RwontReadSymlinks.md

Given:

source ${IRAP_DIR}/irap_setup.sh
realpath /nfs/production3/ma/home/atlas3-production/bioentity_properties/ensembl/arabidopsis_thaliana.ensgene.go.tsv

/nfs/production3/ma/home/atlas3-production/bioentity_properties/archive/ensembl_87_34/arabidopsis_thaliana.ensgene.go.tsv

This is problematic:

source ${IRAP_DIR}/irap_setup.sh && irap_GSE_piano --tsv=/nfs/production3/ma/home/atlas3-production/analysis/differential/microarray/experiments/E-ATMX-20/E-ATMX-20_A-AFFY-2-analytics.tsv --pvalue-col=4 --foldchange-col=6 --title=" Sample title" --pvalue=0.05 --gs_fdr=0.1 --method=fisher-exact --dup-use-best --plot-annot-only --top=10 --minsize 5 --maxsize 100 --descr /var/tmp/goIdToTerm.tsv --go=/nfs/production3/ma/home/atlas3-production/bioentity_properties/ensembl/arabidopsis_thaliana.ensgene.go.tsv --out=/var/tmp/E-ATMX-20.g1_g2.go.gsea

[ERROR] Empty file /nfs/production3/ma/home/atlas3-production/bioentity_properties/ensembl/arabidopsis_thaliana.ensgene.go.tsv?

This is fine:

irap_GSE_piano --tsv=/nfs/production3/ma/home/atlas3-production/analysis/differential/microarray/experiments/E-ATMX-20/E-ATMX-20_A-AFFY-2-analytics.tsv --pvalue-col=4 --foldchange-col=6 --title=" Sample title" --pvalue=0.05 --gs_fdr=0.1 --method=fisher-exact --dup-use-best --plot-annot-only --top=10 --minsize 5 --maxsize 100 --descr /var/tmp/goIdToTerm.tsv --go=/nfs/production3/ma/home/atlas3-production/bioentity_properties/archive/ensembl_87_34/arabidopsis_thaliana.A-AFFY-2.tsv --out=/var/tmp/E-ATMX-20.g1_g2.go.gsea

*** science proceeds ****

Caused by this bit in irap_GSE_piano:

tryCatch(gene2go <- read.table(opt$go.file,sep="\t",header=F,comment.char="!",quote="\""),error=function(x) NULL)
if ( is.null(gene2go) ) {
  perror("Empty file ",opt$go.file,"?")
  q(status=2)
}