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
### 7. Future logins
For future logins, you must reactivate all conda environments. This means launching these commands:
For future logins, you must reactivate all conda environments. This means launching these commands:
