diff --git a/README.md b/README.md index 0c8a5ea5a3ab1ad6f8c44e8986e2ab4020869edc..57d5364a5b95dfb3bee9ff088ac47e8a480159f5 100755 --- a/README.md +++ b/README.md @@ -26,10 +26,10 @@ PanACoTA is a software providing tools for large scale comparative genomics: PanACoTA is written in **python3**. So, you need python3 (and pip3 for installation) to run it. Its external dependencies are: -- [**prokka**](https://github.com/tseemann/prokka) (to annotate the genomes) and/or [**prodigal**](https://github.com/hyattpd/Prodigal) -- [**mmseqs**](https://github.com/soedinglab/MMseqs2) (to generate pangenomes) -- [**mafft**](http://mafft.cbrc.jp/alignment/software/) (to align persistent genome) -- At least one of those softwares, to infer a phylogenetic tree: +- [**prokka**](https://github.com/tseemann/prokka) and/or [**prodigal**](https://github.com/hyattpd/Prodigal) (for 'annotate module' - to uniformly annotate your genomes) +- [**mmseqs**](https://github.com/soedinglab/MMseqs2) ('pangenome module' - to generate pangenomes) +- [**mafft**](http://mafft.cbrc.jp/alignment/software/) ('align module' - to align persistent genome) +- At least one of those softwares, to infer a phylogenetic tree ('tree module'): - [**IQ Tree**](http://www.iqtree.org/) - [**FastTreeMP**](http://www.microbesonline.org/fasttree/#Install): We advise to download C code, and compile as described here above. - [**FastME**](http://www.atgc-montpellier.fr/fastme/binaries.php) @@ -102,7 +102,7 @@ If you installed it by downloading a zip file, [Uninstall it](#uninstall), and [ `PanACoTA` contains 6 different subcommands: -- `prepare` (download and prepare your dataset, with several controls) +- `prepare` (download genomes from refseq if you want to, or give your input database, to run a filtering quality control) - `annotate` (annotate all genomes of the dataset, after a quality control) - `pangenome` (generate pan-genome) - `corepers` (generate core-genome or persistent-genome) @@ -132,7 +132,7 @@ You can find more information in [PanACoTA documentation](http://aperrin.pages.p 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). -PanACoTA is also hosted in gitlab, where all CI is done. Here is the link: https://gitlab.pasteur.fr/aperrin/pipeline_annotation.git +PanACoTA is also hosted in gitlab, where all CI is done. Here is the link: https://gitlab.pasteur.fr/aperrin/pipeline_annotation ## Installing `PanACoTA` (development mode) diff --git a/doc/source/about.rst b/doc/source/about.rst index 4ebcc19e8cb1a6a9cdf24acace87db8c1e2f9c00..526b7fb5ffd259c1694d91c5f2fc053f64e8fda6 100644 --- a/doc/source/about.rst +++ b/doc/source/about.rst @@ -3,7 +3,7 @@ About PanACoTA ============== -PanACoTA program is available at `<https://gitlab.pasteur.fr/aperrin/PanACoTA>`_. +PanACoTA program is available at `<https://github.com/gem-pasteur/PanACoTA>`_. Copyright © `GEM <https://research.pasteur.fr/fr/team/microbial-evolutionary-genomics/>`_ - Institut Pasteur, CNRS UMR3525 diff --git a/doc/source/develop.rst b/doc/source/develop.rst index 00b35ce6ed0c195090090e367179190e62c04c55..971a5e575c8f8408004565fe83d5a15172ad66ab 100755 --- a/doc/source/develop.rst +++ b/doc/source/develop.rst @@ -4,6 +4,8 @@ Work on PanACoTA code This part is for people who want to work on developing `PanACoTA` package: adding new features, correcting bugs etc. +PanACoTA is also hosted in gitlab, where all CI is done. Here is the link: https://gitlab.pasteur.fr/aperrin/pipeline_annotation + Installing ``PanACoTA`` in development mode =========================================== diff --git a/doc/source/starting.rst b/doc/source/starting.rst index 935637a1d58884f8e29d0771c3b525ddc1359424..1bfad9e7049280ee111484be2b57aa60ea23087a 100755 --- a/doc/source/starting.rst +++ b/doc/source/starting.rst @@ -3,19 +3,18 @@ Starting with PanACoTA ====================== -``PanACoTA`` is a Python package, developed in Python 3. +``PanACoTA`` is a Python package, developed in Python 3.6. Downloading and updating ======================== -You can download ``PanACoTA`` source code by downloading an archive (zip, tar.gz), or by cloning its github repository. 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: +You can download ``PanACoTA`` source code by downloading an archive of a given release (zip, tar.gz), or by cloning its github repository. 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: .. code-block:: bash git clone https://github.com/gem-pasteur/PanACoTA.git - -When asked, give your github login, and password. +ve your github login, and password. This will create a repository called ``PanACoTA``. Go inside this repository (``cd PanACoTA``) to install the software, as described hereafter. @@ -39,10 +38,10 @@ Dependencies There are several external dependencies, and you can install only the ones you need for your study: -- `prokka <https://github.com/tseemann/prokka>`_ and/or `prodigal <https://github.com/hyattpd/Prodigal>`_ (if you want to uniformly annotate your genomes) -- `mmseqs <https://github.com/soedinglab/MMseqs2>`_ (if you want to generate pangenomes) -- `mafft <http://mafft.cbrc.jp/alignment/software/>`_ (if you want to align persistent genome) -- At least one of those softwares, if you want to infer a phylogenetic tree: +- `prokka <https://github.com/tseemann/prokka>`_ and/or `prodigal <https://github.com/hyattpd/Prodigal>`_ (for 'annotate module' - to uniformly annotate your genomes) +- `mmseqs <https://github.com/soedinglab/MMseqs2>`_ ('pangenome module' - to generate pangenomes) +- `mafft <http://mafft.cbrc.jp/alignment/software/>`_ ('align module' - to align persistent genome) +- At least one of those softwares, if you want to infer a phylogenetic tree ('tree module'): - `IQtree <http://www.iqtree.org/>`_ - `FastTreeMP <http://www.microbesonline.org/fasttree/#Install>`_: We advise to download C code, and compile as described :ref:`here above <fasttree>`. @@ -90,6 +89,7 @@ just as any other software. .. warning:: If you plan to work on the scripts, choose the development installation (see :doc:`Developer documentation <develop>`). +.. _uninstall: Uninstalling ``PanACoTA`` ---------------------------- @@ -116,6 +116,8 @@ If you want to install a new version of ``PanACoTA``: .. note:: If you have permission issues, and installed the package as root, use ``sudo`` before the second command line (``sudo ./make upgrade``) to upgrade. Or, if you installed the package locally, use ``./make upgrade --user`` to upgrade this local version. +If you installed it by downloading a zip file, see :ref:`Uninstall it <uninstall>`), and install the new version (by cloning gitlab repository, or downloading the new zip file). + Quick run =========