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 Ulf On 28/07/14 09:43, Peter Cock wrote: > On Mon, Jul 28, 2014 at 8:28 AM, Ulf Schaefer <ulf.schae...@phe.gov.uk> 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 > ************************************************************************** The information contained in the EMail and any attachments is confidential and intended solely and for the attention and use of the named addressee(s). It may not be disclosed to any other person without the express authority of Public Health England, or the intended recipient, or both. If you are not the intended recipient, you must not disclose, copy, distribute or retain this message or any part of it. This footnote also confirms that this EMail has been swept for computer viruses by Symantec.Cloud, but please re-sweep any attachments before opening or saving. http://www.gov.uk/PHE ************************************************************************** ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
