Docerizing

Changes to be committed:
	modified:   .gitignore
	new file:   Dockerfile
	new file:   docker-compose.yml
	deleted:    lib/censu-scope.py
	new file:   lib/censuscope.py
	new file:   lib/process_blast_file_chunk.py

.gitignore

@@ -161,3 +161,7 @@ cython_debug/
 #  and can be added to the global gitignore or merged into this file.  For a more nuclear
 #  option (not recommended) you can uncomment the following to ignore the entire idea folder.
 #.idea/
+
+.vscode
+/temp_dirs
+/test_data

Dockerfile

@@ -0,0 +1,30 @@
+# Dockerfile
+
+FROM python:3.10-slim
+RUN apt-get update && apt-get install -y \
+    wget \
+    gcc \
+    make \
+    zlib1g-dev \
+    build-essential \
+    ca-certificates \
+    && rm -rf /var/lib/apt/lists/*
+
+# Install NCBI BLAST+
+RUN apt-get update && apt-get install -y ncbi-blast+ \
+    && rm -rf /var/lib/apt/lists/*
+
+# Install Seqtk
+RUN wget https://github.com/lh3/seqtk/archive/refs/tags/v1.3.tar.gz && \
+    tar -xzvf v1.3.tar.gz && \
+    cd seqtk-1.3 && \
+    make && \
+    mv seqtk /usr/local/bin/ && \
+    cd .. && \
+    rm -rf seqtk-1.3 v1.3.tar.gz
+
+WORKDIR /app
+
+COPY . .
+
+CMD ["python", "lib/censuscope.py"]

docker-compose.yml

@@ -0,0 +1,20 @@
+# docker-compose.yml 
+
+services:
+  censuscope:
+    build: .
+    image: censuscope_image
+    container_name: censuscope_container
+    command: >
+      python3 lib/censuscope.py 
+      -i 10 
+      -s 5 
+      -t 5 
+      -q /app/input_files/GW-04_S4_L001_R1_001.fastq
+      -d /app/input_files/blast_db/gfkb/HumanGutDB-v2.6.fasta 
+      
+    volumes:
+      - /tmp/test:/app/input_files
+      - /tmp/test/outputs:/app/temp_dirs
+    stdin_open: true
+    tty: true