...
Dostupne verzije i moduli
Verzije | Module |
---|
RepeatModeler2 2.0.4 RepeatMasker 4.1.5 RepeatExplorer2 2.3.8 | bioinfo/RepeatTools/repeat_env |
Primjeri aplikacija:
Testni podaci: https://www.ncbi.nlm.nih.gov/datasets/taxonomy/9785/
Code Block |
---|
language | bash |
---|
title | RepeatModeler2 |
---|
|
#!/bin/shbash
#$ -N modeler
#$ -pe *mpisingle 20
#$ -cwd
module load bioinfo/RepeatTools/repeat_env
#Prije pokretanja potrebno je kreirati bazu
BuildDatabase -name elephant GCF_000001905.1_Loxafr3.0_genomic.fna
RepeatModeler -database elephant -threads $NSLOTS -LTRStruct >& run.out |
Code Block |
---|
language | bash |
---|
title | RepeatMasker |
---|
|
#!/bin/shbash
#$ -N masker
#$ -pe *mpisingle 20
#$ -cwd
module load bioinfo/RepeatTools/repeat_env
RepeatMasker --species Loxodonta_africana GCF_000001905.1_Loxafr3.0_genomic.fna -pa $NSLOTS |
Code Block |
---|
language | bash |
---|
title | RepeatExplorer2 |
---|
|
#!/bin/shbash
#$ -N explorer
#$ -pe *mpisingle 20
#$ -cwd
#$ -l memory=2
module load bioinfo/RepeatTools/repeat_env
seqclust -c $NSLOTS -r 41943040 GCF_000001905.1_Loxafr3.0_genomic.fna |
Note |
---|
title | RepeatExplorer memorija |
---|
|
Repeat explorer koristi cijelu dostupnu memoriju po zadanim postavkama. Potrebno je odrediti broj maksimalne količine memorije u kB, u primjeru smo odredili 20(CPU) * 2 GB RAM-a = 40 GB ili 41943040 kB. |