Commit b39ce478 authored by Robert Bossy's avatar Robert Bossy
Browse files

Update README.md

parent 12742d42
>> This is work in progress, contact us if you have any questions
>> This is work in progress, [contact us](mailto:mouhamadou%DOT%ba%AT%inrae%DOT%fr) if you have issues and questions.
# About
......@@ -6,10 +6,18 @@ This project is designed to extract entities (i.e., `taxa`, `phenotypes`, `habit
The project contains a workflow based on Framework [AlvisNLP](https://github.com/Bibliome/alvisnlp) and uses the Ontobiotope Ontology and NCBI taxonomy.
## Requirements
* GNU Bash 4.4.X
* A git client
* [singularity](https://sylabs.io/) 3.4.X ([how to install singularity ?](https://sylabs.io/guides/3.4/user-guide/quick_start.html#quick-installation-steps))
In order to run the workflow you will need a host with at least 16Gb RAM.
## Usage
The workflow works on all OS (e.g., Ubuntu, CentOs) supporting `GNU bash version 4.4.x` and `singularity version 3.4.x` ([how to install singularity ?](https://sylabs.io/guides/3.4/user-guide/quick_start.html#quick-installation-steps)).
The current version is compatible with [`AlvisNLP version 0.7.1`](https://github.com/Bibliome/alvisnlp/tree/0.7.1) provided via [singularity](https://sylabs.io/) images/containers.
The current version is compatible with [`AlvisNLP version 0.7.1`](https://github.com/Bibliome/alvisnlp/tree/0.7.1).
Installation of AlvisNLP is not required, it is provided in the singularity images.
Run in command line the following steps to test the workflow,
a test corpus is provided here `corpus/pesv/Xylella-test/txt/`, `16Go` RAM is required to process the test corpus).
......@@ -17,54 +25,57 @@ a test corpus is provided here `corpus/pesv/Xylella-test/txt/`, `16Go` RAM is re
1. clone the project.
```sh
$ git clone https://forgemia.inra.fr/bibliome/pesv-tm.git
```
git clone https://forgemia.inra.fr/bibliome/pesv-tm.git
cd pesv-tm
```
2. pull the singularity image of AlvisNLP (the image size is ~4Go, pulling may take a while)
2. pull the singularity image of AlvisNLP (the image size is ~4Go, pulling may take time...)
> `login` and `password` could be asked to pull some AlvisNLP singularity image from forgemia, please contact the maintainer if you have any permission problems.
> If you encounter permission issues to pull the singularity image, or if the server asks for authentification, then please contact the [maintainer](mailto:mouhamadou%DOT%ba%AT%inrae%DOT%fr).
```
cd pesv-tm/
```sh
$ cd pesv-tm
singularity pull alvisnlp-0.7.1.sif oras:registry.forgemia.inra.fr/bibliome/pesv-tm/alvisnlp:0.7.1
$ singularity pull alvisnlp-0.7.1.sif oras:registry.forgemia.inra.fr/bibliome/pesv-tm/alvisnlp:0.7.1
```
3. run the workflow.
> execute the workflow with the test corpus `corpus/pesv/Xylella-test/txt/3IO4RO27QI.txt`, the results will be stored into `corpus/pesv/Xylella-test/`
```
cd pesv-tm/
./alvisnlp-0.7.1.sif -J-Xmx16G -verbose -cleanTmp \
-alias input corpus/pesv/Xylella-test/txt/3IO4RO27QI.txt \
-outputDir corpus/pesv/Xylella-test/ \
-entity ontobiotope resources/BioNLP-OST+EnovFood \
-feat inhibit-syntax inhibit-syntax \
plans/PESV_workflow.plan
```
4. check the results from `corpus/Xylella/visualisation_html`
You will need a corpus to process.
The image contains a test corpus in `corpus/pesv/Xylella-test/txt/3IO4RO27QI.txt`.
```sh
$ ./alvisnlp-0.7.1.sif -J-Xmx16G -verbose -cleanTmp \
-alias input corpus/pesv/Xylella-test/txt/3IO4RO27QI.txt \
-outputDir corpus/pesv/Xylella-test/ \
-entity ontobiotope resources/BioNLP-OST+EnovFood \
-feat inhibit-syntax inhibit-syntax \
plans/PESV_workflow.plan
```
firefox corpus/Xylella/visualisation_html/index.html
```
*. You may browser the results using option `-browser`: run the following command, check the logs and goto [http://localhost:8878](http://localhost:8878)
AlvisNLP will process the corpus.
In this example, the output is stored in `corpus/pesv/Xylella-test/`.
4. check the results
```sh
$ firefox corpus/Xylella/visualisation_html/index.html
```
cd pesv-tm/
./alvisnlp-0.7.1.sif -J-Xmx16G -verbose -cleanTmp \
-browser
-alias input corpus/pesv/Xylella-test/txt/3IO4RO27QI.txt \
-outputDir corpus/pesv/Xylella-test/ \
-entity ontobiotope resources/BioNLP-OST+EnovFood \
-feat inhibit-syntax inhibit-syntax \
plans/PESV_workflow.plan
You can run AlvisNLP with the browser mode:
```sh
$ firefox http://localhost:8878
$ ./alvisnlp-0.7.1.sif -J-Xmx16G -verbose -cleanTmp \
-browser
-alias input corpus/pesv/Xylella-test/txt/3IO4RO27QI.txt \
-outputDir corpus/pesv/Xylella-test/ \
-entity ontobiotope resources/BioNLP-OST+EnovFood \
-feat inhibit-syntax inhibit-syntax \
plans/PESV_workflow.plan
```
Then refresh the page in the browser.
## Maintainer
Mouhamadou Ba : mouhamadou.ba@inrae.fr
\ No newline at end of file
[Mouhamadou Ba](mailto:mouhamadou%DOT%ba%AT%inrae%DOT%fr)
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