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runTEdenovo
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#python
module load python/2.7.15-201901021238
module load blast/2.2.22
# The name of the FASTA file you are working with
export PROJECT_NAME=DmelChr4
# The latest version of gcc needs to be loaded for the latest version of GLIBC
module load gcc/5.3.0
# Runs all of the steps of the TEdenovo pipeline
# Step 1
rm -rf ${PROJECT_NAME}_db/
TEdenovo.py -P ${PROJECT_NAME} -C TEdenovo.cfg -S 1
# Step 2
rm -rf ${PROJECT_NAME}_Blaster/
TEdenovo.py -P ${PROJECT_NAME} -C TEdenovo.cfg -S 2 -s Blaster
# Step 2 structural
rm -rf ${PROJECT_NAME}_LTRharvest
TEdenovo.py -P ${PROJECT_NAME} -C TEdenovo.cfg -S 2 --struct
# Step 3
rm -rf ${PROJECT_NAME}_Blaster_Grouper/
TEdenovo.py -P ${PROJECT_NAME} -C TEdenovo.cfg -S 3 -s Blaster -c Grouper
rm -rf ${PROJECT_NAME}_Blaster_Recon/
TEdenovo.py -P ${PROJECT_NAME} -C TEdenovo.cfg -S 3 -s Blaster -c Recon
rm -rf ${PROJECT_NAME}_Blaster_Piler/
TEdenovo.py -P ${PROJECT_NAME} -C TEdenovo.cfg -S 3 -s Blaster -c Piler
# Step 3 structural
rm -rf ${PROJECT_NAME}_LTRharvest_Blastclust/
TEdenovo.py -P ${PROJECT_NAME} -C TEdenovo.cfg -S 3 --struct
# Step 4
rm -rf ${PROJECT_NAME}_Blaster_Grouper_Map/
TEdenovo.py -P ${PROJECT_NAME} -C TEdenovo.cfg -S 4 -s Blaster -c Grouper -m Map
rm -rf ${PROJECT_NAME}_Blaster_Recon_Map/
TEdenovo.py -P ${PROJECT_NAME} -C TEdenovo.cfg -S 4 -s Blaster -c Recon -m Map
rm -rf ${PROJECT_NAME}_Blaster_Piler_Map/
TEdenovo.py -P ${PROJECT_NAME} -C TEdenovo.cfg -S 4 -s Blaster -c Piler -m Map
# Step 4 structural
rm -rf ${PROJECT_NAME}_LTRharvest_Blastclust_Map
TEdenovo.py -P ${PROJECT_NAME} -C TEdenovo.cfg -S 4 --struct -m Map
# Step 5
rm -rf ${PROJECT_NAME}_Blaster_GrpRecPil_Struct_Map_TEclassif/
TEdenovo.py -P ${PROJECT_NAME} -C TEdenovo.cfg -S 5 -s Blaster -c GrpRecPil -m Map --struct
# Step 6
rm -rf ${PROJECT_NAME}_Blaster_GrpRecPil_Struct_Map_TEclassif/classifConsensus
TEdenovo.py -P ${PROJECT_NAME} -C TEdenovo.cfg -S 6 -s Blaster -c GrpRecPil -m Map --struct
# Step 7
rm -rf ${PROJECT_NAME}_Blaster_GrpRecPil_Struct_Map_TEclassif_Filtered
TEdenovo.py -P ${PROJECT_NAME} -C TEdenovo.cfg -S 7 -s Blaster -c GrpRecPil -m Map --struct
# Step 8
rm -rf ${PROJECT_NAME}_Blaster_GrpRecPil_Struct_Map_TEclassif_Filtered_Blastclust
TEdenovo.py -P ${PROJECT_NAME} -C TEdenovo.cfg -S 8 -s Blaster -c GrpRecPil -m Map --struct -f Blastclust
rm -rf ${PROJECT_NAME}_Blaster_GrpRecPil_Struct_Map_TEclassif_Filtered_MCL
TEdenovo.py -P ${PROJECT_NAME} -C TEdenovo.cfg -S 8 -s Blaster -c GrpRecPil -m Map --struct -f MCL