Verified Commit 91961e4e authored by Laurent Modolo's avatar Laurent Modolo
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CONTRIBUTION.md: fix typo

parent 6357c052
# Contributing
To contribute to this repository, you can first [fork it](https://gitlab.biologie.ens-lyon.fr/PSMN/modules/forks/new).
To contribute to this repository, you need to [fork it](https://gitlab.biologie.ens-lyon.fr/PSMN/modules/forks/new).
## Development on the PSMN
To install your forked version of the LBMC modules repository on the PSMN run following command o:
To install your forked version of the LBMC modules repository on the PSMN run following command:
```
git clone git@gitlab.biologie.ens-lyon.fr:<your_login>/modules.git ~/privatemodules_dev
module use ~/privatemodules_dev
```
If you don’t have a `.ssh/config` file and if you like typing your password you can instead use after defining your [Gitlab password](https://gitlab.biologie.ens-lyon.fr/profile/password/edit).
If you don’t have a `.ssh/config` file and if you like typing your password, you can instead use the following clone command, after defining your [Gitlab password](https://gitlab.biologie.ens-lyon.fr/profile/password/edit).
```sh
git clone -c http.sslVerify=false https://gitlab.biologie.ens-lyon.fr:<your_login>/modules.git ~/privatemodules_dev
......@@ -22,7 +22,7 @@ the software required by the module you want to use.
### New version of an existing module
To propose a version of a module, start by running the following commands:
To propose a new version of a module, start by running the following commands:
```sh
cd ~/privatemodules_dev/apps/<software_name>/
......@@ -34,7 +34,7 @@ without error on the PSMN to create a proper installation of the software in
the folder ``/apps/<software_name>/<version>`.
You must add a line `apps/<software_name>/<version>` in the `.gitignore` file,
otherwise the installation files will be committed to your repository.
otherwise the installation files could be committed to your repository.
Then, create the corresponding module file with the following commands:
......@@ -46,20 +46,24 @@ sed -i `s/<existing_version>/<new_version>/g` <new_version>.lua
### New module
To propose a new module, use an existing module as a template to build the
corresponding `apps/<software>/<version>` and `modulefiles/<software>/<version>` directory.
To propose a new module, you can use an existing module as a template to write your `apps/<software>/<version>_install.sh` script and `modulefiles/<software>/<version>.lua` file.
You can look at the following modules to have examples of :
- Python tools : [MultiQC install.sh](https://gitlab.biologie.ens-lyon.fr/PSMN/modules/blob/master/apps/MultiQC/install_1.0.sh) and [MultiQC .lua](https://gitlab.biologie.ens-lyon.fr/PSMN/modules/blob/master/modulefiles/MultiQC/1.0.lua)
- Compiled tools : [UrQt install.sh](https://gitlab.biologie.ens-lyon.fr/PSMN/modules/blob/master/apps/UrQt/install_d62c1f8.sh)
- Java tools : [Trimmomatic install.sh](https://gitlab.biologie.ens-lyon.fr/PSMN/modules/blob/master/apps/Trimmomatic/install_0.36.sh) and [nextflow .lua](https://gitlab.biologie.ens-lyon.fr/PSMN/modules/blob/master/modulefiles/nextflow/0.28.2.lua)
- Java tools : [Trimmomatic install.sh](https://gitlab.biologie.ens-lyon.fr/PSMN/modules/blob/master/apps/Trimmomatic/install_0.36.sh) and [nextflow.lua](https://gitlab.biologie.ens-lyon.fr/PSMN/modules/blob/master/modulefiles/nextflow/0.28.2.lua)
## Making your module available to the LBMC
To make your module available to the LBMC you must have a `install_<new_version>.sh` script working without errors on the E5 compilation servers and you must be able to load the correspond module and run it.
To make your module available to the LBMC you must have a `install_<new_version>.sh` script working without errors on the E5 compilation servers and you must be able to load the correspond module and run it with the commands:
Then after pushing your modification on your forked repository, you can make a Merge Request to the [PSMN/modules](https://gitlab.biologie.ens-lyon.fr/PSMN/modules) **dev** branch. Where it will be tested and
```sh
module use ~/privatemodules_dev
ml <module_name>/<module_version>
```
After pushing your modifications to your forked repository, you can make a Merge Request to the [PSMN/modules](https://gitlab.biologie.ens-lyon.fr/PSMN/modules) **dev** branch. Where it will be tested and
integrated to the **master** branch.
## Migrate old module to the new module system
......
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