Commit 542930fb authored by Tommy Tang's avatar Tommy Tang
Browse files

add phantompeakqual as dependency

parent 2cb7943d
......@@ -50,6 +50,7 @@ Rscript sraDownload.R -a 'ascp -QT -l 300m -i ~/.aspera/connect/etc/asperaweb_i
* [ROSE](http://younglab.wi.mit.edu/super_enhancer_code.html) for calling superEnhancer. ROSE has to be run inside the installation folder. now I hard coded the path in the Snakefile. (you will have to change that to the ROSE directory in your cluster). Todo: expose the path to the `config.yaml` file that one can change.
* [macs1](https://pypi.python.org/pypi/MACS/1.4.2) v1.4.2 and [macs2](https://github.com/taoliu/MACS) v2.1.1 for calling peaks (macs2 for broad peaks).
* [multiQC](http://multiqc.info/)
* [phantompeakqual](https://github.com/kundajelab/phantompeakqualtools)
`macs1`, `macs2` and `ROSE` are python2.x, see this [Using Snakemake and Macs2](https://groups.google.com/forum/#!searchin/snakemake/macs%7Csort:relevance/snakemake/60txGSq81zE/NzCUTdJ_AQAJ) in the snakemake google group.
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