PanACoTA is written in **python3**. So, you need python3 (and pip3 for installation) to run it.
PanACoTA has several dependencies. Install only the one(s) you need, according to the module you want to use:
Then, PanACoTA has several external dependencies. If you use [`singularity`](#singularity) installation (for ex. to run on a cluster), you do not need to install any dependency. Otherwise, install only the one(s) you need, according to the module(s) you want to use:
- For prepare module: [**mash**](https://mash.readthedocs.io/en/latest/)(to filter genomes)
- For annotate module: [**prokka**](https://github.com/tseemann/prokka) and/or [**prodigal**](https://github.com/hyattpd/Prodigal)(to uniformly annotate your genomes)
- For pangenome module: [**mmseqs**](https://github.com/soedinglab/MMseqs2)(to generate pangenomes)
...
...
@@ -72,55 +86,78 @@ For FastTree, we advise to download C code from [here](http://www.microbesonline
You can then add the output `FastTreeMP` to your `$PATH` to be able to run it from everywhere.
## <a name="install"></a> Installing `PanACoTA` and update
You have different possibilities to install `PanACoTa`.
**Warning:** If you plan to work on the scripts, choose the development installation (see [Development section](#develop)).
## Downloading and updating `PanACoTA`
### <a name="pypi"></a> From pypi
You can download `PanACoTA` source code by downloading a [zip file](https://github.com/gem-pasteur/PanACoTA/archive/master.zip), or by cloning its github repository (which is more recommended). By cloning the github repository, you will then be able to update the code to new versions very easily and quickly. Here is how to clone the repository:
A very simple way to install the last stable version. This will install files in your python site-packages folder.
pip install panacota
And to get new version:
pip install panacota --upgrade
If you have permission issues, you can either use 'sudo' before the previous command lines to install it as root, or add the `--user` option to install it locally.
### <a name="clone"></a> From github repository
This allows you to get the very last version, and be able to test the last enhancements before they are uploaded to the other platforms. For that, go to where you want to install it `(<your_dir>)`, and type:
This will create a repository called `PanACoTA`. Go inside this repository to install `PanACoTA`, as described hereafter.
This will create a repository called `PanACoTA`, containing the content of this github repository. To install PanACoTA:
cd PanACoTA
./make
If you have permission issues, you can either use 'sudo' before the previous command lines to install it as root, or add the `--user` option to install it locally.
If a new version of `PanACoTA` is released, and you want to use it, type the following command to update the source code:
To upload to new version, go back to your repository:
cd <your_dir>/PanACoTA
git pull
./make update
Then, you will be able to upgrade to the new version (see bellow).
To install `PanACoTA`, and all its dependencies, from the root directory, type:
Very useful if you do not have permission rights on the computer, such as, for example, on a cluster. The other advantage is that you do not need to install any dependence (except singularity itself of course). Singularity image includes all of them. You just have to download 1 file, and nothing will be installed anywhere on your computer.
If you want a specific version, like version 1.0, specify `shub://gem-pasteur/PanACoTA:1.0`.
You will then be able to use the package from any directory in your computer,
just as any other software.
To get latest version:
If you have permission issues, you can either use 'sudo' before the previous command lines to install it as root, or add the `--user` option to install it locally.
It will replace your file panacota.img by a new one corresponding to the latest version.
If you don't want `PanACoTA` anymore, or if you want to install a newer version, uninstall it by typing:
### From zip version
./make uninstall
For people wanting to download source code of a specific version, we provide releases. You can download last one here: [](https://github.com/gem-pasteur/PanACoTA/releases)
If you want to install a new version of `PanACoTA` (and you got it by cloning the gitlab repository):
- update source code to the new version (`git pull`)
- upgrade installation to the new version (`./make upgrade`)
If you don't want `PanACoTA` anymore uninstall it by typing:
If you installed it by downloading a zip file, [Uninstall it](#uninstall), and [install](#install) the new version (by cloning gitlab repository, or downloading the new zip file).
pip unintall panacota # If you installed from pip
./make uninstall # If you installed from github repository
Or, if you used singularity, just remove the downloaded image: `rm -r panacota.img`
# Running `PanACoTA`
# <a name="run"></a> Running `PanACoTA`
## Quick run
...
...
@@ -141,36 +178,23 @@ Each subcommand has its own options and inputs. To get the list of required argu
PanACoTA <subcommand> -h
## Examples
When using singularity, just replace `PanACoTA` by `./panacota.img`:
We provide a folder, `Examples`, containing genomic sequences (in `Examples/genomes`) and examples of input files (in `Examples/input_files`) for the software.
In the [example part of documentation](http://aperrin.pages.pasteur.fr/pipeline_annotation/html-doc/examples.html), you will find information explaining you how to run the different modules of `PanACoTA` with this dataset, so that you can try the software. We also describe the results that should be created by each command line.
**Note:** the provided genomic sequences are taken from real genomes, but then modified and drastically shortened in order to have an example showing different situations, but running very fast. Hence, the examples results should not be interpreted biologically!
## Documentation
## <a name="doc"></a> Documentation
You can find more information in [PanACoTA documentation](http://aperrin.pages.pasteur.fr/pipeline_annotation/html-doc)!
If you want a specific version, like version 1.0, specify `shub://gem-pasteur/PanACoTA:1.0`. If you want the latest version, use `shub://gem-pasteur/PanACoTA`or `shub://gem-pasteur/PanACoTA:latest`
Then, you can run PanACoTA as previously:
./panacota.img -h # to get help on the whole PanACoTA program
./panacota.img <subcommand_name> <arguments_for_subcommand> # to run a module of PanACoTA on your data.
# <a name="develop"></a> Development
This part is for people who want to work on developing `PanACoTA` package. In the documentation, there is a part dedicated to [developers](http://aperrin.pages.pasteur.fr/pipeline_annotation/html-doc/develop.html).
...
...
@@ -179,9 +203,7 @@ PanACoTA is also hosted in gitlab, where all CI is done. Here is the link: https
## Installing `PanACoTA` (development mode)
If you want to install `PanACoTA` while still working on modifying the scripts, type:
./make develop
If you want to install `PanACoTA` while still working on modifying the scripts, use `./make develop` instead of `./make install` once you have cloned the repository.
Your changes will then be taken into account. As you installed the package, you will be able to run it from any directory in your computer.
