:78 Function create_function() is deprecated [8192]

adding checks to the script that gets the data for the Oxytricha

Marcelo Ponce [2019-06-28 18:26:24]
adding checks to the script that gets the data for the Oxytricha
Filename
datasets/get_OXYchIPseq-files.sh
diff --git a/datasets/get_OXYchIPseq-files.sh b/datasets/get_OXYchIPseq-files.sh
old mode 100644
new mode 100755
index 92b82f2..55296ab
--- a/datasets/get_OXYchIPseq-files.sh
+++ b/datasets/get_OXYchIPseq-files.sh
@@ -4,11 +4,34 @@
 # This script is part of
 # RACS v1.0 (2018/2019) -- Open source tools for Analizing ChIP-Seq data

-# It requires the "NSBI SRA toolkit" to download the data
+# It requires the "NCBI SRA (Sequence Read Archive)" to download the data
+# whcioh can be obtained from	https://github.com/ncbi/sra-tools

 # set PATH to add "SRA toolkit"
 PATH=$PATH:/scratch1/mponce/RESEARCH/Tetrahymena_Ryerson/TOOLS/NCBI_SRA_toolkit/sratoolkit.2.9.6-1-ubuntu64/bin

+#######################################################
+# check that the script is not being sourced!!!
+if [[ $0 == '-bash' ]]; then
+        echo "Please do not 'source' this script; ie. run it as PATHtoRACS/core/SCRIPTname arguments"
+        return 1
+fi
+
+# setting preamble, detecting scripts location
+scriptsDIR=`dirname $0`
+
+
+# load auxiliary fns for integrity checks and message/error handling
+if [[ -f $scriptsDIR/../core/auxs/auxFns.sh ]]; then
+        . $scriptsDIR/../core/auxs/auxFns.sh --source-only;
+else
+        echo "Error auxiliary file: " $scriptsDIR/auxs/auxFns.sh "NOT found!"
+        return 11
+fi
+#######################################################
+
+checkTools fastq-dump gzip
+
 # Oxytricha files:
 srxFiles="SRX483016 SRX483017"
ViewGit