diff --git a/README.md b/README.md index 270a02e5019d41f3d1662ce788c3561cd393fbdd..c83f4ef5ff86902546fc97f1fb99794d59387520 100644 --- a/README.md +++ b/README.md @@ -38,20 +38,6 @@ $ conda create --name cnvpipeline --file requirements.yaml source activate cnvpipeline ``` - -### 6. Additional softwares to install - -You also need to install the RepBase (http://www.girinst.org/server/archive/RepBase21.12/ - choose this version as more recent ones are not compatible with 4.0.6 version of RepeatMaster). Download the Repbase-derived RepeatMasker libraries (repeatmaskerlibraries-20160829.tar.gz) Uncompress it in your save folder. It will create a Library folder. Then define the path to the Library folder inside the application.properties file (see below). - -If you run simulation, you need additional python modules: matplotlib and seaborn. Once you loaded your conda environment, just install them like that: - - pip install matplotlib==2.2.* seaborn==0.8.* - -Special case of genologin cluster (genotoul): - -* Lumpy is already available through bioinfo/lumpy-v0.2.13. Just add it in the application.properties file. -* For genomestrip, you can use this folder: `/usr/local/bioinfo/src/GenomeSTRiP/svtoolkit_2.00.1774` (see configuration part, sv_dir point) - ### 7. Future logins For future logins, you must reactivate all conda environments. This means launching these commands: