add script for local

test/test_local.sh

@@ -0,0 +1,63 @@
+#! /bin/bash
+
+set -euo pipefail
+
+test_script_dir="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
+debug_dir="$test_script_dir/../../Debug_atlas"
+
+mkdir -p $debug_dir
+cd $debug_dir
+
+
+reads_dir="test_reads"
+
+snakemake_args=" --quiet rules $@ " 
+
+# if test_reads doean't exist download it
+
+if [ ! -d "$reads_dir" ]; then
+    echo "Downloading test reads"
+    wget https://zenodo.org/record/3992790/files/test_reads.tar.gz
+    tar -xzf test_reads.tar.gz 
+    rm test_reads.tar.gz
+fi
+
+WD='wd'
+
+
+rm -f $WD/samples.tsv
+
+#
+atlas init $reads_dir -w $WD 
+
+atlas run None screen -w $WD qc  $snakemake_args
+
+echo "\n\nFinished screen\n\n"
+
+atlas run -w $WD qc  $snakemake_args
+
+echo "\n\nFinished qc\n\n"
+
+
+atlas run assembly -w $WD $snakemake_args
+
+echo "\n\nFinished assembly\n\n"
+
+atlas run binning -w $WD $snakemake_args
+
+echo "\n\nFinished binning\n\n"
+
+atlas run genecatalog --omit-from combine_egg_nogg_annotations combine_dram_genecatalog_annotations -w $WD $snakemake_args
+
+echo "\n\nFinished genecatalog\n\n"
+
+# atlas run genomes -w $WD $@
+
+# echo "\n\nFinished genomes\n\n"
+
+# atlas run strains -w $WD $@
+
+# echo "\n\nFinished strains\n\n"
+
+
+