diff --git a/Dockerfile b/Dockerfile index 714748a5d7c2fc964bbc7498370b48afa90f8013..29286755704a07a701f7ef28537e12a307fda927 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,4 +1,4 @@ -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 \ diff --git a/Readme.md b/Readme.md index c7e9445ee35730e4a0f1bd4f62f390af1d4fa90c..7b839d99a32bfdac502545c48967f2623583d002 100644 --- a/Readme.md +++ b/Readme.md @@ -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/cgetools ./ +docker build --platform linux/amd64 -t registry.gitlab.unige.ch/amr-genomics/fatools ./ ```