Dear All
I am trying to move our Galaxy installation to new hardware and at the
same time to a new version (the original is "15.10",minor version "2"
via mercurial; the new is "16.04" via github):
So far, I am making good progress, but I am struggling with a tool which
was written by someon
Hi Hans,
see my comment below.
On 16/08/16 09:51, Hans-Rudolf Hotz wrote:
Dear All
I am trying to move our Galaxy installation to new hardware and at the
same time to a new version (the original is "15.10",minor version "2"
via mercurial; the new is "16.04" via github):
So far, I am making
Forget about my previous comment, I should have read your email better,
sorry!
Your code similar to bowtie_wrapper is also used by
https://github.com/galaxyproject/tools-iuc/blob/master/tools/rgrnastar/rg_rnaStar.xml
and I think it should work, not sure if it's a regression in Galaxy.
Cheers
I've tested bowtie_wrapper on Galaxy release_16.04: type="from_data_table" name="bowtie_indexes" column="1" offset="0">
works fine for me.
Cheers,
Nicola
On 16/08/16 11:42, Nicola Soranzo wrote:
Forget about my previous comment, I should have read your email
better, sorry!
Your code similar
Hi Nicola
Many thanks for your comments/suggestions. I've just tested the rnaStar
wrapper, and it works as well.
I will try to dig deeper
Hans-Rudolf
On 08/16/2016 01:38 PM, Nicola Soranzo wrote:
I've tested bowtie_wrapper on Galaxy release_16.04:
works fine for me.
Cheers,
Nicola
On
Hi Nicola and others on the list
It looks like it has something to do with the 'conditional'
I took the rnaStar xml file, and reduced it to the bare bones, just to
reproduce the issue (see attachment: rg_rnaStar.simple ). This works. It
picks up the right dbkey.
I made the xml file even simp
Yup - thanks for the bug report. I have used your rna example to build
a minimal-ish example to fit into Galaxy's test tools framework here
https://github.com/galaxyproject/galaxy/pull/2795. I also tested in
16.01 and it worked - so this clearly broke in 16.04. I'll see if I
can track it down and w
Hi Ray,
Sorry I missed this mail.
On 23. juni 2016 10:27, Raymond Wan wrote:
> Dear all,
>
> I'm trying to run the JBrowse tool within Galaxy. The installation
> was fine (I think), but when I run the tool, I get this error:
>
>
> Fatal error: Exit code 1 () Traceback (most recent call last): Fil
Hi Galaxy-devs
I've created a workflow that processes some NGS data. Since many of the
intermediate files are really large, is it possible to automatically delete
(rather than just hide) some of these files? I've seen that you can delete
intermediate files that aren't used as inputs to other tools
Hi Eric,
On Wed, Aug 17, 2016 at 4:31 AM, Eric Rasche wrote:
> Hi Ray,
>
> Sorry I missed this mail.
No problem! Thanks for getting back to me!
> On 23. juni 2016 10:27, Raymond Wan wrote:
> I'm trying to run the JBrowse tool within Galaxy. The installation
> was fine (I think), but when I
Hi John and Nicola
Thank you very much for working on this and presenting a solution so fast!
Hans-Rudolf
PS: https://github.com/galaxyproject/galaxy/pull/2800
On 08/16/2016 04:40 PM, John Chilton wrote:
Yup - thanks for the bug report. I have used your rna example to build
a minimal-ish exa
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