Snakemake file test working

.devcontainer/devcontainer.json

@@ -44,7 +44,8 @@
 				"ms-python.python",
 				"julialang.language-julia",
 				"ms-azuretools.vscode-docker",
-				"vscodevim.vim"
+				"vscodevim.vim",
+				"DavidAnson.vscode-markdownlint"
 			]
 		}
 	},
@@ -71,5 +72,6 @@
 		// "oryx build -p virtualenv_name=.venv --log-file /tmp/oryx-build.log --manifest-dir /tmp || echo 'Could not auto-build. Skipping.'",
 		// "python -m bash_kernel.install",
 		// "rvm rvmrc warning ignore all.rvmrcs"
+		"sudo jupyter lab --allow-root"
 	]
 }

.gitignore

@@ -7,3 +7,5 @@ docs/build/
 *.md_checkpoints
 *.ipynb.md
 docs/src
+data
+.snakemake

Dockerfile

@@ -15,6 +15,9 @@ USER root
 # COPY requirements.txt .
 # pip install requirements.txt
 
+RUN conda install -c conda-forge mamba
+RUN mamba install -c conda-forge -c bioconda snakemake
+
 # conda
 # write out current installations
 # conda list --explicit > spec-file.txt
@@ -25,8 +28,8 @@ USER root
 # RUN conda install --file spec-file.txt
 
 # install R & R kernel
-RUN conda install -y -c conda-forge r-base
-RUN conda install -y -c r r-essentials
+RUN mamba install -y -c conda-forge r-base
+# RUN conda install -y -c r r-essentials
 ENV PATH=/opt/conda/bin:$PATH
 RUN Rscript -e 'install.packages("IRkernel",repos = "http://cran.us.r-project.org");IRkernel::installspec()'
 # install additional R packages here
@@ -52,5 +55,20 @@ RUN julia -e 'import Pkg; Pkg.instantiate()'
 # install bash kernel
 # RUN pip install bash_kernel
 
+# Install jupyter templates
+RUN pip install jupyter_contrib_nbextensions
+RUN jupyter contrib nbextension install
+RUN pip install jupyterlab_templates
+RUN jupyter labextension install jupyterlab_templates
+RUN jupyter serverextension enable --py jupyterlab_templates
+
+# copy templates into this directory for them to automatically pop up
+# /usr/local/share/jupyter/labextensions/jupyterlab_templates
+
+# adding templates
+#  https://github.com/jpmorganchase/jupyterlab_templates#adding-templates
+
+# install papermill, which will be our script driver
+
 WORKDIR $CODESPACE_VSCODE_FOLDER
 USER codespace

Snakefile

@@ -1,11 +1,23 @@
-rule bwa_map:
-    input:
-        "data/genome.fa",
-        "data/samples/{sample}.fastq"
+# https://papermill.readthedocs.io/en/latest/usage-cli.html
+# run `snakemake some_target --delete-all-output` to clean outputs from target
+# run `snakemake --delete-all-output --cores all` to clean all outputs
+# run `snakemake --cores all` to run whole workflow
+# run `snakemake some_target --cores all` to run up to and through target
+
+rule hello_world:
     output:
-        "mapped_reads/{sample}.bam"
+        "data/test.txt"
     shell:
-        "bwa mem {input} | samtools view -Sb - > {output}"
+        "mkdir -p data && echo 'this is a test' > data/test.txt"
+
+# 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: