From 461262b763c316fef92c3943f578f4444be4b44e Mon Sep 17 00:00:00 2001 From: Sibbe Bakker Date: Fri, 29 Aug 2025 15:22:49 +0200 Subject: [PATCH] add docker file --- Dockerfile | 19 +++++++++++++++++++ FungAMR_db/README.md | 3 +++ README.md | 7 ++++++- environment.yml | 10 ++++++++++ files/README.md | 0 5 files changed, 38 insertions(+), 1 deletion(-) create mode 100644 Dockerfile create mode 100644 FungAMR_db/README.md create mode 100644 environment.yml create mode 100644 files/README.md diff --git a/Dockerfile b/Dockerfile new file mode 100644 index 0000000..9d8b702 --- /dev/null +++ b/Dockerfile @@ -0,0 +1,19 @@ +FROM continuumio/miniconda +WORKDIR /app +COPY . . + +# Extract the database and move its contents up one level +RUN mkdir -p /app/FungAMR_db && \ + tar -xvzf /app/FungAMR_db/db-v20250811.tgz -C /app/FungAMR_db && \ + mv /app/FungAMR_db/db-v0.6.0/* /app/FungAMR_db/ && \ + rm -rf /app/FungAMR_db/db-v0.6.0 && \ + rm /app/FungAMR_db/db-v20250811.tgz +RUN rm /app/FungAMR_db/README.md + +# Create the conda environment +RUN conda env create -f environment.yml + +# Set up the shell and entrypoint +SHELL ["conda", "run", "-n", "ChroQueTas", "/bin/bash", "-c"] +ENV TERM=xterm-256color +ENTRYPOINT ["conda", "run", "-n", "ChroQueTas", "bash", "bin/ChroQueTas.sh"] diff --git a/FungAMR_db/README.md b/FungAMR_db/README.md new file mode 100644 index 0000000..3ec916f --- /dev/null +++ b/FungAMR_db/README.md @@ -0,0 +1,3 @@ +# README + +db-v20250811.tgz holds the species database. diff --git a/README.md b/README.md index e7e1a38..b8a8769 100644 --- a/README.md +++ b/README.md @@ -144,7 +144,12 @@ rm -r ChroQueTas/FungAMR_db.tgz ``` ### 3.3 Via Docker -> Intructions will be added shortly, sorry for the inconveniences + +Usage via docker works as follows. + +``` +docker run --rm -it $IMAGE_NAME --list_species +```
diff --git a/environment.yml b/environment.yml new file mode 100644 index 0000000..a1b2a58 --- /dev/null +++ b/environment.yml @@ -0,0 +1,10 @@ +name: ChroQueTas +channels: + - conda-forge + - bioconda +dependencies: + - blast + - mafft + - miniprot + - emboss + - seqkit diff --git a/files/README.md b/files/README.md new file mode 100644 index 0000000..e69de29