Hi Ross,
I tried installing again it shows no item..
Also i couldn't find any .log file or the (
/htseq/0.5.4p3/fubar/htseq_bams_to_count_matrix) in the tool dependency
directory.
Thanks
On Wed, Aug 21, 2013 at 12:13 PM, Ross wrote:
> Sridhar,
> Kindly try rerunning the failed job to confir
Hi,
I am having trouble uploading files to a Data Library, and I'm not sure
where to begin troubleshooting. I'm uploading from a URL (but I had a
similar issue from the desktop). The symptom is that the datasets in the
library have the message "This job is queued" and never seem to progress.
I am
Sorry, missed some information: there are a handful of files, 35MB
(gzipped) each. The issue occurs even if I only try to upload one of them
though. The server is a 16-core machine.
On 21 August 2013 17:08, Clare Sloggett wrote:
> Hi,
>
> I am having trouble uploading files to a Data Library, a
Sridhar,
Tool shed installations always create those log files, even when they fail.
I am unable to offer any further assistance without seeing the installation
log for the dependency.
What does:
find [your tool dependency directory] -name "INSTALLATION.log"
show?
If necessary, try navigating th
Hi Clare
a few points to start:
- do you define the 'File Format'?
(don't use 'Auto-detect' for big files)
- and similar to a recent question on the list: check your proxy
settings
Regards, Hans-Rudof
On 08/21/2013 09:09 AM, Clare Sloggett wrote:
Sorry, missed some information: th
Why the dislike for quick turnover? Could somebody present the arguments for
people not having been at the BOF?
People don't have to upgrade - unless its breaking changes that e.g. disable
the possibility to download from the public toolshed which forced me to upgrade.
The alternative to freque
On Wednesday, August 21, 2013, Ido Tamir wrote:
> Why the dislike for quick turnover? Could somebody present the arguments
> for people not having been at the BOF?
>
> People don't have to upgrade - unless its breaking changes that e.g.
> disable the possibility to download from the public toolshe
On Tue, Aug 20, 2013 at 8:34 PM, Greg Von Kuster wrote:
> Peter and Ross,
>
> I've not been able to reproduce this behavior, most likely because I am not
> following the precise steps you've used when you see it. Can you clarify
> what you do when you encounter it?
>
> Thanks!
>
> Greg Von Kuster
On Tue, Aug 20, 2013 at 9:15 PM, Dave Bouvier wrote:
> Peter,
>
> I believe this was again due to the installation of an earlier repository
> hanging until the testing framework canceled the build. I've added the
> repository in question to the exclude list, and hopefully your blast
> repositories
Hi Hans and all,
The issue turned out to be a more general one with our job runners (it was
also stopping non-data-transfer jobs running, if I'd noticed). Yep, I do
specify file format when uploading.
Thanks for your help!
Clare
On 21 August 2013 17:38, Hans-Rudolf Hotz wrote:
> Hi Clare
>
>
Hi Dannon,
I'm seeing a problem which seems very similar to the one Bjoern
had back in June with the same workflow (which appeared to have
been fixed according to the old IUC thread "Workflow import is not
working").
This server is running the current galaxy-dist release,
$ sudo -u galaxy hg hea
Hi all,
I have found two potential bugs with how workflow actions are
described to the user when running a workflow.
I am looking over the "run workflow" dialogue for this workflow,
(I currently get a warning due to the filter tool having a new
"Number of header lines to skip" option)
http://tool
On Wed, Aug 21, 2013 at 10:54 AM, Peter Cock wrote:
> On Tue, Aug 20, 2013 at 9:15 PM, Dave Bouvier wrote:
>> Peter,
>>
>> I believe this was again due to the installation of an earlier repository
>> hanging until the testing framework canceled the build. I've added the
>> repository in question
Peter,
Thanks for noticing this -- the text in the UI should definitely reflect
which output it's referring to. "Hide output_pos", etc.
https://trello.com/c/KAtwLSiV/1069-workflow-actions-cosmetic-issues
-Dannon
On Wed, Aug 21, 2013 at 7:16 AM, Peter Cock wrote:
> Hi all,
>
> I have found two
Hey Peter,
I've reproduced this here, thanks. Unfortunately this got missed
previously, once we had the import itself working. To be clear, though,
the workflow itself is still completely functional, imports and runs, and
the only issue is the inability to view the svg?
I think what's causing t
Peter,
Here is the relevant log output for the installation of ncbi_blast_plus.
A quick google informs me that exit code 64 means "command line usage
error", for what it's worth.
install_and_test_repositories INFO 2013-08-20 23:34:43,270 Installing
and testing revision 946749c8605f of reposi
Quick followup on this one -- had you manually tweaked this workflow prior
to upload? I see all of the tool identifiers are the short form 'signalp3'
and not the long-form toolshed included versions.
On Wed, Aug 21, 2013 at 8:25 AM, Dannon Baker wrote:
> Hey Peter,
>
> I've reproduced this here
On Wed, Aug 21, 2013 at 1:45 PM, Dave Bouvier wrote:
> Peter,
>
> Here is the relevant log output for the installation of ncbi_blast_plus. A
> quick google informs me that exit code 64 means "command line usage error",
> for what it's worth.
>
> install_and_test_repositories INFO 2013-08-20 23:34:
> On Wed, Aug 21, 2013 at 8:25 AM, Dannon Baker
> wrote:
>>
>> Hey Peter,
>>
>> I've reproduced this here, thanks. Unfortunately this got missed
>> previously, once we had the import itself working. To be clear, though, the
>> workflow itself is still completely functional, imports and runs, and
On Wed, Aug 21, 2013 at 9:10 AM, Peter Cock wrote:
> Via the Tool Shed I couldn't see the import workflow action... from
> memory it was on the broken SVG page?
>
Yep, that's where it was.
These are not tweaked - it is an old workflow created with manually
> installed tools which therefore have
Thanks Peter,
As soon as I can get the steps to produce "white ghost", I'll get a fix
committed - I've not been able to produce one yet.
Greg Von Kuster
On Aug 21, 2013, at 5:41 AM, Peter Cock wrote:
> On Tue, Aug 20, 2013 at 8:34 PM, Greg Von Kuster wrote:
>> Peter and Ross,
>>
>> I've not
I've made a note on the Trello issue Ross filed for this,
https://trello.com/c/SqrjrnNg/986
On Wed, Aug 7, 2013 at 4:16 PM, Greg Von Kuster wrote:
> Hi Peter,
>
> This is a known issue ( not a Tool Shed issue, but a Galaxy issue )
> related to the Select list that gets automatically populated wit
Hello Bjoern,
On Aug 21, 2013, at 2:51 AM, Bjoern Gruening wrote:
> Hi Greg,
>
> a first test seems to work as expected for me, will test again with the
> whole CTB.
Great - thanks!
> If I understood your commit you are searching now for the next valid
> 'installable' revision, aka a revisi
Thanks Peter, I've added some comments as well, and relabeld the Trello card as
trivial bug: Using Galaxy select lists fail unless the "Select one" option
removed first.
since this is not a tool shed issue, but a Selectlist issue in the Galaxy
formbuilder framework. The tool shed simply inheri
Hey Peter,
The reason it's actually failing has to do with the tool Filter1, and your
particular version of the filter tool not having the header lines
parameter. This was added in 8678:a14006775b08. In this instance, we
should have just used the default value.
Once all tools and versions are i
n Wed, Aug 21, 2013 at 2:59 PM, Dannon Baker wrote:
> Hey Peter,
>
> The reason it's actually failing has to do with the tool Filter1, and your
> particular version of the filter tool not having the header lines parameter.
> This was added in 8678:a14006775b08. In this instance, we should have ju
Hi all,
I'm trying to update one of my saved workflows which was created
using an old version of the filter tool BEFORE this tool had the
option "Number of header lines to skip". In order to get rid of the
nag message on using the tool, I want to re-save the workflow
using the default 0 for this.
Hi,
I didn't know this was possible, thanks!
Unfortunately I can't use this in my case because I can only use param
with type="hidden" for a data source...
Anthony
On 21/08/2013 08:51, Hans-Rudolf Hotz wrote:
Hi Anthony
I doubt it will solve your problem, but just as a general hint: you
can
Hi all,
I've seen several unicode issues reported recently, so here is
another one: I just tried to log in and naively copy and pasted
my password from one browser to another:
This upset Galaxy,
143.234.100.162 - - [21/Aug/2013:15:47:55 +0100] "POST
/galaxy/user/login?use_panels=False H
Hi all,
I was trying to update this workflow repository on the Test Tool Shed,
http://testtoolshed.g2.bx.psu.edu/view/peterjc/secreted_protein_workflow
Attempting to upload the tar-ball appeared to fail as follows:
URL:
http://testtoolshed.g2.bx.psu.edu/upload/upload?repository_id=eb13e537583cd
Hi Peter,
You are probably using a mac if you are seeing this, so can you check to see if
your .ga file permissions include an @ sign?
This an Apple osx issue, and you'll need to do the following:
xattr -d com.apple.quarantine
When you do this, it will fix the permissions, and uploading to the
On Wed, Aug 21, 2013 at 4:30 PM, Greg Von Kuster wrote:
> Hi Peter,
>
> You are probably using a mac if you are seeing this, so can you check to see
> if your .ga file permissions include an @ sign?
Yes, I am, and yes, they have an '@' sign.
> This an Apple osx issue, and you'll need to do the f
On Mon, Aug 19, 2013 at 3:34 PM, Peter Cock wrote:
> Filed on Trello,
> https://trello.com/c/HaQnZGvW/1060-embedding-help-text-in-workflows-ideally-rich-text-with-markup
>
> Peter
On Fri, May 10, 2013 at 5:07 PM, Jeremy Goecks wrote:
>> Do you think we could add a new 'rich text' field for a wo
On Wed, Aug 21, 2013 at 5:40 PM, Peter Cock wrote:
> On Mon, Aug 19, 2013 at 3:34 PM, Peter Cock wrote:
>> Filed on Trello,
>> https://trello.com/c/HaQnZGvW/1060-embedding-help-text-in-workflows-ideally-rich-text-with-markup
>>
>> Peter
>
>
> On Fri, May 10, 2013 at 5:07 PM, Jeremy Goecks
> wro
Hi Shane,
please find a new bismark version with an updated dependency on samtools
0.1.19 here:
http://toolshed.g2.bx.psu.edu/view/bgruening/bismark
Thanks for reporting that issue,
Bjoern
> I've had a bit of a time trying to get Bismark working on our Galaxy
> instance. The install doesn'
Hi Greg,
seems to work fine!
> Hello Bjoern,
>
>
> On Aug 21, 2013, at 2:51 AM, Bjoern Gruening
> wrote:
>
> > Hi Greg,
> >
> > a first test seems to work as expected for me, will test again with the
> > whole CTB.
>
> Great - thanks!
>
>
> > If I understood your commit you are searching
We should create a Tool Shed Hackathon, I'm an expert in producing
'white ghosts' :)
> Thanks Peter,
>
> As soon as I can get the steps to produce "white ghost", I'll get a fix
> committed - I've not been able to produce one yet.
>
> Greg Von Kuster
>
> On Aug 21, 2013, at 5:41 AM, Peter Cock
Hello Bjoern,
On Aug 21, 2013, at 1:27 PM, Bjoern Gruening wrote:
> Hi Greg,
>
> seems to work fine!
>
>> Hello Bjoern,
>>
>>
>> On Aug 21, 2013, at 2:51 AM, Bjoern Gruening
>> wrote:
>>
>>> Hi Greg,
>>>
>>> a first test seems to work as expected for me, will test again with the
>>> whol
Hi,I am using the latest version of galaxy at my local installation and I try to use trackster to display a simple BED file, but it invariably complains about not having a converter for this datatype and it tells me to check my datatypes_conf.xml which I did (not sure what I should be looking for,
Hi Anthonius,
Do you have the BEDTools installed and its directory added to your PATH
environment variable? Trackster uses compressed file formats to reduce the
amount of data transfers.
I hope this helps,
Sam
On Wed, Aug 21, 2013 at 4:11 PM, Anthonius deBoer wrote:
> Hi,
>
> I am using the
Hi Bjoern,
I've upgraded our machine and confirmed it now works fine. Thanks for that!
Shane
On 22/08/2013, at 5:17 AM, Bjoern Gruening wrote:
>
> Hi Shane,
>
> please find a new bismark version with an updated dependency on samtools
> 0.1.19 here:
>
> http://toolshed.g2.bx.psu.edu/view/bg
I've just created a repository in the sandbox and have been trying to test the
installation of a dependency my tool needs. The tool needs the python module
"requests" and I've written code. I get an error:
STDERR
python: can't open file 'setup.py': [Errno 2] No such file or directory
I've mo
Yep...$ bedtools --versionbedtools v2.17.0ThonOn Aug 21, 2013, at 01:40 PM, sam guerler wrote:Hi Anthonius,Do you have the BEDTools installed and its directory added to your PATH environment variable? Trackster uses compressed file formats to reduce the amount of data transfers.I hope this helps,S
Curt,
I tried installing the ingtest repository on a local instance of Galaxy,
and the requests python module installed without errors. Which revision
of Galaxy are you trying to install this repository into, and what kind
of environment are you running on that system?
--Dave B.
On 2013-08
Hi Dave,
I made changes giving the suggestions of Ross, I got a different error and
that gave me insight as to what was going on. I uploaded new xml:
http://pypi.python.org/packages/source/r/requests/re
quests-1.2.3.tar.gz
$INSTALL_DIR
For the record, I'd noticed that the change of working directory following
a download_by_url disappears if you include any other action tags before
you run setup.py
Reordering fixes this so arguably it's not really a bug although it took me
some time and headscratching to realise that was the prob
Curt,
I'm happy to hear that everything is now working. If you encounter any
further issues, please don't hesitate to contact us.
--Dave B.
On 2013-08-21 21:31, Curt Palm wrote:
Hi Dave,
I made changes giving the suggestions of Ross, I got a different error and
that gave me insight as to w
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