forked from kjellp/SMRT-Analysis
-
Notifications
You must be signed in to change notification settings - Fork 0
Job fails if a soft link resolves to 2 different paths
pb-jlandolin edited this page Mar 7, 2013
·
1 revision
If you try to run Celera Assembler where $SEYMOUR_HOME is a soft link that resolves to two different paths, the job will fail.
Theoretically, you can solve this problem by using the pathMap= parameter in the \*.spec to circumvent the $FindBin::RealBin check by explicitly stating the location of the binaries. However, in practice this does not work for the error correction step (P_PacBioToCA) in the current version of Celera Assembler.
This was fixed in the newest release of Celera Assembler, and will be included in a later release of SMRT Pipe.