Dear Nate, dear Peter

Again, sorry for the delay in replying.

Yes I can. It looks like this

[galaxy@srv ~]$ cat /galaxy/database/files/081/dataset_81002.dat
[galaxy@srv ~]$ ls /galaxy/database/files/081/dataset_81002_files/
blastdb.nhd  blastdb.nhi  blastdb.nhr  blastdb.nin  blastdb.nog 
blastdb.nsd  blastdb.nsi  blastdb.nsq

I think the simplest solution would be to put something in the primary 
file. Just a short string that gets the file size above 0.

I personally have followed you initial suggestion and made the dbs 
available globally via the .loc file.

Thanks again

On 28/07/14 09:43, Peter Cock wrote:
> On Mon, Jul 28, 2014 at 8:28 AM, Ulf Schaefer <> wrote:
>> Dear Nate, dear Peter
>> Sorry for the delay in replying.
>> I can import both HTML and blastdb from a history to a data library. If
>> I try to get the data out of the library into anothre history, I am
>> successful for the html but not for the blastdb. The problem seems to be
>> that the primary data file (the /path/dataset_12345.dat) is empty for
>> the blastdb, while the html primary file has something in it.
> OK. Can you tell where Galaxy thinks the library files are on disk,
> and check to see if the folder of BLAST database files is actually
> there?
>> When I try to import the blastdb (from library to history) there is a
>> message along the lines of "can't import empty file". I hypothesise
>> (admittedly without having looked at a line of code) that there is a
>> test for file size 0 somewhere that is either altogether unnecessary or,
>> more likely, does not take into account that for composite datatypes it
>> might be completely legitimate for the primary file to be empty.
> This guess makes sense - but I've not yet tried to trace through
> the code either.
>> Or is my primary blastdb file not supposed to be empty in the first
>> place? I can blast against it just fine.
> The BLAST databases do not define/populate a primary file, so
> Galaxy seems to create a dummy empty file on its own. I have
> wondered about altering the BLAST database datatype definition
> to have a human readable text file as the "primary file" (i.e. the
> information currently saved as a text log file when creating a
> database).
>> Thanks a lot for your help
>> Ulf
> You too - you've found an "interesting" bug...
> Peter

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