From ce5bf603c5aa375f7fc04d9f6b1fab49b80bd299 Mon Sep 17 00:00:00 2001
From: Julien Prados <julien.prados@unige.ch>
Date: Wed, 18 Dec 2024 12:42:33 +0100
Subject: [PATCH] change registry to gitlab
---
Dockerfile | 14 ++------------
Readme.md | 8 ++++----
2 files changed, 6 insertions(+), 16 deletions(-)
diff --git a/Dockerfile b/Dockerfile
index 4c7087e..714748a 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -42,19 +42,9 @@ RUN mkdir -p /db \
ENV CGE_RESFINDER_RESGENE_DB=/db/resfinder_db/
ENV CGE_RESFINDER_RESPOINT_DB=/db/pointfinder_db/
ENV CGE_DISINFINDER_DB=/db/disinfinder_db/
-RUN pip install -U biopython==1.73 tabulate \
- && curl -sSL https://pdm-project.org/install-pdm.py | python3 - \
- && git -C /usr/src/ clone --depth 1 https://bitbucket.org/genomicepidemiology/cgecore.git \
- && cd /usr/src/cgecore && python3 setup.py install \
- && git -C /usr/src/ clone --depth 1 https://bitbucket.org/genomicepidemiology/cgelib.git \
- && cd /usr/src/cgelib && python3 setup.py install \
+RUN curl -sSL https://pdm-project.org/install-pdm.py | python3 - --path /usr/local \
&& git -C /usr/src/ clone --depth 1 https://bitbucket.org/genomicepidemiology/resfinder.git \
- && cd /usr/src/resfinder && /root/.local/bin/pdm build && pip3 install dist/*.whl
-
-#RUN pip install -U biopython==1.73 tabulate cgecore \
-# && pip install --no-cache-dir resfinder
-
-
+ && cd /usr/src/resfinder && pdm build && pip3 install dist/*.whl
diff --git a/Readme.md b/Readme.md
index e1058ca..c7e9445 100644
--- a/Readme.md
+++ b/Readme.md
@@ -12,9 +12,9 @@ databases (mlst,plasmidfinder,resfinder).
To use the tool, you need to mount the working directory on `/cwd`. Example:
```bash
-docker run --rm -v .:/cwd unigebsp/cgetools plasmidfinder.py
-docker run --rm -v .:/cwd unigebsp/cgetools mlst.py
-docker run --rm -v .:/cwd unigebsp/cgetools python3 -m resfinder
+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
```
@@ -22,7 +22,7 @@ docker run --rm -v .:/cwd unigebsp/cgetools python3 -m resfinder
To build the container, run:
```bash
-docker build -t unigebsp/cgetools ./
+docker build --platform linux/amd64 -t registry.gitlab.unige.ch/amr-genomics/cgetools ./
```
--
GitLab