GFLS (Galaxy For Life Science) ➖✨✨4️⃣🌿🔬➖ BIOS4BIOL

📊 GFLS_Stats_Explorer :

This repository concern the GFLS_Stats_Explorer part of the GFLS project. It is made in collaboration with the statistics group of the CATI "BIOS4BIOL". All the R, Perl and XML scripts are made by this team.

[:heavy_exclamation_mark:Last Update] We improved the wrappers with best practices of Galaxy community. The dependencies are managed with Conda. Tools are avaible in the Toolshed (see below). Tools are available on some French bioinformatics platform (see below).

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• The aim of the GFLS is to :

  • Enhance the wrappers of the tools
  • Package their dependencies
  • Make them at disposition of everyone into different instances (Galaxy servers, Cloud)

• There is 3+1 tool on this project :

  • summary_statistics : This tool produces simple descriptive statistics from a numerical table. Statistical measures are computed for each column in the table. ✉️ @contact melanie.petera[a]inra.fr
  • h_clust : This tool allows to generate hierarchical cluster analysis on a numeric data table according to differents parameters. ✉️ @contact luc.jouneau[a]inra.fr
  • pcaFactoMineR This tool launch a Principal Component Analysis (PCA) as done in the FactoMineR package ✉️ @contact marie.tremblay-franco[a]inra.fr
  • normalization : This last one (the +1) was made during the GFLS project after an enhancement discussion of the differents tools with the stats group. It propose the user different normalization method to preprocess data tables (in tabular format). ✉️ @contact luc.jouneau[a]inra.fr

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• ✉️ Contacts :
  • Manager of the GFLS project : olivier.inizan[a]inra.fr
  • Manager of the GFLS_Stats_Explorer project : sarah.maman[a]inra.fr
  • Developper for the GFLS project : valentin.marcon[a]inra.fr

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• 📂 Toolshed repository :

  • Summary Statistics : Toolshed

  • Hierarchical Clustering : Toolshed

  • PCAFactoMineR Toolshed)

  • Normalization : Toolshed

  • suite_statsexplorer_gfls_1_0 : Toolshed (Allow you to install all four tools at a time)

• 💻 Instance :

  Tools are available on this instances (in the "statistics" category):

  • Galaxy Sigenae/Genotool : http://sigenae-workbench.toulouse.inra.fr/galaxy/
  • Galaxy Migale : http://migale.jouy.inra.fr/galaxy/

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💻 Dev processus :

To work on this project you need to clone it (html or ssh way)

git clone https://github.com/IFB-ElixirFr/GFLS.git # With html

git clone git@github.com:IFB-ElixirFr/GFLS.git # With SSH

git fetch origin dev:dev # Get the "dev" branch

Then, you will need to follow the Versionning strategy as descibed bellow :

• To make a change on a file, you need to create your own branch of developement ("Branch X"), based on the "Master" one.

git checkout master # Change branch to Master

git pull origin master # Recover the last changes

git checkout -b branchMyName # Create a new branch named "branchMyNale" from the Master branch

or update your branch

git checkout branchMyName # Change branch to your own

git pull origin master:master # Recover the last changes from Master

• Make your developement on your branch, and then commit and push to your branch

git commit -a -m "YourMessage" # Record changes to the repository

git pull origin branchYourName # EXCEPTIONAL : If another member use it to develop (or if you use several developement environment), recover the last changes in your branch

git push origin branchYourName # Push to the dev branch

• Merge with the "Dev" branch

git checkout dev # Change branch to Dev

git pull origin dev # Recover the last changes from Dev

git merge branchMyName # Merge your change with the dev branch

• If it's ok, push on the remote dev branch

git push origin dev # Push to the dev branch

• : Inform the administrator, and ask him to make the test with the dev branch if you are not able to
• Finally if the developement work, the administrator will push on the master branch
• The adminstrator will create a "tag" to the master node, corresponding to the new release of the project

Developer Admin