Merge pull request #16 from psteinb/snakemake-lesson-code

add code for snakemake lesson

Author: psteinb

commands.mk

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+files/snakemake-lesson.tar.gz: files/snakemake-lesson/*py
+	@rm -vf $@ && cd files && tar vczf ../$@ snakemake-lesson/*py snakemake-lesson/books/* snakemake-lesson/matplotlibrc snakemake-lesson/cluster.json snakemake-lesson/.Snakefile
+
+files/snakemake-lesson.zip: files/snakemake-lesson/*py
+	@rm -vf $@ && cd files && zip ../$@ snakemake-lesson/*py snakemake-lesson/books/* snakemake-lesson/matplotlibrc snakemake-lesson/cluster.json snakemake-lesson/.Snakefile
+
+## prep-release     : compress contents of snakemake-lesson for release
+prep-release: files/snakemake-lesson.zip files/snakemake-lesson.tar.gz

files/snakemake-lesson.tar.gz

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+# This is a "hidden" version of the final Snakefile if students want/need 
+# to run the instructor's copy.
+
+# our zipf analysis pipeline
+DATS = glob_wildcards('books/{book}.txt').book
+
+localrules: all, clean, make_archive
+
+rule all:
+    input:
+        'zipf_analysis.tar.gz'
+
+# delete everything so we can re-run things
+# deletes a little extra for purposes of lesson prep
+rule clean:
+    shell:  
+        '''
+        rm -rf results dats plots __pycache__
+        rm -f results.txt zipf_analysis.tar.gz *.out *.log *.pyc
+        '''
+
+# count words in one of our "books"
+rule count_words:
+    input:  
+        wc='wordcount.py',
+        book='books/{file}.txt'
+    output: 'dats/{file}.dat'
+    threads: 4
+    log: 'dats/{file}.log'
+    shell:
+        '''
+        echo "Running {input.wc} with {threads} cores on {input.book}." &> {log} &&
+            python {input.wc} {input.book} {output} &>> {log}
+        '''
+
+# create a plot for each book
+rule make_plot:
+    input:
+        plotcount='plotcount.py',
+        book='dats/{file}.dat'
+    output: 'plots/{file}.png'
+    resources: gpu=1
+    shell: 'python {input.plotcount} {input.book} {output}'
+
+# generate summary table
+rule zipf_test:
+    input:  
+        zipf='zipf_test.py',
+        books=expand('dats/{book}.dat', book=DATS)
+    output: 'results.txt'
+    shell:  'python {input.zipf} {input.books} > {output}'
+
+# create an archive with all of our results
+rule make_archive:
+    input:
+        expand('plots/{book}.png', book=DATS),
+        expand('dats/{book}.dat', book=DATS),
+        'results.txt'
+    output: 'zipf_analysis.tar.gz'
+    shell: 'tar -czvf {output} {input}'
+