From e3dbb9f39b611e09f00ffd7ee9bed45086b8c64e Mon Sep 17 00:00:00 2001
From: Laura Cook <l.cook2@student.unimelb.edu.au>
Date: Thu, 15 Oct 2020 10:50:22 +1100
Subject: [PATCH] first commit
---
.../scripts/array_wrapper.slurm | 48 +++++++++++++++++++
.../scripts/changeFilenameLoop.sh | 15 ++++++
cross_species_comparison/scripts/lastz.sh | 2 +-
3 files changed, 64 insertions(+), 1 deletion(-)
create mode 100644 cross_species_comparison/scripts/array_wrapper.slurm
create mode 100644 cross_species_comparison/scripts/changeFilenameLoop.sh
diff --git a/cross_species_comparison/scripts/array_wrapper.slurm b/cross_species_comparison/scripts/array_wrapper.slurm
new file mode 100644
index 0000000..e350115
--- /dev/null
+++ b/cross_species_comparison/scripts/array_wrapper.slurm
@@ -0,0 +1,48 @@
+#!/bin/bash
+
+### Author: Laura E Cook, University of Melbourne, 22/01/2020
+### Last update: 07/02/2020
+### Purpose: basic array wrapper script
+
+# Array set up:
+#SBATCH --array=618-718
+
+# Partition for the job:
+
+# The project ID which this job should run under:
+#SBATCH -A punim0586
+
+# Maximum number of tasks/CPU cores used by the job:
+#SBATCH --mem=50000
+
+#SBATCH --partition mig
+
+# Send yourself an email when the job:
+# aborts abnormally (fails)
+#SBATCH --mail-type=FAIL
+# ends successfully
+#SBATCH --mail-type=END
+
+#SBATCH --mail-user=lecook@student.unimelb.edu.au
+
+# The maximum running time of the job in days-hours:mins:sec
+#SBATCH --time=50:00:00
+
+# The name of the job:
+#SBATCH --job-name=array
+
+# Output control:
+#SBATCH --error="/data/projects/punim0586/lecook/chipseq-pipeline/cross_species/logs/lastz_%a.stderr"
+#SBATCH --output="/data/projects/punim0586/lecook/chipseq-pipeline/cross_species/logs/lastz_%a.stdout"
+
+# Load modules:
+
+module load foss
+module load lastz
+conda activate wga
+
+# Run the simulations:
+command=`head -n $SLURM_ARRAY_TASK_ID /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/scripts/lastz_commands.sh | tail -n 1`
+echo "SLURM_ARRAY_TASK_ID: " $SLURM_ARRAY_TASK_ID
+echo $command
+eval $command
\ No newline at end of file
diff --git a/cross_species_comparison/scripts/changeFilenameLoop.sh b/cross_species_comparison/scripts/changeFilenameLoop.sh
new file mode 100644
index 0000000..e41606c
--- /dev/null
+++ b/cross_species_comparison/scripts/changeFilenameLoop.sh
@@ -0,0 +1,15 @@
+##!/usr/bin/env bash
+
+## Change file names in a loop
+
+TRA=($(for file in *.fa.masked; do echo $file |cut -d "." -f 1;done))
+
+echo ${TRA[@]}
+
+for tr in ${TRA[@]};
+
+do
+
+mv ${tr}.fa.masked ${tr}.fa
+
+done
\ No newline at end of file
diff --git a/cross_species_comparison/scripts/lastz.sh b/cross_species_comparison/scripts/lastz.sh
index 6eed081..41baef6 100644
--- a/cross_species_comparison/scripts/lastz.sh
+++ b/cross_species_comparison/scripts/lastz.sh
@@ -12,6 +12,6 @@ for tr in ${TRA[@]};
do
-echo 'lastz_32 /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/mm10.fa[multiple] /data/projects/pun$
+echo 'lastz_32 /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/mm10.fa[multiple] /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/smiCra1_RM/'${tr}.fa 'H=2000 K=2400 L=3000 Y=9400 --format=maf > /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/maf/'${tr}_mm10.smiCra1.maf
done
--
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