From 82c7d553a770bcdb56f408b4bec0b889b892e78e Mon Sep 17 00:00:00 2001 From: Kevin Brick Date: Mon, 20 Dec 2021 11:29:09 -0500 Subject: [PATCH] Update bind-paths --- conf/nihbiowulf.config | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/conf/nihbiowulf.config b/conf/nihbiowulf.config index 5c035ba..6159f0d 100644 --- a/conf/nihbiowulf.config +++ b/conf/nihbiowulf.config @@ -34,5 +34,9 @@ singularity { enabled = true autoMounts = true envWhitelist='https_proxy,http_proxy,ftp_proxy,DISPLAY,SLURM_JOBID' - runOptions = ' -B /lscratch -B /fdb/igenomes/ --env TMPDIR="/lscratch/$SLURM_JOBID" ' -} \ No newline at end of file + + //As names change, the bind paths required may change too. To chack that everything is being captured: + //Run '. /usr/local/current/singularity/app_conf/sing_binds' to populate $SINGULARITY_BINDPATH + //Check that each folder in $SINGULARITY_BINDPATH is listed with -B in the runOptions below. If not, add it. + runOptions = ' -B /gs10 -B /gs11 -B /gs12 -B /gs4 -B /gs6 -B /gs7 -B /gs8 -B /gs9 -B /vf -B /spin1 -B /data -B /fdb -B /lscratch -B /fdb/igenomes/ --env TMPDIR="/lscratch/$SLURM_JOBID" ' +}