Hi All,
I installed the toolshed htseq_bams_to_count_matrix repository , i gave the
gene model gtf file(ex: tss.gtf file) Gene model (GFF) file to count reads
over from your current history: in this section and all bam files.
it gives error as
empty
format: tabular, database: hg19
Traceback
Sridhar,
The error message you provide suggests that the HTSeq python module is not
available when Galaxy tries to run the tool.
Please confirm that you installed that tool through the admin interface
from the test toolshed and that the admin interface for toolshed installed
tools shows the
Hi Greg,
that bug was fixed I think!
Thanks,
Bjoern
Hello Peter and Bjoern,
Can you clarify the tool shed bug to which you are referring with the
statement:
Still that TS bug needs to be fixed I think before the next stable
release.
I'll take a look as soon as I get
Hi,
also fixed, yes!
Good start in a day, to write positive mails :)
Bjoern
Hello Bjoern,
I believe this issue was corrected in changeset 10412:29ab5a6d75a7, which was
committed to the stable branch and is running on both tool sheds. At least I
am unable to reproduce the behavior you
Hi Ross,
i Installed through admin interface .
for pysam and freetype it showed new... and rest installed..
Thanks
On Wed, Aug 21, 2013 at 11:47 AM, Ross ross.laza...@gmail.com wrote:
Sridhar,
The error message you provide suggests that the HTSeq python module is not
available when
Morning Greg,
seems to be also fixed in latest release. Will reopen the thread if I
encounter it again.
Thanks a lot,
Bjoern
Hello Peter and Bjoern,
I believe this issue was handled in the August Galaxy release, but the
main tool shed had not yet been upgraded to that release when you
Sridhar,
Kindly try rerunning the failed job to confirm that it still fails now that
the tool installation should have well and truly finished - it does take a
while.
If it still fails the same way, please send me a copy of the installation
log for the htseq dependency found in:
[your
Hi Greg,
a first test seems to work as expected for me, will test again with the
whole CTB.
If I understood your commit you are searching now for the next valid
'installable' revision, aka a revision with metadata. Does it make sense
to have revisions for Tool dependency definition. Only one
Hi Anthony
I doubt it will solve your problem, but just as a general hint: you can
use the email address for filtering. In our case, the user gets a
different list of groups he/she can select from, eg:
param name=group type=select label=Select your group
options
Hi Dave
two months is a good time between releases.
Much more important than the release cycle length is fixing identified
bugs on the release branch as well.
Regards, Hans-Rudolf
On 08/20/2013 08:36 PM, Dave Clements wrote:
Hello all,
At one of the GCC2013 Birds of a Feather sessions
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 ross.laza...@gmail.com wrote:
Sridhar,
Kindly try rerunning the
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 s...@unimelb.edu.au wrote:
Hi,
I am having trouble uploading files to
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
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:
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
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 toolshed
On Tue, Aug 20, 2013 at 8:34 PM, Greg Von Kuster g...@bx.psu.edu 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
On Tue, Aug 20, 2013 at 9:15 PM, Dave Bouvier d...@bx.psu.edu 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
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 h...@fmi.ch wrote:
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 head
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)
On Wed, Aug 21, 2013 at 10:54 AM, Peter Cock p.j.a.c...@googlemail.com wrote:
On Tue, Aug 20, 2013 at 9:15 PM, Dave Bouvier d...@bx.psu.edu 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
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 p.j.a.c...@googlemail.comwrote:
Hi
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
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
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 dannon.ba...@gmail.comwrote:
Hey Peter,
I've
On Wed, Aug 21, 2013 at 1:45 PM, Dave Bouvier d...@bx.psu.edu 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
On Wed, Aug 21, 2013 at 8:25 AM, Dannon Baker dannon.ba...@gmail.com
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
On Wed, Aug 21, 2013 at 9:10 AM, Peter Cock p.j.a.c...@googlemail.comwrote:
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
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 p.j.a.c...@googlemail.com wrote:
On Tue, Aug 20, 2013 at 8:34 PM, Greg Von Kuster g...@bx.psu.edu
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 g...@bx.psu.edu 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
Hello Bjoern,
On Aug 21, 2013, at 2:51 AM, Bjoern Gruening bjoern.gruen...@gmail.com 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'
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
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
n Wed, Aug 21, 2013 at 2:59 PM, Dannon Baker dannon.ba...@gmail.com 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,
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
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 name of your exported.ga file
When you do this, it will fix the
On Wed, Aug 21, 2013 at 4:30 PM, Greg Von Kuster g...@bx.psu.edu 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
On Mon, Aug 19, 2013 at 3:34 PM, Peter Cock p.j.a.c...@googlemail.com 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 jeremy.goe...@emory.edu wrote:
Do you think we
On Wed, Aug 21, 2013 at 5:40 PM, Peter Cock p.j.a.c...@googlemail.com wrote:
On Mon, Aug 19, 2013 at 3:34 PM, Peter Cock p.j.a.c...@googlemail.com 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,
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't
Hi Greg,
seems to work fine!
Hello Bjoern,
On Aug 21, 2013, at 2:51 AM, Bjoern Gruening bjoern.gruen...@gmail.com
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
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 bjoern.gruen...@gmail.com wrote:
Hi Greg,
seems to work fine!
Hello Bjoern,
On Aug 21, 2013, at 2:51 AM, Bjoern Gruening bjoern.gruen...@gmail.com
wrote:
Hi Greg,
a first test seems to work as expected for me, will
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 mydatatypes_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 thondeb...@me.com wrote:
Hi,
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 bjoern.gruen...@gmail.com wrote:
Hi Shane,
please find a new bismark version with an updated dependency on samtools
0.1.19 here:
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
Yep...$ bedtools --versionbedtools v2.17.0ThonOn Aug 21, 2013, at 01:40 PM, sam guerler aysam.guer...@gmail.com 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
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
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:
?xml version=1.0?
tool_dependency
package name=requests version=1.2.3
install version=1.0
actions
action
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
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