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Add readme note about Linux
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agitter committed Nov 14, 2019
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Expand Up @@ -5,7 +5,9 @@ Parameter advising for biological pathway creation algorithms.

## Dependencies

Pathway parameter advising was written and tested using Python 3.6 and requires the packages `networkx` and `numpy`. The `runPPA.sh` and `setupPGD.sh` scripts require git.
Pathway parameter advising was written and tested using Python 3.6 and requires the packages `networkx` and `numpy`.
The `runPPA.sh` and `setupPGD.sh` scripts require git.
These scripts have only been tested in a Linux environment initially.

## Usage

Expand Down Expand Up @@ -50,5 +52,6 @@ Unzip the Reactome pathway graphlets file `reactomeGraphlets.zip` before running
Graphlet decomposition files are created with the [Parallel Graphlet Decomposition library](http://nesreenahmed.com/graphlets/).
Files are the piped output from the pgd script: `./pgd -f inputGraphFile >> graphletOutputFile.gOut`.

`scripts/setupPGD.sh` installs the PGD library into the `lib` directory, which is created if none exists. PGD is cloned from its [github repository](https://github.com/nkahmed/pgd) and complied using `make`. It can then be run from the base pathway-parameter-advising directory as `lib/pgd/pgd -f inputGraphFile`.

`scripts/setupPGD.sh` installs the PGD library into the `lib` directory, which is created if none exists.
PGD is cloned from its [github repository](https://github.com/nkahmed/pgd) and complied using `make`.
It can then be run from the base pathway-parameter-advising directory as `lib/pgd/pgd -f inputGraphFile`.

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