add docker file

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"]

FungAMR_db/README.md

@@ -0,0 +1,3 @@
+# README
+
+db-v20250811.tgz holds the species database.

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
+```
 
 <br> 
 

environment.yml

@@ -0,0 +1,10 @@
+name: ChroQueTas
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - blast
+  - mafft
+  - miniprot
+  - emboss
+  - seqkit