@@ -50,13 +51,13 @@ You can then add the output `FastTreeMP` to your `$PATH` to be able to run it fr
## Downloading and updating `PanACoTA`
You can download `PanACoTA` source code by downloading a [zip file](https://gitlab.pasteur.fr/aperrin/pipeline_annotation/repository/archive.zip?ref=master), or by cloning its gitlab repository. By cloning the gitlab repository, you will then be able to update the code to new versions very easily and quickly. Here is how to clone the repository:
You can download `PanACoTA` source code by downloading a [zip file](https://gitlab.pasteur.fr/aperrin/pipeline_annotation/repository/archive.zip?ref=master), or by cloning its gitlab repository (which is more recommended). By cloning the gitlab repository, you will then be able to update the code to new versions very easily and quickly. Here is how to clone the repository:
If you don't want `PanACoTA` anymore, or if you want to install a newer version, uninstall it by typing:
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@@ -94,24 +91,20 @@ If you don't want `PanACoTA` anymore, or if you want to install a newer version,
## Upgrade to new version
If you want to install a new version of `PanACoTA` (and you downloaded it by cloning the gitlab repository):
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 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).
## Cleaning dependencies
If you installed the dependencies (such as prokka) via our installation script, but now want to install your own version, you can remove all dependencies downloaded and installed by `make` by doing:
./make clean
# Running `PanACoTA`
## Quick run
`PanACoTA` contains 5 different subcommands:
`PanACoTA` contains 6 different subcommands:
-`prepare` (download and prepare your dataset, with several controls)
-`annotate` (annotate all genomes of the dataset, after a quality control)
-`pangenome` (generate pan-genome)
-`corepers` (generate core-genome or persistent-genome)
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@@ -131,7 +124,7 @@ Each subcommand has its own options and inputs. To get the list of required argu
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 shortened in order to have an example showing different situations, but running very fast. Hence, the examples results should not be interpreted biologically!
**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
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@@ -139,7 +132,7 @@ You can find more information in [PanACoTA documentation](http://aperrin.pages.p
# <a name="develop"></a> Development
This part is for people who want to work on developing `PanACoTA` package.
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).
## Installing `PanACoTA` (development mode)
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@@ -149,16 +142,13 @@ If you want to install `PanACoTA` while still working on modifying the scripts,
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.
If you don't want to install the software, you can still test it, and contribute to the tests and documentation
by installing the libraries needed for the software, and those
If you don't want to install the software, you can still test it, and contribute to the tests and documentation by installing the libraries needed for the software, and those
needed for development by running:
pip3 install -r requirements.txt # dependencies used by PanACoTA
pip3 install -r requirements-dev.txt # libraries used to run tests, generate documentation etc.
**Note:** biopython is only used for 'tree' subcommand, with option ``--soft fastme`` or ``--soft quicktree``. If you do not
plan to use this, you do not need to install biopython. You can comment the ``biopython>=1.60`` line in
``requirements.txt`` (add a ``#`` at the beginning of the line).
**Note:** biopython is only used for 'tree' subcommand, with option ``--soft fastme`` or ``--soft quicktree``. If you do not plan to use this, you do not need to install biopython. You can comment the ``biopython>=1.60`` line in ``requirements.txt`` (add a ``#`` at the beginning of the line).
