Eric Lyons issues

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                                            Eric Lyons

Space in file name causing failure for workflow when loading genome.

CoGe's reported error: ######################### Sorting FASTA file Job: /opt/apache2/coge/scripts/sort_fasta.pl Pa_scaffold 0_7.fa > Pa_scaffold 0_7.fa.sorted Submitted at: 02/09/20 at 01:19:13AM Completed at: 02/09/20 at 01:19:14AM Execution time: 0.026153 sec Assigned to...

spaces in iRODS folder names causing failures

If there are spaces in iRODS folder names, CoGe's workflow will fail: Fetching /iplant/home/arabiflora/coge_data/Concatenated AFG data/A02concat_R1.fastq Job: mkdir -p /scratch/coge/tmp/uploads/arabiflora/FCFBB44EEBD611EAA59889A743376945/irods/iplant/home/arabiflora/coge_data/Concatenated AFG data && export irodsEnvFile='/opt/apache2/coge/irodsEnv' && iget -fT '/iplant/home/arabiflora/coge_data/Concatenated AFG...