From 0009d1754a723528dd49009b9145b36326af2e1f Mon Sep 17 00:00:00 2001 From: Anthony Gitter Date: Thu, 14 Nov 2019 17:07:55 -0600 Subject: [PATCH] Add readme note about Linux --- README.md | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/README.md b/README.md index eebac90..8a34e4e 100644 --- a/README.md +++ b/README.md @@ -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 @@ -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`.