Mccalluc/doc tweaks (#52)

* Syntax highlighting on bash snippets (grey comments)

* typo: "tests" -> "test"

* Running tests created these, but probably should not be committed?

* Does not seem like it could actually write to output before.
(Docker does not actually run for me: #51)

* Rename to take advantage of MD rendering

* link to examples

COMMANDS → COMMANDS.md

@@ -1,5 +1,6 @@
 ### Calculating gene coverage
 
+```
 bedtools makewindows -g ~/projects/negspy/negspy/data/hg19/chromInfo.txt -w 1000 > ~/data/genbank-data/hg19/bins_hg19_1000.bed
 
 awk '{ if ($6 == "-") print }' ~/data/genbank-data/hg19/geneAnnotationsExonUnions.bed > ~/data/genbank-data/hg19/geneAnnotationsExonUnions.-.bed
@@ -10,29 +11,38 @@ bedtools coverage -b ~/data/genbank-data/hg19/geneAnnotationsExonUnions.-.bed -a
 
 clodius convert bedfile_to_multivec ~/data/genbank-data/hg19/annotationsCoverage.+.bed --assembly hg19 --starting-resolution 1000
 clodius convert bedfile_to_multivec ~/data/genbank-data/hg19/annotationsCoverage.-.bed --assembly hg19 --starting-resolution 1000
+```
 
 ### Converting bedfile to multivec
 
+```
 clodius convert bedfile_to_multivec test/sample_data/sample.bed.gz  --has-header --assembly hg38 --base-resolution 10
 clodius aggregate multivec test/sample_data/sample.bed.multivec --assembly hg38 --base-resolution 10
+```
 
 ### Getting gene summaries
 
+```
 cat ~/data/genbank-data/mm9/gene_summaries_*.tsv > ~/data/genbank-data/mm9/all_gene_summaries.tsv
+```
 
 ### Building the documentation
 
+```
 make publish  # upload to PyPI
 
 sphinx-build -b html docs docs/_build/html/
 
 for file in $(ls ~/projects/francesco-tad-calls/TADcalls/Rao/GM12878/*.txt); do clodius aggregate bedpe --assembly hg19 --chr1-col 1 --from1-col 2 --to1-col 3 --chr2-col 1 --from2-col 2 --to2-col 3 $file; done;
 
 for file in $(ls ~/projects/francesco-tad-calls/TADcalls/Rao/IMR90/*.txt); do clodius aggregate bedpe --assembly hg19 --chr1-col 1 --from1-col 2 --to1-col 3 --chr2-col 1 --from2-col 2 --to2-col 3 $file; done;
+```
 
 ### Multivec files
 
+```
 cat ~/Dropbox/paper-data/Danielles-data/drosophila.chromSizes.orig | awk '{print $1 "\t" $NF}'  > ~/Dropbox/paper-data/Danielles-data/drosophila.chromSizes
 clodius aggregate multivec --output-file ~/Dropbox/paper-data/Danielles-data/drosophila.multivec.hdf5 --chromsizes-filename ~/Dropbox/paper-data/Danielles-data/drosophila.chromSizes ~/Dropbox/paper-data/Danielles-data/drosophila.hdf5
 
 python setup.py sdist upload -r pypi
+```

README.md

@@ -4,32 +4,34 @@
 
 Install the clodius package:
 
-```
+```shell
 pip install clodius
 ```
 
 And use it aggregate a bigWig file:
 
-```
+```shell
 clodius aggregate bigwig ~/Downloads/E116-DNase.fc.signal.bigwig
 ```
 
 The output files can then be displayed using the [higlass-docker container](https://github.com/hms-dbmi/higlass-docker). For more information about viewing these types of files take a look at the [higlass wiki](https://github.com/hms-dbmi/higlass/wiki#bigwig-files).
 
+[More examples](COMMANDS.md) are available.
+
 ## Development
 
 
 The recommended way to develop `clodius` is to use a [conda](https://conda.io/docs/intro.html) environment and
 install `clodius` with develop mode:
 
-```
+```shell
 python setup.py develop
 ```
 
 Note that making changes to the `clodius/fast.pyx` [cython](http://docs.cython.org/en/latest/src/quickstart/cythonize.html) module requires an
 explicit recompile step:
 
-```
+```shell
 python setup.py build_ext --inplace
 ```
 
@@ -38,36 +40,38 @@ python setup.py build_ext --inplace
 
 The unit tests for clodius can be run using [nosetests](http://nose.readthedocs.io/en/latest/):
 
-    nosetests tests
+```shell
+nosetests test
+```
 
 Individual unit tests can be specified by indicating the file and function
 they are defined in:
 
-```
+```shell
 nosetests test/cli_test.py:test_clodius_aggregate_bedgraph
 ```
 
 ## Quick start with Docker
 
 If you don't have your own, get some sample data:
-```
+```shell
 mkdir -p /tmp/clodius/input
 mkdir -p /tmp/clodius/output
 curl https://raw.githubusercontent.com/hms-dbmi/clodius/develop/test/sample_data/geneAnnotationsExonsUnions.short.bed \
-  > /tmp/clodius/input/sample.short.bed 
+  > /tmp/clodius/input/sample.short.bed
 ```
 Then install Docker, and pull and run the Clodius image:
-```
-docker stop clodius; 
+```shell
+docker stop clodius;
 docker rm clodius;
 
 docker pull gehlenborglab/clodius # Ensure that you have the latest.
 
-docker run -v /tmp/clodius/input:/tmp/ \
+docker run -v /tmp/clodius/:/tmp/ \
            gehlenborglab/clodius \
-           clodius aggregate bigwig /tmp/file.bigwig
-           
-ls /tmp/clodius/input # Should contain the output file
+           clodius aggregate bigwig /tmp/input/file.bigwig
+
+ls /tmp/clodius/output # Should contain the output file
 ```
 
 If you already have a good location for your input and output files,