nicolasdelhomme / laccariabicolorecmdev

The molecular timecourse of hybrid aspen/Laccaria bicolor ectomycorrhiza development

laccariaBicolorEcmDev

The molecular timecourse of hybrid aspen/Laccaria bicolor ectomycorrhiza development

Abstract

The project aims at deciphering the molecular timecourse of the establishment of Laccaria bicolor ectomycorrhiza on hybrid aspen (Populus tremula x Populus tremuloides, T89). Samples collected from various stage of the ectomycorrhiza have been collected and sequenced

Setup

Repository

In the terminal, clone both project and its submodules

git clone --recurse-submodules [email protected]:nicolasDelhomme/laccariaBicolorEcmDev.git  

Or in two steps:

git clone [email protected]:nicolasDelhomme/laccariaBicolorEcmDev.git
cd laccariaBicolorEcmDev
git submodule init
git submodule update

Data

ln -s /mnt/picea/projects/aspseq/jfelten/T89-Laccaria-bicolor data

Reference

ln -sf /mnt/picea/storage/reference/Laccaria-bicolor/Lacbi2 fungi
ln -sf /mnt/picea/storage/reference/Populus-tremula/v2.2 aspen

Seidr Gold Standard

ln -s /mnt/picea/projects/functional-genomics-course/summer2018/goldStandard .

Update

To update the submodule when doing git pull, you need to run extra commands:

cd laccariaBicolorEcmDev
git submodule update --remote

Note that this will overwrite anyt local changes, also commited, by the content of the UPSCb-common repository

Therefore any changes to be done to these common scripts is best done directly in the UPSCb-common repository