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Environment variables are not set correctly
pb-jlandolin edited this page Mar 7, 2013
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All environment variables used by SMRT Analysis are specified in /opt/smrtanalysis/analysis/etc/smrtpipe.rc. A common error occurs when the TMP and SHARED_DIR variables are set to directories that do not exist on your file system. To correct the error, create the directories in the local file system, and give the directories write permissions.
sudo mkdir /scratch/
sudo chmod +x /scratch/
sudo mkdir /opt/smrtanalysis/common/userdata/shared_dir/
sudo chmod +x opt/smrtanalysis/common/userdata/shared_dir/
Then assign those directories to the environment variables by editing smrtpipe.rc:
TMP=/scratch/
SHARED_DIR=/opt/smrtanalysis/common/userdata/shared_dir/