-
Notifications
You must be signed in to change notification settings - Fork 5
/
Copy pathDockerfile
51 lines (40 loc) · 2.41 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
FROM vanallenlab/miniconda:3.12
WORKDIR /
RUN apt-get update && apt-get install -y
COPY requirements.txt /
RUN pip install --upgrade pip
RUN pip install -r requirements.txt
COPY example_data/ /example_data/
COPY example_output/ /example_output/
RUN mkdir /moalmanac/
RUN mkdir /datasources
RUN mkdir /docs/
COPY moalmanac/test/ moalmanac/test/
COPY datasources/acmg/ /datasources/acmg/
COPY datasources/cancergenecensus/ /datasources/cancergenecensus/
COPY datasources/cancerhotspots/ /datasources/cancerhotspots/
COPY datasources/clinvar/ /datasources/clinvar/
COPY datasources/cosmic/ /datasources/cosmic/
COPY datasources/exac/ /datasources/exac/
COPY datasources/gsea_gene_sets/ /datasources/gsea_gene_sets/
COPY datasources/hereditary/ /datasources/hereditary/
COPY datasources/lawrence/ /datasources/lawrence/
COPY datasources/oncotree/ /datasources/oncotree/
COPY moalmanac/templates/ /moalmanac/templates/
COPY moalmanac/*.py moalmanac/*.ini /moalmanac/
COPY datasources/moalmanac/ /datasources/moalmanac/
COPY datasources/preclinical/README.md /datasources/preclinical/README.md
COPY datasources/preclinical/generate-dictionary.ipynb /datasources/preclinical/generate-dictionary.ipynb
COPY datasources/preclinical/cell-lines.pkl /datasources/preclinical/cell-lines.pkl
COPY datasources/preclinical/formatted/almanac-gdsc-mappings.json /datasources/preclinical/formatted/almanac-gdsc-mappings.json
COPY datasources/preclinical/formatted/cell-lines.summary.txt /datasources/preclinical/formatted/cell-lines.summary.txt
COPY datasources/preclinical/annotated/cell-lines.somatic-variants.annotated.txt /datasources/preclinical/annotated/cell-lines.somatic-variants.annotated.txt
COPY datasources/preclinical/annotated/cell-lines.copy-numbers.annotated.txt /datasources/preclinical/annotated/cell-lines.copy-numbers.annotated.txt
COPY datasources/preclinical/annotated/cell-lines.fusions.annotated.txt /datasources/preclinical/annotated/cell-lines.fusions.annotated.txt
COPY datasources/preclinical/annotated/cell-lines.fusions.annotated.gene1.txt /datasources/preclinical/annotated/cell-lines.fusions.annotated.gene1.txt
COPY datasources/preclinical/annotated/cell-lines.fusions.annotated.gene2.txt /datasources/preclinical/annotated/cell-lines.fusions.annotated.gene2.txt
COPY datasources/preclinical/formatted/sanger.gdsc.txt /datasources/preclinical/formatted/sanger.gdsc.txt
COPY docs/* /docs/
COPY README.md /
COPY LICENSE /
COPY Dockerfile /