latest version. We should use specific version, tag or commit.
WORKDIR /downloads/vcftools
RUN git clone --depth 1 https://github.com/vcftools/vcftools.git /downloads/vcftools && \
./autogen.sh && \
./configure --prefix=/opt/vcftools && \
make -j `nproc` && \
make -j `nproc` install
ENV PATH="/opt/vcftools/bin:$PATH"
# builder-freebayes
FROM builder-base as builder-freebayes
ARG FREEBAYESS_VERSION
WORKDIR /opt/freebayes/bin
RUN curl -fsSL "https://github.com/freebayes/freebayes/releases/download/v${FREEBAYESS_VERSION}/freebayes-${FREEBAYESS_VERSION}-linux-amd64-static.gz" -o "freebayes-${FREEBAYESS_VERSION}-linux-amd64-static.gz" && \
gunzip freebayes-${FREEBAYESS_VERSION}-linux-amd64-static.gz && \
chmod 755 freebayes-${FREEBAYESS_VERSION}-linux-amd64-static && \
ln -s freebayes-${FREEBAYESS_VERSION}-linux-amd64-static freebayes
ENV PATH="/opt/freebayes/bin:$PATH"
# builder-snpeff
FROM builder-base as builder-snpeff
WORKDIR /opt
ADD third-party/snpEff.tar.gz /opt
COPY data/snpEff /opt/snpEff
# builder-python
# Here goes all packages installed as python packages.
# - Pangolin
# - PycoQC
FROM builder-base as builder-python
ARG PANGOLIN_VERSION
COPY requirements.txt /
RUN pip install -r /requirements.txt
WORKDIR /downloads
RUN curl -fsSL https://github.com/cov-lineages/pangolin/archive/refs/tags/v${PANGOLIN_VERSION}.tar.gz -o v${PANGOLIN_VERSION}.tar.gz && \
tar -zxvf v${PANGOLIN_VERSION}.tar.gz && \
rm v${PANGOLIN_VERSION}.tar.gz
WORKDIR /downloads/pangolin-${PANGOLIN_VERSION}
RUN python setup.py install && \
pip freeze && \
pip uninstall --yes pangolin_data
# builder-nextclade
FROM builder-base as builder-nextclade
ARG NEXTCLADE_VERSION
WORKDIR /opt/nextclade/bin
RUN curl -fsSL "https://github.com/nextstrain/nextclade/releases/download/${NEXTCLADE_VERSION}/nextclade-x86_64-unknown-linux-gnu" -o "nextclade" && \
chmod +x nextclade
RUN mkdir -p /SARS-CoV2/
ENV PATH="/opt/nextclade/bin:$PATH"
RUN nextclade dataset get --name='sars-cov-2' --output-dir=/SARS-CoV2/nextclade/
# builder-picard
FROM builder-base as builder-picard
ARG PICARD_VERSION
WORKDIR /opt/picard
RUN curl -fsSL "https://github.com/broadinstitute/picard/releases/download/${PICARD_VERSION}/picard.jar" -o "picard.jar"
# builder-gofasta
FROM builder-base as builder-gofasta
ARG GOFASTA_VERSION
WORKDIR /opt/gofasta/bin
RUN curl -fsSL "https://github.com/virus-evolution/gofasta/releases/download/v${GOFASTA_VERSION}/gofasta-linux-amd64" -o "gofasta" && \
chmod +x gofasta
ENV PATH="/opt/gofasta/bin:$PATH"
# builder-faToVcf
# TODO: We consider this as unstable resource, so we should store it locally in third-party directory.
FROM builder-base as builder-faToVcf
WORKDIR /opt/blat/bin
RUN curl -fsSL "https://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/faToVcf" -o "faToVcf" && \
chmod +x faToVcf
ENV PATH="/opt/blat/bin:$PATH"
# builder-isa-l
# This lib is a dependency of one of Usher binaries, we don't use it but it is still needed for building usher.
# We do not copy that unnecesary binary to production image, and also we don't copy this i-sal lib, either.
FROM builder-base as builder-isa-l
ARG ISA_VERSION
WORKDIR /downloads
RUN apt install -y --no-install-recommends nasm && \
curl -fsSL "https://github.com/intel/isa-l/archive/refs/tags/v${ISA_VERSION}.tar.gz" -o "v${ISA_VERSION}.tar.gz" && \
tar -zxf v${ISA_VERSION}.tar.gz && \
rm v${ISA_VERSION}.tar.gz
WORKDIR /downloads/isa-l-${ISA_VERSION}
RUN ./autogen.sh && \
./configure --prefix "/opt/isa-l" && \
make -j $(nproc) && \
make -j $(nproc) install
# builder-usher
FROM builder-base as builder-usher
ARG USHER_VERSION
ARG TBB_VERSION
COPY --from=builder-isa-l /opt/isa-l /opt/isa-l
WORKDIR /downloads
RUN git clone --depth 1 --branch v${USHER_VERSION} https://github.com/yatisht/usher.git && \
cd usher && \
mkdir build
WORKDIR /downloads/usher/build
RUN apt -y --no-install-recommends install gfortran-12 \
ibverbs-providers \
libboost1.74-dev \
libboost-date-time1.74-dev \
libboost-date-time1.74.0 \
libboost-date-time-dev \
libboost-dev \
libboost-filesystem1.74-dev \
libboost-filesystem1.74.0 \
libboost-filesystem-dev \
libboost-iostreams1.74-dev \
libboost-iostreams1.74.0 \
libboost-iostreams-dev \
libboost-program-options1.74-dev \
libboost-program-options1.74.0 \
libboost-program-options-dev \
libboost-regex1.74-dev \
libboost-regex1.74.0 \
libboost-serialization1.74-dev \
libboost-serialization1.74.0 \
libboost-system1.74-dev \
libboost-system1.74.0 \
libfabric1 \
libgfortran-12-dev \
libhwloc15 \
libhwloc-dev \
libhwloc-plugins \
libibverbs1 \
libibverbs-dev \
libjs-jquery-ui \
libjs-jquery \
libmunge2 \
libnl-3-200 \
libnl-3-dev \
libnl-route-3-200 \
libnl-route-3-dev \
libnuma-dev \
libopenmpi3 \
libopenmpi-dev \
libpciaccess0 \
libpmix2 \
libpmix-dev \
libprotobuf32 \
libprotobuf-dev \
libprotobuf-lite32 \
libprotoc32 \
libprotoc-dev \
libpsm2-2 \
libpsm-infinipath1 \
librdmacm1 \
libucx0 \
libxnvctrl0 \
ocl-icd-libopencl1 \
openmpi-bin \
openmpi-common \
protobuf-compiler
RUN curl -fsSL "https://github.com/oneapi-src/oneTBB/archive/${TBB_VERSION}.tar.gz" -o "${TBB_VERSION}.tar.gz" && \
tar -zxf ${TBB_VERSION}.tar.gz && \
rm ${TBB_VERSION}.tar.gz && \
cmake -DCMAKE_INSTALL_PREFIX=/opt/usher \
-DTBB_DIR=${PWD}/oneTBB-2019_U9 \
-DISAL_LIB=/opt/isa-l/lib/libisal.so \
-DCMAKE_CXX_FLAGS=-I/opt/isa-l/include .. && \
make -j $(nproc) && \
make -j $(nproc) install && \
mkdir -p /opt/tbb/lib && \
cp /downloads/usher/build/tbb_cmake_build/tbb_cmake_build_subdir_release/libtbb_preview.so.2 /opt/tbb/lib
# builder-kraken2
FROM builder-base as builder-kraken2
ARG KRAKEN2_VERSION
WORKDIR /downloads
RUN git clone --depth 1 --branch ${KRAKEN2_VERSION} https://github.com/DerrickWood/kraken2.git
WORKDIR /downloads/kraken2
RUN mkdir -p /opt/kraken2 && \
./install_kraken2.sh /opt/kraken2/bin
# builder-modeller
FROM builder-base as modeller
ADD third-party/modeller/modeller.tar.gz /opt
ADD third-party/modeller/config.py /opt/modeller/modlib/modeller/config.py
# main
FROM python:3.11.8-slim-bookworm AS main
LABEL maintainer="Michal Lazniewski <[email protected]>"
LABEL maintainer="Michał Kadlof <[email protected]>"
RUN echo 'alias ls="ls --color --group-directories-first"' >> /root/.bashrc && \
echo "PS1='\[\033[36m\][\[\033[m\]\[\033[34m\]\[\e[1m \u@\h \e[0m\] \[\033[32m\]\W\[\033[m\]\[\033[36m\]]\[\033[m\]# '" >> /root/.bashrc
ENV LD_LIBRARY_PATH="/opt/htslib/lib:/opt/tbb/lib:/opt/isa-l/lib:${LD_LIBRARY_PATH}"
ENV PYTHONPATH="/home/external_databases/pangolin"
RUN apt update && \
apt install --yes --no-install-recommends bc\
openjdk-17-jre-headless \
libdeflate-dev \
libcurl3-gnutls\
libboost-program-options1.74.0 \
libboost-iostreams1.74.0 \
libboost-filesystem1.74.0 \
libprotobuf32 \
libgsl27 \
minimap2 \
libcurl4 \
libgomp1 \
procps \
seqtk
ADD third-party/mafft/mafft_7.520-1_amd64.deb /
RUN dpkg -i mafft_7.520-1_amd64.deb && \
rm -f /mafft_7.520-1_amd64.deb
COPY --from=builder-base /opt /opt
COPY --from=builder-python /opt/venv /opt/venv
COPY --from=builder-samtools /opt/samtools /opt/samtools
COPY --from=builder-bcftools /opt/bcftools /opt/bcftools
COPY --from=builder-htslib /opt/htslib /opt/htslib
COPY --from=builder-bedtools /downloads/bedtools2 /opt/bedtools
COPY --from=builder-vcftools /opt/vcftools /opt/vcftools
COPY --from=builder-snpeff /opt/snpEff /opt/snpEff
COPY --from=builder-picard /opt/picard /opt/picard
COPY --from=builder-gofasta /opt/gofasta /opt/gofasta
COPY --from=builder-faToVcf /opt/blat /opt/blat
# Usher builds with several binaries, but pelines use only a one. We copy only that one.
COPY --from=builder-usher /opt/usher/bin/usher /opt/usher/bin/usher
COPY --from=builder-usher /opt/tbb /opt/tbb
COPY --from=builder-nextclade /opt/nextclade /opt/nextclade
COPY --from=builder-varscan /opt/varscan /opt/varscan
COPY --from=builder-kraken2 /opt/kraken2 /opt/kraken2
COPY --from=modeller /opt/modeller /opt/modeller
ENV GENOME_ID="MN908947.3"
ENV GENOME_FASTA="/home/data/genome/sarscov2.fasta"
ENV PYTHONPATH="/home/external_databases/pangolin"
ENV VIRTUAL_ENV=/opt/venv
ENV PATH /opt/modeller/bin:\
/opt/kraken2/bin:\
/opt/usher/bin:\
/opt/blat/bin:\
/opt/gofasta/bin:\
/opt/bwa/bin:\
/opt/FastQC:\
/opt/nextclade/bin:\
/opt/freebayes/bin:\
/opt/vcftools/bin:\
/opt/lofreq/bin:\
/opt/ivar/bin:\
/opt/bedtools/bin:\
/opt/htslib/bin:\
/opt/bcftools/bin:\
/opt/samtools/bin:\
$VIRTUAL_ENV/bin:\
/usr/local/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
## Kopiowanie wymaganych plikow
COPY data/genome/SarsCov2 /home/data/genome
COPY data/primers /home/data/primers
COPY data/coinfections /home/data/coinfections
COPY data/modeller /home/data/modeller
#ADD data/generic/generic_data.tar.gz /home/SARS-CoV2
WORKDIR /home
# updater container
FROM python:3.11.8-slim-bookworm AS updater
LABEL maintainer="Michal Lazniewski <[email protected]>"
LABEL maintainer="Michał Kadlof <[email protected]>"
COPY --from=builder-nextclade /opt/nextclade /opt/nextclade
RUN apt update && \
apt install -y --no-install-recommends git wget && \
apt clean && \
rm -rf /var/lib/apt/lists/* && \
pip install --no-cache-dir boto3==1.34.75
ADD bin/update.sh /home/update.sh
ADD bin/kraken_updater.py /home/kraken_updater.py
WORKDIR /home/pangolin
WORKDIR /home/nextclade
WORKDIR /home/kraken
WORKDIR /home/freyja
RUN chown -R 1000:1000 /home && chmod 777 /home/pangolin /home/nextclade /home/kraken /home/freyja
WORKDIR /home
ENTRYPOINT ["/home/update.sh"]