On Wed, Oct 24, 2012 at 4:46 PM, Greg Von Kuster wrote:
> Hello Peter,
>
> Thanks very much for this - I'm sure many will find it very helpful. I've
> applied your patch to changeset revision 8096:0c56502c7fd7, which
> will be included in the next Galaxy release currently scheduled for
> next Fri
Hello Peter,
Thanks very much for this - I'm sure many will find it very helpful. I've
applied your patch to changeset revision 8096:0c56502c7fd7, which will be
included in the next Galaxy release currently scheduled for next Friday (not
today's currently scheduled release).
Thanks again,
G
FAO the Galaxy dev team,
I've tested a patch (at end of email) which issues a warning if loading
a loc file with inconsistent numbers of tabs. In the case of blastdb_p.loc
this would result in showing the warning three times, since currently
Galaxy appears to reload a *.loc file for each tool usin
Yes, have to agree there, an error would be more informative.
chris
On Oct 20, 2012, at 2:38 PM, Shane Sturrock wrote:
> That would certainly have saved me a fair bit of time since the only
> indication I got was an empty set of quotes in the error log. I always feel
> like tabs aren't the b
That would certainly have saved me a fair bit of time since the only indication
I got was an empty set of quotes in the error log. I always feel like tabs
aren't the best separators for these sorts of files anyway since they are
usually invisible but since that isn't likely to change, making it
On Saturday, October 20, 2012, Fields, Christopher J wrote:
> On Oct 4, 2012, at 3:11 PM, Peter Cock
> >
> wrote:
>
> > On Thu, Oct 4, 2012 at 8:56 PM, Shane Sturrock
> > >
> wrote:
> >> I've just been setting up our internal galaxy server and following
> >> the instructions to get the NCBI BLAS
On Oct 4, 2012, at 3:11 PM, Peter Cock wrote:
> On Thu, Oct 4, 2012 at 8:56 PM, Shane Sturrock wrote:
>> I've just been setting up our internal galaxy server and following
>> the instructions to get the NCBI BLAST+ tool working but I kept
>> getting stuck with it passing -db "" in rather than th
Thanks Peter!
Shane
Sent from my iPad
On 20/10/2012, at 4:00 AM, Peter Cock wrote:
> On Fri, Oct 5, 2012 at 8:43 AM, Peter Cock wrote:
>>
>>
>> On Thursday, October 4, 2012, Shane Sturrock wrote:
>>>
>>> This section:
>>>
>>> #Your blastdb_p.loc file should include an entry per line for e
On Fri, Oct 5, 2012 at 8:43 AM, Peter Cock wrote:
>
>
> On Thursday, October 4, 2012, Shane Sturrock wrote:
>>
>> This section:
>>
>> #Your blastdb_p.loc file should include an entry per line for each "base
>> name"
>> #you have stored. For example:
>> #
>> #nr_05Jun2010 NCBI NR (non redundant) 05
On Sun, Oct 7, 2012 at 3:02 PM, Shane Sturrock wrote:
> using xemacs, just the terminal based one. And typing a raw
> tab involves a tedious control sequence... there probably is an
> easier way, but I don't edit these loc files very often.
>
>
> Just hit 'Tab' in vi.
Somehow I don't think this w
Hi Peter,
On 5/10/2012, at 8:43 PM, Peter Cock wrote:
>
>
> On Thursday, October 4, 2012, Shane Sturrock wrote:
>
> There are two tabs between the 2010 and /data
>
> Sigh. I've been using emacs to edit these files on our server, and
> it doesn't show non-printing characters like tabs in a vis
On Thursday, October 4, 2012, Shane Sturrock wrote:
> Hi Peter,
>
> Thanks for the quick reply.
>
No problem.
> This section:
>
> #Your blastdb_p.loc file should include an entry per line for each "base
> name"
> #you have stored. For example:
> #
> #nr_05Jun2010 NCBI NR (non redundant) 05 Jun
Hi Peter,
Thanks for the quick reply.
On 5/10/2012, at 9:11 AM, Peter Cock wrote:
> On Thu, Oct 4, 2012 at 8:56 PM, Shane Sturrock wrote:
>>
>> examples in the blastdb_p.loc file, I had put two tabs in just
>> as in the sample doc. This doesn't work. It has to be one tab.
>
> You're seeing
On Thu, Oct 4, 2012 at 8:56 PM, Shane Sturrock wrote:
> I've just been setting up our internal galaxy server and following
> the instructions to get the NCBI BLAST+ tool working but I kept
> getting stuck with it passing -db "" in rather than the actual
> database name. It turns out, because I ha
I've just been setting up our internal galaxy server and following the
instructions to get the NCBI BLAST+ tool working but I kept getting stuck with
it passing -db "" in rather than the actual database name. It turns out,
because I had copied the examples in the blastdb_p.loc file, I had put t
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