I included a new tool in galaxy and I get the following debug msg:
galaxy.metadata DEBUG ... setting metadata externally failed for HistoryDatasetAssociation 860: 'samtools returned with error 1: stdout=, stderr=samtools index: failed to create index for ".../galaxy/database/files/000/dataset_859.dat"\n'.
[E::hts_idx_push] Unsorted positions on sequence #1: 205803679 followed by 25375294
These numbers appear to be from the output bam of my tool.
I fixed this by adding:
samtools sort output.bam > a && mv a output.bam in the last line of CDATA section.
Is there a elegant way of doing the same? For instance could
dependency_resolvers_conf.xml have something to do?