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AMR-genomics
cgetools
Commits
05f15db0
Commit
05f15db0
authored
1 month ago
by
Julien.Prados
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add docker.io to FROM directive
parent
19633999
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Pipeline
#98127
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1 month ago
Stage: build
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Dockerfile
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-1
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Dockerfile
Readme.md
+4
-8
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Readme.md
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and
9 deletions
Dockerfile
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View file @
05f15db0
FROM
python:3.10-slim-bullseye
FROM
docker.io/
python:3.10-slim-bullseye
RUN
apt-get update
-qq
&&
apt-get
install
-y
-qq
\
git
\
...
...
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Readme.md
+
4
−
8
View file @
05f15db0
...
...
@@ -2,19 +2,15 @@
# Introduction
`cgetools`
is s docker container with an installation of several
[
CGE
](
[https://bitbucket.org/genomicepidemiology/]
)
softwares and associated
databases (mlst,plasmidfinder,resfinder).
`fatools`
is s docker container with several command to handle FASTA files.
# Usage
To use the tool, you need to mount the working directory on
`/cwd`
. Example:
```
bash
docker run
--rm
-v
.:/cwd registry.gitlab.unige.ch/amr-genomics/cgetools plasmidfinder.py
docker run
--rm
-v
.:/cwd registry.gitlab.unige.ch/amr-genomics/cgetools mlst.py
docker run
--rm
-v
.:/cwd registry.gitlab.unige.ch/amr-genomics/cgetools python3
-m
resfinder
docker run
--rm
-v
.:/cwd registry.gitlab.unige.ch/amr-genomics/fatools fa_reheader
docker run
--rm
-v
.:/cwd registry.gitlab.unige.ch/amr-genomics/fatools fa_rotate
```
...
...
@@ -22,7 +18,7 @@ docker run --rm -v .:/cwd registry.gitlab.unige.ch/amr-genomics/cgetools python3
To build the container, run:
```
bash
docker build
--platform
linux/amd64
-t
registry.gitlab.unige.ch/amr-genomics/
cge
tools ./
docker build
--platform
linux/amd64
-t
registry.gitlab.unige.ch/amr-genomics/
fa
tools ./
```
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