Add/snakemake flux (#25)

* adding darshan

this likely should be added as a view that can be used on the fly,
but this container should be an OK start (and we can adjust as needed)

Signed-off-by: vsoch <[email protected]>* wrong container tag

.github/workflows/build-matrices.yaml

@@ -67,7 +67,7 @@ jobs:
     name: Build ${{ matrix.result.container_name }} ${{ matrix.arch[0] }}
     steps:
     - name: Checkout Repository
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
     - uses: actions/setup-go@v3
 
     - name: GHCR Login

snakemake/Dockerfile

@@ -0,0 +1,34 @@
+ARG tag=3.11
+FROM python:${tag}
+
+# docker build -t snakemake .
+# command: snakemake --cores 1 --flux --jobs 1
+# workdir: /workflow
+
+RUN apt-get update
+ENV DEBIAN_FRONTEND="noninteractive"
+RUN apt-get update && \
+    apt-get -y install \
+    git \
+    curl \
+    && apt-get clean \
+    && apt-get autoremove \
+    && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
+
+# Wrappers to ensure we source the mamba environment!
+RUN git clone --depth 1 https://github.com/snakemake/snakemake-tutorial-data /workflow
+WORKDIR /workflow
+
+# This wraps the existing entrypoint
+COPY ./Snakefile ./
+RUN mkdir ./scripts
+COPY ./scripts/plot-quals.py ./scripts/plot-quals.py
+
+# instead of altering the entrypoint to active the environment!
+RUN pip install snakemake && \
+    pip install git+https://github.com/snakemake/snakemake-interface-common && \
+    pip install git+https://github.com/snakemake/snakemake-executor-plugin-flux && \
+    pip install git+https://github.com/snakemake/snakemake-interface-executor-plugins && \
+    pip install git+https://github.com/snakemake/snakemake-executor-flux
+
+WORKDIR /code

snakemake/README.md

@@ -0,0 +1,15 @@
+# Flux Snakemake Example
+
+This is an example container where you can build (optional) and run
+the [Snakemake tutorial workflow](https://snakemake.readthedocs.io/en/stable/tutorial/tutorial.html):
+
+```bash
+$ docker build -t snakemake .
+```
+
+or with a tag for the restful API:
+
+```bash
+$ docker build --no-cache --build-arg app="latest" -t snakemake .
+```
+

snakemake/Snakefile

@@ -0,0 +1,56 @@
+SAMPLES = ["A", "B"]
+
+
+rule all:
+    input:
+        "plots/quals.svg"
+
+
+rule bwa_map:
+    input:
+        "data/genome.fa",
+        "data/samples/{sample}.fastq"
+    output:
+        "mapped_reads/{sample}.bam"
+    shell:
+        "bwa mem {input} | samtools view -Sb - > {output}"
+
+
+rule samtools_sort:
+    input:
+        "mapped_reads/{sample}.bam"
+    output:
+        "sorted_reads/{sample}.bam"
+    shell:
+        "samtools sort -T sorted_reads/{wildcards.sample} "
+        "-O bam {input} > {output}"
+
+
+rule samtools_index:
+    input:
+        "sorted_reads/{sample}.bam"
+    output:
+        "sorted_reads/{sample}.bam.bai"
+    shell:
+        "samtools index {input}"
+
+
+rule bcftools_call:
+    input:
+        fa="data/genome.fa",
+        bam=expand("sorted_reads/{sample}.bam", sample=SAMPLES),
+        bai=expand("sorted_reads/{sample}.bam.bai", sample=SAMPLES)
+    output:
+        "calls/all.vcf"
+    shell:
+        "bcftools mpileup -f {input.fa} {input.bam} | "
+        "bcftools call -mv - > {output}"
+
+
+rule plot_quals:
+    input:
+        "calls/all.vcf"
+    output:
+        "plots/quals.svg"
+    script:
+        "scripts/plot-quals.py"

snakemake/scripts/plot-quals.py

@@ -0,0 +1,9 @@
+import matplotlib
+matplotlib.use("Agg")
+import matplotlib.pyplot as plt
+from pysam import VariantFile
+
+quals = [record.qual for record in VariantFile(snakemake.input[0])]
+plt.hist(quals)
+
+plt.savefig(snakemake.output[0])

snakemake/uptodate.yaml

@@ -0,0 +1,6 @@
+dockerbuild:
+  build_args:
+    tag:
+      key: python
+      versions:
+       - "3.11"