generate commands to run array scripts for lastz and repeatMasker

cross_species_comparison/scripts/lastz.sh

+##!/usr/bin/env bash
+
+## This script loops through all scaffolds in the dunnart genome and
+## generates a separate lastz command for each scaffold
+## These commands are then used in a slurm array script to run jobs in parallel
+
+TRA=($(for file in *.fa; do echo $file |cut -d "." -f 1;done))
+
+echo ${TRA[@]}
+
+for tr in ${TRA[@]};
+
+do
+
+echo 'lastz_32 /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/mm10.fa[multiple] /data/projects/pun$
+
+done

cross_species_comparison/scripts/repeatMasker.sh

+##!/usr/bin/env bash
+
+## This script loops through all scaffolds in the dunnart genome and
+## generates a separate RepeatMasker command for each scaffold
+## These commands are then used in a slurm array script to run jobs in parallel
+
+TRA=($(for file in *.fa; do echo $file |cut -d "." -f 1;done))
+
+echo ${TRA[@]}
+
+for tr in ${TRA[@]};
+
+do
+
+echo 'RepeatMasker -q -xsmall smiCra1/'${tr}'.fa -default_search_engine hmmer -trf_prgm /home/lecook/.conda/envs/wga/bin/trf -hmmer_dir /home/lecook/.conda/envs/wga/bin/'
+
+
+done