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Nikos Pappas
pvogs_function
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48f8c2ff
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48f8c2ff
authored
4 years ago
by
Nikos Pappas
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remove X server description for ete3 from README
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README.md
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48f8c2ff
...
...
@@ -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).
...
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@@ -174,7 +175,7 @@ results
│ ├── N10.RF.pkl ---------------------- * Best model obtained when optimizing with each negative set
.....
.....
└
── scores.tsv ----------------------------- *
Master t
able with feature values for all possible pVOGs combinations
│
── scores.tsv ----------------------------- *
T
able with feature values for all possible pVOGs combinations
│── predictions_annotations_features.tsv ---- * Master table that contains all results.
```
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