:78 Function create_function() is deprecated [8192]
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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"