From 96f874c5012c276e4279f926d003fc1adefa3c99 Mon Sep 17 00:00:00 2001
From: Julien Prados <julien.prados@unige.ch>
Date: Wed, 13 Nov 2024 16:12:21 +0100
Subject: [PATCH] fix resfinder installation
---
Dockerfile | 18 ++++++++++++++++--
Readme.md | 4 ++--
2 files changed, 18 insertions(+), 4 deletions(-)
diff --git a/Dockerfile b/Dockerfile
index b7b5cb8..4c7087e 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -5,6 +5,7 @@ RUN apt-get update -qq && apt-get install -y -qq \
build-essential \
libz-dev \
ncbi-blast+ \
+ curl \
&& rm -rf /var/cache/apt/* /var/lib/apt/lists/*
# KMA
@@ -41,6 +42,19 @@ 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 cgecore \
- && pip install --no-cache-dir resfinder
+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 \
+ && 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
+
+
+
+
diff --git a/Readme.md b/Readme.md
index befcbe2..e1058ca 100644
--- a/Readme.md
+++ b/Readme.md
@@ -3,7 +3,7 @@
# Introduction
`cgetools` is s docker container with an installation of several
-(CGE)[https://bitbucket.org/genomicepidemiology/] softwares and associated
+[CGE]([https://bitbucket.org/genomicepidemiology/]) softwares and associated
databases (mlst,plasmidfinder,resfinder).
@@ -14,7 +14,7 @@ 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 resfinder.py
+docker run --rm -v .:/cwd unigebsp/cgetools python3 -m resfinder
```
--
GitLab