+ date=2019-10-01
+ data_source=data_sources
+ organism='Homo sapiens'
+ study=LUAD
+ org=tcga
+ dsource=tcga
+ preds_file=
+ perl -e '$study="LUAD"; $study=~/(..)$/; $lo=$1; `mkdir -p $lo/$study`; print "$lo/$study\n";'
++ cat LUAD.dir
+ dir=AD/LUAD
+ head -1 samples.tsv
+ cat samples.tsv.header /dev/fd/63
++ fgrep '	LUAD	' samples.tsv
+ cut_cols=1-3
+ [[ tcga == \m\o\u\s\e ]]
+ [[ tcga == \h\u\m\a\n ]]
+ [[ tcga == \g\t\e\x ]]
+ [[ tcga == \t\c\g\a ]]
+ date=2019-12-01
+ gzip
+ cut -f 1-840 AD/LUAD/samples.tsv.LUAD
+ cut -f 1-3,841- AD/LUAD/samples.tsv.LUAD
+ gzip
+ proj_header='rail_id	external_id	study	project	organism	file_source	metadata_source	date_processed'
+ dsource_path=data_sources/tcga
+ extra_proj_cols='Homo sapiens	data_sources/tcga	data_sources/tcga	2019-12-01'
+ gzip
+ cat /dev/fd/63 /dev/fd/62
++ echo 'rail_id	external_id	study	project	organism	file_source	metadata_source	date_processed'
++ tail -n+2 AD/LUAD/samples.tsv.LUAD
++ cut -f 1-3
++ perl -ne 'chomp; $f=$_; ($rid,$run,$study)=split(/\t/,$f); print "$f\t$study\tHomo sapiens	data_sources/tcga	data_sources/tcga	2019-12-01\n";'
+ [[ -n '' ]]
+ rm AD/LUAD/samples.tsv.LUAD