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allenday/get open-cannabis SRR IDs.bash

Last active March 27, 2017 22:00
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get open-cannabis SRR IDs.bash
for i in `wget -O - -q 'http://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?save=efetch&rettype=runinfo&db=sra&term=PRJNA347566' | head | grep SRR | perl -ne 'chomp;@F=split/,/;$F[9]=~s#.+/##;print $F[9],"\n"'` ; do
echo $i ;
~/sratoolkit.2.8.1-2-ubuntu64/bin/fastq-dump --split-files -F $i ;
java -jar ~/bin/picard.jar FastqToSam F1=$i.fastq O=$i.bam SAMPLE_NAME=$i ;
gsutil cp $i.bam gs://$BUCKET_NAME/open-cannabis/samples/;
rm -v $i*;
done
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