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nchenche committed Nov 12, 2022
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**.idea
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Expand Up @@ -15,6 +15,7 @@ RUN wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh \
&& rm Miniconda3-latest-Linux-x86_64.sh

ADD . /ORFmine/
RUN rm -r /ORFmine/docs

RUN chmod +x /ORFmine/orfribo/RiboDoc_BAM2Reads/RiboDoc_BAM2Reads.sh /ORFmine/install.sh

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212 changes: 55 additions & 157 deletions README.md
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## Overview
# Overview

Recent studies attribute a new role to the noncoding genome in the production of novel peptides. The widespread transcription of noncoding regions and the pervasive translation of the resulting RNAs offer a vast reservoir of novel peptides to the organisms.
OMICS studies attribute a new role to the noncoding genome in the production of novel peptides. The widespread transcription
of noncoding regions and the pervasive translation of the resulting RNAs offer a vast reservoir of novel peptides to the organisms.

ORFmine is an open-source package that aims at extracting, annotating, and characterizing the fold potential and the structural properties of all Open Reading Frames (ORF) encoded in a genome (including coding and noncoding sequences). ORFmine consists of two independent programs, ORFtrack and ORFold that can be used together or independently (see here for an example of application).

Both these tools have been developed in python3 (version >= 3.6).
The install.sh script will install both ORFtrack and ORFold with their dependancies.
They can be used together or independently.
ORFmine[1][2] is an open-source package that aims at extracting, annotating, and characterizing the sequence and structural properties of
all Open Reading Frames (ORFs) of a genome (including coding and noncoding sequences) along with their translation activity. ORFmine consists of several independent programs that can be used together or independently:
- ORFtrack
- ORFold
- ORFribo
- ORFdate

## Documentation
You will find complete documentation on [https://i2bc.github.io/ORFmine/](https://i2bc.github.io/ORFmine/)
## Built with
- python 3.6
- miniconda
- pyHCA [1]
- R
- bash
- Docker

## Installation

### 1. Download and uncompress the latest release
All programs and dependencies are listed [here](docs/dependencies.md).


You can clone the whole project with the following command:
```
git clone https://github.com/i2bc/ORFmine.git
```
# Getting started

Alternatively, you can click [here](https://github.com/i2bc/ORFmine/releases/latest/) to access the latest release.
## Prerequisites

Then uncompress the archive. If you downloaded:
* the *.zip* file: ```unzip ORFmine-x.x.x.zip```
* the *.tar.gz* file: ```tar xzvf ORFmine-x.x.x.tar.gz```
- [Docker](https://docs.docker.com/engine/install/) or [Singularity](https://singularity-tutorial.github.io/01-installation/)
- [IUPred](https://iupred2a.elte.hu/download_new) [2,3,4] (optional)
- [Tango](http://tango.crg.es) [5,6,7] (optional)

<br>

## Installation

### 2. Create an isolated environment
Although not strictly necessary, this step is highly recommended
(it will allow you to work on different projects without having any conflicting library versions).
If you do not want to create a virtual environment, please go directly to the [install section](#general_install).

#### Install virtualenv
``` python
python3 -m pip install virtualenv
```
Simply pull the ORFmine image from Dockerhub.

#### Create a virtual environment
For docker:
```bash
virtualenv -p python3 orfmine_env
# pull the ORFmine docker image from Dockerhub
docker pull annelopes94/orfmine:v0.8.6
```

#### Activate the created environment
For singularity:
```bash
source orfmine_env/bin/activate
# this will build a sif image named orfmine_v0.8.6.sif that will be located in YOUR_PATH (to adapt)
singularity build YOUR_PATH/orfmine_v0.8.6.sif docker://annelopes94/orfmine:v0.8.6
```

Once activated, any python library you will install using pip
will be installed solely in this isolated environment.
You must activate this environment any time you need libraries installed
in this environment.

Once you are done working on your project,
simply type `deactivate` to exit the environment.


<div class="admonition note">
<p class="first admonition-title">
Note
</p>
<p class="last">
To delete definitely your virutal environment, you can simply
remove the directory with the following instruction:
<code>rm -r orfmine_env/</code>
</p>
</div>

<div class="admonition note">
<p class="first admonition-title">
Note
</p>
<p class="last">
We remind to the user that some external packages used in ORFmine
(such as Biopython) require python version >= 3.6. Before creating
your virtual environment make sure that your python version is up-to-date.
</p>
</div>

<a name="general_install"></a>

### 3. Install ORFMine

#### Preparation before the Installation

Please note that we will refer below to the root directory of ORFmine as ORFmine-x-x-x where x-x-x refers to the version downloaded from an archive file (either .zip or .tar.gz).
If you just cloned the project, the root directory of ORFmine will be ORFmine instead.

If you just want to use **ORFtrack** in order to annotate all
the possible ORFs of a genome, you have no other dependencies
to install, and you simply have to **Launch the Installation**
presented [below](#launch_install).

The installation of **ORFold** becomes a bit more demanding as
there are some external tools to be downloaded and/or installed
before launching the installation.

Firstly, **ORFold** is based on the HCA method for the calcluation of the
fold potential. As a result [pyHCA](https://github.com/T-B-F/pyHCA)
[[1](https://www.biorxiv.org/content/10.1101/249995v1)]
is essential to be pre-installed in your machine before installing
**ORFold**. You can [download](https://github.com/T-B-F/pyHCA) for free and install **pyHCA** using
the instructions of the developers.
<br>
If you are not interested in the calculation of the disorder
and/or aggregation propensities with **ORFold** and you already
have installed pyHCA, you can simply launch the installation
presented [below](#launch_install).

However, in the case you want to use [IUPred](https://iupred2a.elte.hu)
[2][3][4] and/or [Tango](http://tango.crg.es) [5][6][7] with **ORFold** you have to
first contact their developers through the respective links and have access
to their programs. These two softwares are not freely available for
non-academic users.

Once you have access to the IUPred and Tango you have to place them in a directory
called ```softwares``` placed in the path: ```ORFmine-x.x.x/orfold_v1/orfold/```. To do so:


* First create the ```softwares``` directory if not already created:
If you have any error, it might come from a permissions problem so you should try using these commands with sudo as prefix.

```bash
mkdir ORFmine-x.x.x/orfold_v1/orfold/softwares
```

* Move the IUPred source code and data (provided by the developer):

mv iupred2a.py ORFmine-x.x.x/orfold_v1/orfold/softwares
mv iupred2a.py ORFmine-x.x.x/orfold_v1/orfold/softwares
mv data ORFmine-x.x.x/orfold_v1/orfold/softwares

* Move Tango source code:
* For MacOS:
mv tango2_3_1 ORFmine-x.x.x/orfold_v1/orfold/softwares

* For linux:

mv tango_x86_64_release ORFmine-x.x.x/orfold_v1/orfold/softwares

* For windows:
mv Tango.exe ORFmine-x.x.x/orfold_v1/orfold/softwares

<div class="admonition note">
<p class="first admonition-title">
Note
</p>
<p class="last">
The calculation of the disorder or aggregation propensities are both optional and
complementary to the HCA score. As a result, IUPred and
Tango tools are not mandatory for the installation of ORFold. In addition,
they are not necessarily coupled together. ORFold will properly be
installed without them or even with only one of them.
</p>
</div>
<a name="launch_install"></a>


#### Installation

If you use a virtual environment, be sure that your virtual environment is activated.
Then, in any case, follow the procedure described below:


```bash
cd ORFmine-x.x.x
chmod u+x install.sh
./install.sh
```
# Usage

For usage examples, please check the [Quick start](https://i2bc.github.io/ORFmine/orfmine_quickstart.html) section of our documentation page.


This script will first uninstall ORFmine if it was already installed and will
re-install it. In addition, it will install all the dependency packages needed for
ORFtrack and ORFold.
# Documentation

Our full documentation is accessible [here](https://i2bc.github.io/ORFmine/)


# Contact

Anne Lopes - [email protected]


# Citing

Yet to come.


# Licence

The ORFmine project is under the MIT licence. Please check [here](LICENSE.md) for more details.


## References
Expand All @@ -188,3 +84,5 @@ ORFtrack and ORFold.
6. Linding, R., Schymkowitz, J., Rousseau, F., Diella, F. & Serrano, L. A comparative study of the relationship between protein structure and β-aggregation in globular and intrinsically disordered proteins. Journal of molecular biology 342, 345–353 (2004).
7. Rousseau, F., Schymkowitz, J. & Serrano, L. Protein aggregation and amyloidosis: confusion of the kinds? Current opinion in structural biology 16, 118–126 (2006).


`singularity shell --pwd /workdir/ -B workdir:/workdir/ -B database:/database/ -B fastq:/fastq/ -B ~/tango:/ORFmine/orfold_v1/orfold/softwares/ ../../ORFmine/orfmine_test.sif`
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