Blast Production vs Test

Remark on Blast-tool differences between Production and Test

On Test Galaxy-tool-Blast has been updated to Python3.
For the sake of continuity (the updated tool should be thoroughly
tested first), Production is still Python2. Because of limitations
in disk size, not all blastdbs of Production are installed on Test,
thus causing a difference in the respective xml files.

Ongoing updates of the Snakefile

When updating GenBank-blastdb subsets (COI, 12S, ect.) these can
become larger than anticipated in the Snakefile. This will result in
a MissingOutputException. In that case adjust:

output/12S/12S.fa.nhr to output/12S/12S.fa.01.nhr

When creating a custom script to mine Bold (especially because there's
an issue with the Api which prevents downloading the complete dataset
for Arthropods), the same MissingOutputException occured. In this
case it was caused by the fact that the Snakefile required a 'XXX.fa.nal'
file. It turns out that such a file is only created for larger blastdbs,
or when a blastdb is created from multiple input files.

Another issue is the size of the blastdb exceeding the default (1 Gb).
To increase the size of the blastdb (max 4 Gb) add -max_file_sz option
to the affected makeblastdb command in the Snakefile (for 2 Gb):

shell("makeblastdb2.8.1 ... -max_file_sz 2000000000")

Modified file examples

Production.xml vs Test.xml
Old Snakefile vs New Snakefile