#83 Invalid workflow_run_dir
When running through the eragtis tutorial for a "single machine" (no-grid) install, saving a pipeline crashed telling me that the workflow_run_dir could not be found (even though it can be) and check_installation.pl passed the directory...
In the Browser was: "Invalid workflow_run_dir (doesn't exist) in ergatis.ini: workflow_run_dir"
Think it might be a bug /opt/ergatis-v2r10b1/lib/Ergatis/Pipeline.pm??
...in sub run
near...
## create a directory from which to run this pipeline
if ( -d $run_dir ) {
## make sure the scripts directory exists. this is where the pipeline execution shell
# files are written
if ( ! -d $pipeline_scripts_dir ) {
mkdir $pipeline_scripts_dir || croak "filed to create pipeline scripts directory: $pipeline_scripts_dir : $!";
}
# make a subdirectory for this pipelineid
# Here? ########################################################################
if (!$args{ergatis_cfg}->val('grid', 'vappio_data_placement')){
$run_dir .= '/' . $self->id;
################################################################################
For our single machine we could get functionality by commenting out
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
;;;vappio_data_placement = n
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
in the ergatis.ini file
Maybe this goes away when we move to a grid_enabled=1 ...
Proceeding to configure the software.config to begin making realistic pipelines…
THANK YOU FOR A REALLY COOL SYSTEM!!!
Daniel J McGoldrick Ph.D.
Associate Scientist, Bioinformatics
St Jude Children's Research Hospital
Invalid workflow_run_dir/Pipeline.pm