I managed to setup my own server (running on Ubuntu) and managed to perform the necessary analyses succesfully (i.e. no errors anymore and got the files I wanted WGS SNPs analyses). I converted it to a workflow and ran into various issues when I wanted to use the workflow, advice would be greatly appreciated!
1. Reference FASTA file not selectable anymore with Realigner Target creator, Realigner, Mpileup, while Map with BWA can find the reference FASTA OK. did check the name and uploading as custom build did not help as I couldn't select the custom build.
2. While FASTQC groomer and BWA runs OK, the function "Select on Data 6" I get: tool error; failure preparing job. when I rerun the failed history manually again (not changing anything) it runs OK but my workflow is stopped. The error says:
OperationalError: (OperationalError) database is locked u'UPDATE job SET update_time=?, command_line=? WHERE job.id = ?' ('2015-04-21 12:53:08.691793', "python /home/t4admin/galaxy/tools/filters/grep.py -i /home/t4admin/galaxy/database/files/000/dataset_142.dat -o /home/t4admin/galaxy/database/files/000/dataset_144.dat -pattern '^@' -v true", 118)
Anybody an idea what I am doing wrong?
Many thanks in advance,