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Commit 48f8c2ff authored by Nikos Pappas's avatar Nikos Pappas
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remove X server description for ete3 from README

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......@@ -3,7 +3,6 @@
## TL;DR
```
# Clone this repo
$ git clone https://git.science.uu.nl/n.pappas/pvogs_function.git
......@@ -21,6 +20,7 @@ $ conda activate my_env
```
## Description
The main purpose of this repository is to host the code necessary for full reproducibility.
* Raw data required are hosted on [zenodo sandbox](https://sandbox.zenodo.org/record/666719#.X1c5qoZS_J8). These are automatically
......@@ -53,8 +53,12 @@ These include:
- `negatives`: Specifies the number of negative datasets to create. 10 is used in the manuscript.
>Changing this will most likely break the workflow
- the zenodo dois Until the workflow gets published, I am using the zenodo sandbox for testing.
- the zenodo dois
Until the workflow gets published, I am using the zenodo sandbox for testing.
- `threads` per rule
For the most resource demanding rules included in the config, you can specify the number of cores
each rule will utilize at runtime. I have set these to reasonable values for my own local
setup (`Ubuntu 16.04.1 x86_64` with `120Gb` of RAM and `20` processors) for a good
......@@ -62,13 +66,10 @@ These include:
setup.**
## Usage
---
Currently, this workflow was built and tested on a local machine with an X server available
(i.e. you can do stuff in a GUI).
>If you run this on a remote machine, make sure that you (can) ssh with `ssh -X ...`.
>This is required for the `summarize_intact.py` script, that uses the `ete3` package
>to do some plotting.
Currently, this workflow was built and tested on a local machine.
It should be fairly easy to use a cluster profile, but this has not been tested here.
A couple of options are provided:
### **Option 1. This repo**
......@@ -111,7 +112,7 @@ This will trigger the execution of the rest of the workflow.
The resulting notebook will be saved as `results/logs/processed_notebook.py.ipynb`.
**Note that depending on the changes you make, the results you might get will differ from the default, non-interactive run**.
**Note that depending on the changes you make, the results you get will differ from the default, non-interactive run**.
### Option 2. Archived workflow from zenodo (TO DO).
......@@ -174,7 +175,7 @@ results
│ ├── N10.RF.pkl ---------------------- * Best model obtained when optimizing with each negative set
.....
.....
── scores.tsv ----------------------------- * Master table with feature values for all possible pVOGs combinations
── scores.tsv ----------------------------- * Table with feature values for all possible pVOGs combinations
│── predictions_annotations_features.tsv ---- * Master table that contains all results.
```
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