SOFT : REPET
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Site du soft: https://urgi.versailles.inra.fr/Tools/REPET
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LICENSE:
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CeCILL

See software documentation for more informations.

Location: /usr/local/bioinfo/src/REPET
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Load binaries and environment:
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-> Version v2.5

#Need Python-2.7.2
module load system/Python-2.7.2

#If needed Blast+,RECON,GenomeTools,hmmer3, blastclust (or if need mcl module load bioinfo/mcl-14-137),RepeatMasker,TRF, MAFFT,repeatScout
module load bioinfo/ncbi-blast-2.7.1+ bioinfo/RECON-1.08 bioinfo/genometools-1.5.10 bioinfo/hmmer-3.1b2 bioinfo/blast-2.2.26 bioinfo/RepeatMasker-4-0-7 bioinfo/trf-v4.09 bioinfo/mafft-7.313 bioinfo/RepeatScout-1.0.5

#Load REPET env
module load bioinfo/REPET_v2.5

#Source database variables
source /usr/local/bioinfo/src/REPET/REPET_linux-x64-2.5/config/setEnv.sh (for use shared genotoul database users)

Copy and adapt configuration file (ex: cp $REPET_PATH/config/TEdenovo.cfg .)
 and /usr/local/bioinfo/src/REPET/REPET_linux-x64-2.5/config/setEnv.sh). 
You can use your own database (copy /usr/local/bioinfo/src/REPET/REPET_linux-x64-2.5/config/setEnv.sh  and adapt it) or shared genotoul users  database with:

[repet_env]
repet_version: 2.5
repet_host: mariadb01
repet_user: repet
repet_pw: r1e2p3
repet_db: repet_slurm_2_5
repet_port: 3306
repet_job_manager: SLURM


-> Version v3.0

#Need Python-2.7.2
module load system/Python-2.7.2

#If needed Blast+,RECON,GenomeTools,hmmer3, blastclust (or if need mcl module load bioinfo/mcl-14-137),RepeatMasker,TRF, MAFFT,repeatScout,mreps
module load bioinfo/ncbi-blast-2.7.1+ bioinfo/RECON-1.08 bioinfo/genometools-1.5.10 bioinfo/hmmer-3.1b2 bioinfo/blast-2.2.26 bioinfo/RepeatMasker-4-0-7 bioinfo/trf-v4.09 bioinfo/mafft-7.313 bioinfo/RepeatScout-1.0.5 bioinfo/mreps-2.6.01

#Load REPET env
module load bioinfo/REPET_v3.0

#Source database variables
source /usr/local/bioinfo/src/REPET/REPET_linux-x64-3.0/config/setEnv.sh (for use shared genotoul database users)

Copy and adapt configuration file (ex: cp $REPET_PATH/config/TEdenovo.cfg .)
You can use your own database source /usr/local/bioinfo/src/REPET/REPET_linux-x64-3.0/config/setEnv.sh  and adapt it) or shared genotoul users  database with:

[repet_env]
repet_version: 3.0
repet_host: mariadb01
repet_user: repet
repet_pw: r1e2p3
repet_db: repet_slurm_3_0
repet_port: 3306
repet_job_manager: SLURM


Warning! For TEannot: position yourself in the project directory to start the job and indicate -C TEannot.cfg (If you indicate the full or relative path of TEannot.cfg, error in step 3 of TEannot) 


Example directory for use on cluster:
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/usr/local/bioinfo/src/REPET/example_on_cluster

To submit: sbatch test_REPET_v2.5.sh or cd test_REPET_v3.0 and sbatch test_REPET_v3.0.sh

See software documentation and our FAQ (http://bioinfo.genotoul.fr/index.php/faq/) for more informations.