Skip to content

Commit b916415

Browse files
ahmigahmig
committed
build: update Dockerfile
1 parent e4429e9 commit b916415

1 file changed

Lines changed: 5 additions & 25 deletions

File tree

‎Dockerfile‎

Lines changed: 5 additions & 25 deletions
Original file line numberDiff line numberDiff line change
@@ -1,9 +1,6 @@
11
FROM condaforge/miniforge3:latest
22
LABEL io.github.snakemake.containerized="true"
3-
LABEL io.github.snakemake.conda_env_hash="fb2a04b98efa75d8b830a16722a8717eb91a3c66659e3c78b90b0cee3a50db69"
4-
5-
# Step 2: Retrieve conda environments
6-
3+
LABEL io.github.snakemake.conda_env_hash="64c979b4b8dbf4bcef709ec73814498afe6df09db6fc3631d525802fb0556df1"
74
# Conda environment:
85
# source: workflow/envs/afwdist.yaml
96
# prefix: /conda-envs/9c24a867826615972cc288081976e7fc
@@ -14,7 +11,6 @@ LABEL io.github.snakemake.conda_env_hash="fb2a04b98efa75d8b830a16722a8717eb91a3c
1411
# - afwdist==1.0.0
1512
RUN mkdir -p /conda-envs/9c24a867826615972cc288081976e7fc
1613
COPY workflow/envs/afwdist.yaml /conda-envs/9c24a867826615972cc288081976e7fc/environment.yaml
17-
1814
# Conda environment:
1915
# source: workflow/envs/biopython.yaml
2016
# prefix: /conda-envs/162796cecea22d99c8702138f0c48e2f
@@ -27,7 +23,6 @@ COPY workflow/envs/afwdist.yaml /conda-envs/9c24a867826615972cc288081976e7fc/env
2723
# - pandas==2.0.3
2824
RUN mkdir -p /conda-envs/162796cecea22d99c8702138f0c48e2f
2925
COPY workflow/envs/biopython.yaml /conda-envs/162796cecea22d99c8702138f0c48e2f/environment.yaml
30-
3126
# Conda environment:
3227
# source: workflow/envs/fetch.yaml
3328
# prefix: /conda-envs/9439457f932a4fbca3665c9ea1ac2f0a
@@ -39,7 +34,6 @@ COPY workflow/envs/biopython.yaml /conda-envs/162796cecea22d99c8702138f0c48e2f/e
3934
# - curl
4035
RUN mkdir -p /conda-envs/9439457f932a4fbca3665c9ea1ac2f0a
4136
COPY workflow/envs/fetch.yaml /conda-envs/9439457f932a4fbca3665c9ea1ac2f0a/environment.yaml
42-
4337
# Conda environment:
4438
# source: workflow/envs/freyja.yaml
4539
# prefix: /conda-envs/bb4c5f3a509433cc08861582fab4a705
@@ -50,7 +44,6 @@ COPY workflow/envs/fetch.yaml /conda-envs/9439457f932a4fbca3665c9ea1ac2f0a/envir
5044
# - freyja==2.0.1
5145
RUN mkdir -p /conda-envs/bb4c5f3a509433cc08861582fab4a705
5246
COPY workflow/envs/freyja.yaml /conda-envs/bb4c5f3a509433cc08861582fab4a705/environment.yaml
53-
5447
# Conda environment:
5548
# source: workflow/envs/gisaidr.yaml
5649
# prefix: /conda-envs/3fad3c9cdfa40bee9404f6a2e8fda69f
@@ -64,7 +57,6 @@ COPY workflow/envs/freyja.yaml /conda-envs/bb4c5f3a509433cc08861582fab4a705/envi
6457
RUN mkdir -p /conda-envs/3fad3c9cdfa40bee9404f6a2e8fda69f
6558
COPY workflow/envs/gisaidr.yaml /conda-envs/3fad3c9cdfa40bee9404f6a2e8fda69f/environment.yaml
6659
COPY workflow/envs/gisaidr.post-deploy.sh /conda-envs/3fad3c9cdfa40bee9404f6a2e8fda69f/post-deploy.sh
67-
6860
# Conda environment:
6961
# source: workflow/envs/iqtree.yaml
7062
# prefix: /conda-envs/0a608afb24723cb6fa8aef748f5efbc8
@@ -75,7 +67,6 @@ COPY workflow/envs/gisaidr.post-deploy.sh /conda-envs/3fad3c9cdfa40bee9404f6a2e8
7567
# - iqtree==2.2.2.3
7668
RUN mkdir -p /conda-envs/0a608afb24723cb6fa8aef748f5efbc8
7769
COPY workflow/envs/iqtree.yaml /conda-envs/0a608afb24723cb6fa8aef748f5efbc8/environment.yaml
78-
7970
# Conda environment:
8071
# source: workflow/envs/nextalign.yaml
8172
# prefix: /conda-envs/04a3347f94ddf7e21c34bc49e5246076
@@ -86,7 +77,6 @@ COPY workflow/envs/iqtree.yaml /conda-envs/0a608afb24723cb6fa8aef748f5efbc8/envi
8677
# - nextalign==2.13
8778
RUN mkdir -p /conda-envs/04a3347f94ddf7e21c34bc49e5246076
8879
COPY workflow/envs/nextalign.yaml /conda-envs/04a3347f94ddf7e21c34bc49e5246076/environment.yaml
89-
9080
# Conda environment:
9181
# source: workflow/envs/pangolin.yaml
9282
# prefix: /conda-envs/fb978640cd765c8a63bbcdc01f3a206b
@@ -99,7 +89,6 @@ COPY workflow/envs/nextalign.yaml /conda-envs/04a3347f94ddf7e21c34bc49e5246076/e
9989
# - setuptools<81
10090
RUN mkdir -p /conda-envs/fb978640cd765c8a63bbcdc01f3a206b
10191
COPY workflow/envs/pangolin.yaml /conda-envs/fb978640cd765c8a63bbcdc01f3a206b/environment.yaml
102-
10392
# Conda environment:
10493
# source: workflow/envs/quarto_render.yaml
10594
# prefix: /conda-envs/96f3c1cec4b3ce5d72f708992272e9c1
@@ -114,7 +103,6 @@ COPY workflow/envs/pangolin.yaml /conda-envs/fb978640cd765c8a63bbcdc01f3a206b/en
114103
# - r-heatmaply==1.6.0
115104
RUN mkdir -p /conda-envs/96f3c1cec4b3ce5d72f708992272e9c1
116105
COPY workflow/envs/quarto_render.yaml /conda-envs/96f3c1cec4b3ce5d72f708992272e9c1/environment.yaml
117-
118106
# Conda environment:
119107
# source: workflow/envs/renv.yaml
120108
# prefix: /conda-envs/fe892aca096e6b2883923c8755f9ac77
@@ -136,7 +124,6 @@ COPY workflow/envs/quarto_render.yaml /conda-envs/96f3c1cec4b3ce5d72f708992272e9
136124
# - r-logger==0.2.2
137125
RUN mkdir -p /conda-envs/fe892aca096e6b2883923c8755f9ac77
138126
COPY workflow/envs/renv.yaml /conda-envs/fe892aca096e6b2883923c8755f9ac77/environment.yaml
139-
140127
# Conda environment:
141128
# source: workflow/envs/snpeff.yaml
142129
# prefix: /conda-envs/0adafb79cb1bec58ef4c77bf4cca4f95
@@ -147,7 +134,6 @@ COPY workflow/envs/renv.yaml /conda-envs/fe892aca096e6b2883923c8755f9ac77/enviro
147134
# - snpsift==5.1d
148135
RUN mkdir -p /conda-envs/0adafb79cb1bec58ef4c77bf4cca4f95
149136
COPY workflow/envs/snpeff.yaml /conda-envs/0adafb79cb1bec58ef4c77bf4cca4f95/environment.yaml
150-
151137
# Conda environment:
152138
# source: workflow/envs/tools.yaml
153139
# prefix: /conda-envs/1f283441022c3c9d97669994a3c5e8bb
@@ -159,21 +145,17 @@ COPY workflow/envs/snpeff.yaml /conda-envs/0adafb79cb1bec58ef4c77bf4cca4f95/envi
159145
# - bcftools==1.23
160146
RUN mkdir -p /conda-envs/1f283441022c3c9d97669994a3c5e8bb
161147
COPY workflow/envs/tools.yaml /conda-envs/1f283441022c3c9d97669994a3c5e8bb/environment.yaml
162-
163148
# Conda environment:
164149
# source: workflow/envs/var_calling.yaml
165-
# prefix: /conda-envs/81e46c677a6cc0618c93963d57d17d3f
150+
# prefix: /conda-envs/5150d0f0a91d7f7a789a06f453d63479
166151
# channels:
167152
# - conda-forge
168153
# - bioconda
169154
# dependencies:
170155
# - ivar==1.4.2
171156
# - samtools==1.17
172-
# - bcftools==1.17
173-
RUN mkdir -p /conda-envs/81e46c677a6cc0618c93963d57d17d3f
174-
COPY workflow/envs/var_calling.yaml /conda-envs/81e46c677a6cc0618c93963d57d17d3f/environment.yaml
175-
176-
# Step 3: Generate conda environments
157+
RUN mkdir -p /conda-envs/5150d0f0a91d7f7a789a06f453d63479
158+
COPY workflow/envs/var_calling.yaml /conda-envs/5150d0f0a91d7f7a789a06f453d63479/environment.yaml
177159

178160
RUN conda env create --prefix /conda-envs/9c24a867826615972cc288081976e7fc --file /conda-envs/9c24a867826615972cc288081976e7fc/environment.yaml && \
179161
conda env create --prefix /conda-envs/162796cecea22d99c8702138f0c48e2f --file /conda-envs/162796cecea22d99c8702138f0c48e2f/environment.yaml && \
@@ -187,11 +169,9 @@ RUN conda env create --prefix /conda-envs/9c24a867826615972cc288081976e7fc --fil
187169
conda env create --prefix /conda-envs/fe892aca096e6b2883923c8755f9ac77 --file /conda-envs/fe892aca096e6b2883923c8755f9ac77/environment.yaml && \
188170
conda env create --prefix /conda-envs/0adafb79cb1bec58ef4c77bf4cca4f95 --file /conda-envs/0adafb79cb1bec58ef4c77bf4cca4f95/environment.yaml && \
189171
conda env create --prefix /conda-envs/1f283441022c3c9d97669994a3c5e8bb --file /conda-envs/1f283441022c3c9d97669994a3c5e8bb/environment.yaml && \
190-
conda env create --prefix /conda-envs/81e46c677a6cc0618c93963d57d17d3f --file /conda-envs/81e46c677a6cc0618c93963d57d17d3f/environment.yaml && \
172+
conda env create --prefix /conda-envs/5150d0f0a91d7f7a789a06f453d63479 --file /conda-envs/5150d0f0a91d7f7a789a06f453d63479/environment.yaml && \
191173
conda clean --all -y
192174

193-
# Step 4: Run post-deploy scripts
194-
195175
RUN conda init && . /root/.bashrc && \
196176
conda activate /conda-envs/3fad3c9cdfa40bee9404f6a2e8fda69f && \
197177
bash /conda-envs/3fad3c9cdfa40bee9404f6a2e8fda69f/post-deploy.sh && \

0 commit comments

Comments
 (0)