Hi,
This issue is appearing again, after the upgrade of our Galaxy on October the
23rdanyone experiencing the same?
Thanks,
Pieter.
From: galaxy-dev-boun...@lists.bx.psu.edu
[mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Lukasse, Pieter
Sent: vrijdag 4 april 2014 10:59
I am also having problems when using the option Search and browse toolsheds !
[cid:image001.jpg@01D0040B.AF3C7270]
-Original Message-
From: galaxy-dev-boun...@lists.bx.psu.edu
[mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Peter Briggs
Sent: woensdag 19 november 2014
]
Sent: woensdag 12 november 2014 17:18
To: Lukasse, Pieter
Cc: galaxy-dev@lists.bx.psu.edu; Dave Bouvier
Subject: Re: [galaxy-dev] Tool shed environment dependency - HOW TO do this?
Yes, this is correct. Do you really need to compile it by yourself? This is
really a pain, I tried it during the R2
Ah, great! Please let me know once I can use it.
Thanks,
Pieter
-Original Message-
From: Dave Bouvier [mailto:d...@bx.psu.edu]
Sent: woensdag 12 november 2014 17:27
To: Lukasse, Pieter; 'bjoern.gruen...@googlemail.com'
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] Tool shed
To: galaxy-dev@lists.bx.psu.edu; Lukasse, Pieter; Dave Bouvier
Subject: Re: [galaxy-dev] Tool shed environment dependency - HOW TO do this?
Hi Pieter,
Am 30.10.2014 um 11:15 schrieb Lukasse, Pieter:
Hi,
I have a Bioconductor package which depends on R 3.1.1 , so I think I cannot
use
this from within my
sniff method?
Thanks,
Pieter
From: Ross [mailto:ross.laza...@gmail.com]
Sent: donderdag 30 oktober 2014 11:20
To: Lukasse, Pieter
Cc: John Chilton; galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] strange issue with .RData files
Rdata is binary and serialises R objects so
Formats).
Regards,
Pieter.
From: galaxy-dev-boun...@lists.bx.psu.edu
[mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Lukasse, Pieter
Sent: donderdag 6 november 2014 10:25
To: 'Ross'
Cc: John Chilton; galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] strange issue with .RData files
-Original Message-
From: galaxy-dev-boun...@lists.bx.psu.edu
[mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Lukasse, Pieter
Sent: donderdag 6 november 2014 10:02
To: 'Björn Grüning'; galaxy-dev@lists.bx.psu.edu; Dave Bouvier
Subject: Re: [galaxy-dev] Tool shed environment
if someone
already has thought about such a rule, specifically for RData.
Thanks,
Pieter.
-Original Message-
From: John Chilton [mailto:jmchil...@gmail.com]
Sent: donderdag 23 oktober 2014 3:02
To: Lukasse, Pieter
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] strange issue
Hi,
I have a Bioconductor package which depends on R 3.1.1 , so I think I cannot
use the setup_r_environment trick.
I already got a tool_dependency.xml working that installs R 3.1.1 and the
necessary Bioconductor packages using bioclite method (see attachment). Now my
question is:
*
it finally works!
Thanks again,
Pieter.
-Original Message-
From: Björn Grüning [mailto:bjoern.gruen...@gmail.com]
Sent: vrijdag 24 oktober 2014 16:23
To: Lukasse, Pieter; galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] Dependencies not working on toolshed?
Pieter,
please try to add
Hi ,
I am trying to get a dependency to work in practice (when running a tool after
the installation). But I keep getting the following message when running the
tool:
[sshexec] galaxy.tools.deps DEBUG 2014-10-24 16:04:15,514 Building dependency
shell command for dependency 'R_bioc_metams'
I can confirm it worked on my server as well (recent release)
From: galaxy-dev-boun...@lists.bx.psu.edu [galaxy-dev-boun...@lists.bx.psu.edu]
on behalf of John Chilton [jmchil...@gmail.com]
Sent: Friday, October 24, 2014 3:57 PM
To: James Mullan
Cc:
Struggling with this now...you have my vote!
From: galaxy-dev-boun...@lists.bx.psu.edu
[mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Ross
Sent: donderdag 24 januari 2013 1:04
To: Dan Tenenbaum
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] filtering a param of type 'data'
Hi,
When I upload any .RData file to my Galaxy server it seems to be
unpacking/changing it. The resulting file in my history is different and around
2x larger than the uploaded file. The tool that needs to use it also aborts
with an error due to this erroneous file.
What are the workarounds?
,
Pieter.
-Original Message-
From: John Chilton [mailto:jmchil...@gmail.com]
Sent: donderdag 9 oktober 2014 15:45
To: Lukasse, Pieter
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] HOWTO share tool parameter settings?
How would this be different then the third option you listed
!
Best regards,
Pieter.
-Original Message-
From: John Chilton [mailto:jmchil...@gmail.com]
Sent: donderdag 9 oktober 2014 15:45
To: Lukasse, Pieter
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] HOWTO share tool parameter settings?
How would this be different then the third
Hi,
Do we have a way (or plans) for sharing tool parameter settings in Galaxy?
I know the following workarounds :
* Share a history with all users: so users can import your step and do
rerun to run on their own file with your settings
* Wrap the step in a workflow with all
Hi Carl,
Any news on this?
Thanks,
Pieter.
From: galaxy-dev-boun...@lists.bx.psu.edu
[mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Carl Eberhard
Sent: dinsdag 29 juli 2014 16:35
To: Sajdak, Doris
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] IE 11 issues
That's what I
Hi Dannon,
Thanks for the info. We will test it on our server. Our last update seems to be
from June 5th.
Best regards,
Pieter.
From: Dannon Baker [mailto:dannon.ba...@gmail.com]
Sent: vrijdag 19 september 2014 12:29
To: Lukasse, Pieter
Cc: Carl Eberhard; Sajdak, Doris; galaxy-dev
. I tend to ignore
other messages or temporary(?)hiccups in the installation process web page.
Regards,
Pieter.
From: melissa.s.cl...@gmail.com [mailto:melissa.s.cl...@gmail.com] On Behalf Of
Melissa Cline
Sent: woensdag 3 september 2014 3:23
To: Dave Bouvier
Cc: Lukasse, Pieter; Peter Cock
Hi Melissa,
See also
https://toolshed.g2.bx.psu.edu/view/pieterlukasse/prims_masscomb
or
https://toolshed.g2.bx.psu.edu/view/pieterlukasse/prims_proteomics
Regards,
Pieter.
-Original Message-
From: galaxy-dev-boun...@lists.bx.psu.edu
[mailto:galaxy-dev-boun...@lists.bx.psu.edu] On
that is now planned/going
on(?) for some time on the user interface?
Regards,
Pieter.
-Original Message-
From: Peter Cock [mailto:p.j.a.c...@googlemail.com]
Sent: zaterdag 30 augustus 2014 0:58
To: Lukasse, Pieter
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] when else
Hm...and now I’m completely stuck because apparently a conditional cannot be
set at runtime in a workflow...? Ideas anyone?
Thanks,
Pieter.
From: galaxy-dev-boun...@lists.bx.psu.edu
[mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Lukasse, Pieter
Sent: zaterdag 30 augustus 2014 14
in
my select box. There is no when else option?
Thanks,
Pieter
From: galaxy-dev-boun...@lists.bx.psu.edu
[mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Lukasse, Pieter
Sent: woensdag 27 augustus 2014 22:37
To: galaxy-dev@lists.bx.psu.edu
Subject: [galaxy-dev] refresh_on_change
Hi,
I'm trying to get a wrapper from someone else working and I found this
refresh_on_change attribute in his select boxes which are filled using the
dynamic_options feature:
param name=col_type type=select label=Select column type
refresh_on_change=true
display=radio
Hi Dannon,
I'm facing the same problem now. Could you help me with the steps to delete the
migrate_tmp table manually? I'm trying to use sqlite from command line but get
the following error:
Unable to open database universe.sqlite: file is encrypted or is not a
database
Thanks and regards,
Hi Dannon,
Thanks, this helped.
Just for the record: I did find a small typo in my mail and in your script :
should be migration_tmp instead of migrate_tmp;)
Best regards,
Pieter.
From: Dannon Baker [mailto:dannon.ba...@gmail.com]
Sent: dinsdag 22 april 2014 14:59
To: Lukasse, Pieter
Cc
Hi Alex, all
FYI - I've added the card to https://trello.com/c/ro8knsaa some time ago. Can
you please vote for it?
Thanks,
Pieter.
From: Bossers, Alex
Sent: dinsdag 25 maart 2014 16:52
To: Lukasse, Pieter
Cc: galaxy-dev@lists.bx.psu.edu
Subject: RE: [galaxy-dev] Strange issue with datatypes
Hi,
Apparently a new datatypes bug has been introduced in the Galaxy version of
last week:
I have a tool that generates a csv file. Tool configuration is like this:
outputs
data name=simOut format=msclust.csv label=${tool.name} on ${on_string}
- SIM file/
The datatypes has this entry:
...@lists.bx.psu.edu] On Behalf Of Lukasse, Pieter
Sent: donderdag 30 januari 2014 11:10
To: galaxy-dev@lists.bx.psu.edu
Subject: [galaxy-dev] Question on storage configuration for Galaxy datasets
Hi ,
We would the location of the datasets our Galaxy stores to be determined
dynamically based on a set of rules
Hi ,
We would the location of the datasets our Galaxy stores to be determined
dynamically based on a set of rules. For example: for a specific role we would
like a datasets to be stored in a folder /storage/no_backup and for another
role this should be /storage/with_backup
Is there currently
Hi,
I would like specify a filter based on a role. Does someone know how to do
this? I already have an example on how to do this based on user id (found at
https://wiki.galaxyproject.org/UserDefinedToolboxFilters#For_Administrators)
but now I would like to filter out menu items in case users
else:
# return true for any other tool
return True
From: galaxy-dev-boun...@lists.bx.psu.edu
[mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Lukasse, Pieter
Sent: donderdag 30 januari 2014 14:25
To: galaxy-dev@lists.bx.psu.edu
Subject: [galaxy-dev] Toolbox filtering
in the UI (e.g. when
clicking on one of the repositories again in the list repositories I own).
Regards,
Pieter.
From: Greg Von Kuster [mailto:g...@bx.psu.edu]
Sent: maandag 30 december 2013 16:39
To: Lukasse, Pieter
Cc: galaxy-...@bx.psu.edu
Subject: Re: repository metadata reset not always
Hi Greg,
I found an issue in Toolshed, not sure if it has been reported before.
Steps:
1-Make a repository and add a tool .xml and a README file
2-Reset metadata and check if all information appears in the toolshed UI
3-Now delete the README file from the hg repository
4-
[mailto:p.j.a.c...@googlemail.com]
Sent: woensdag 18 december 2013 17:36
To: Lukasse, Pieter
Cc: Galaxy Dev
Subject: Re: New Galaxy won't start, SQLite (OperationalError) database is
locked
On Wed, Dec 18, 2013 at 12:51 PM, Lukasse, Pieter
pieter.luka...@wur.nlmailto:pieter.luka...@wur.nl wrote:
Hi
Hi Peter,
Thanks for reporting this. I am now facing the same error, but I don't get
it For example: normally it appears when I try to change something in the
DB (e.g. adding a new history), but then suddenly I managed to create one new
history itemand now it is occurring again. It
Hi Peter,
I know that ;) Still I am curious about the possible solution. Any ideas?
Regards,
Pieter.
From: Peter Cock [mailto:p.j.a.c...@googlemail.com]
Sent: woensdag 18 december 2013 13:31
To: Lukasse, Pieter
Cc: Galaxy Dev
Subject: Re: New Galaxy won't start, SQLite (OperationalError
Hi Jeremy, Anna,
I'm having a similar problem here as well. I would like to get a history from
one Galaxy server to another and I followed the export and import steps. I even
did a wget at the destination Galaxy server to check whether it could download
the tar.gz file and this worked. When
[mailto:dannon.ba...@gmail.com]
Sent: maandag 4 november 2013 13:42
To: Lukasse, Pieter
Cc: galaxy-...@bx.psu.edu
Subject: Re: [galaxy-dev] Supporting file sets for running a tool with multiple
input files
Hi Pieter,
We've worked out what we think is the right way to solve this for Galaxy and
expect work
Hi,
Is there any news regarding support for the following scenario in Galaxy:
- User has N files which he would like to process with a Galaxy tool using
the same parameters
- User uploads a (.tar or .zip ?) file to Galaxy and selects this as the
input file for the tool
- Tool
to run some more detailed
validations?
Thanks,
Pieter.
-Original Message-
From: Greg Von Kuster [mailto:g...@bx.psu.edu]
Sent: dinsdag 29 oktober 2013 13:29
To: Lukasse, Pieter
Cc: galaxy-...@bx.psu.edu Dev
Subject: Re: [galaxy-dev] Tool refuses to appear in Toolshed package contents
Hi Bjoern,
Indeed resetting the metadata solved the problem. Thanks!
Best regards,
Pieter.
-Original Message-
From: Bjoern Gruening [mailto:bjoern.gruen...@gmail.com]
Sent: woensdag 30 oktober 2013 15:16
To: Lukasse, Pieter
Cc: Greg Von Kuster (g...@bx.psu.edu); galaxy-...@bx.psu.edu
in the toolshed
package. Are there .xsd files I can check these files against?
Thanks and regards,
Pieter.
From: Greg Von Kuster [g...@bx.psu.edu]
Sent: Friday, October 25, 2013 3:57 PM
To: Lukasse, Pieter
Cc: 'Peter Cock'; galaxy-...@bx.psu.edu
Subject: Re
: donderdag 24 oktober 2013 17:29
To: Lukasse, Pieter
Cc: 'Peter Cock'; galaxy-...@bx.psu.edu
Subject: Re: [galaxy-dev] Tool refuses to appear in Toolshed package contents
Hello Pieter,
There are 2 different issues in 2 of your xml files that make them invalid XML.
1. In your tool_dependencies.xml
]
Sent: vrijdag 25 oktober 2013 15:49
To: Lukasse, Pieter
Cc: Greg Von Kuster; galaxy-...@bx.psu.edu
Subject: Re: [galaxy-dev] Tool refuses to appear in Toolshed package contents
On Fri, Oct 25, 2013 at 2:26 PM, Lukasse, Pieter pieter.luka...@wur.nl wrote:
Hi Greg,
Thanks for the tips
Hi Greg,
Yes, we have an older Mercurial installation (2.0.2 !) . We will try a newer
version.
Thanks!
Pieter.
From: Greg Von Kuster [mailto:g...@bx.psu.edu]
Sent: vrijdag 13 september 2013 13:56
To: Lukasse, Pieter
Cc: Kuijt, Eric; 'galaxy-...@bx.psu.edu'
Subject: Re: problems with toolshed
Hi Greg,
When updating the version number of a tool I noticed that, as expected, both
the old version and the new version of the tool become available in the Galaxy
environment. What I did not expect is that the new version resulted in a new
entry in the menu bar (see screenshot):
revert back to the previous
revision after noticing that this update has an unexpected bug
Regards,
Pieter.
-Original Message-
From: Bjoern Gruening [mailto:bjoern.gruen...@gmail.com]
Sent: donderdag 12 september 2013 13:15
To: Lukasse, Pieter
Cc: 'Greg Von Kuster'; Galaxy Dev
/napq_overview.png
so the variable is not being replaced by the value of the path...is this a
known issue?
Regards,
Pieter.
-Original Message-
From: Bjoern Gruening [mailto:bjoern.gruen...@gmail.com]
Sent: donderdag 12 september 2013 14:31
To: Lukasse, Pieter
Cc: 'Greg Von Kuster'; Galaxy Dev
Hi guys,
We discovered that the problem is at our apache configuration side...working on
it now... ;)
Regards,
Pieter.
-Original Message-
From: galaxy-dev-boun...@lists.bx.psu.edu
[mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Lukasse, Pieter
Sent: donderdag 12 september
Development News
Brief but no background information was given
Thanks and regards,
Pieter.
-Original Message-
From: galaxy-dev-boun...@lists.bx.psu.edu
[mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Lukasse, Pieter
Sent: donderdag 18 oktober 2012 9:19
To: 'joachim.ja...@vib.be
Can anyone give some more information about this?
Thanks,
Pieter.
-Original Message-
From: Joachim Jacob [mailto:joachim.ja...@vib.be]
Sent: donderdag 15 november 2012 9:17
To: Lukasse, Pieter
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] Display of HTML type broken in new
Hi,
Is it possible to do validation of input fields depending on the value of OTHER
input fields?
Example 1
If field A is filled, then field B also should be filled.
Example 2
Field B should be field A
etc
Pieter Lukasse
Wageningen UR, Plant Research International
Departments of
Thanks Joachim, that solved the problem!
-Original Message-
From: Joachim Jacob [mailto:joachim.ja...@vib.be]
Sent: woensdag 17 oktober 2012 10:47
To: Lukasse, Pieter
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] Display of HTML type broken in new Galaxy ?
Hi,
Make sure
Hi,
I noticed that in the new Galaxy version the preview of HTML files seems to be
broken. When I try to preview a HTML file generated by a tool, it displays a
HTML that has all style stripped off. So the HTML display is in fact changing
the generated HTML before displaying it.
Has anyone
Hi,
Is there a way to use validator or perhaps filter options to avoid the
selection of the same dataset twice in different parameters of a tool.
E.g. a tool has 2 data type parameters of the same type, but it should not be
possible for the user to set both parameters to the same dataset. So
Hi,
Is there any way to map an input field from one tool to the input field of
another tool in a workflow?
E.g. let's say tool A has an input field X which tool B also has. If we use
both tool A and B in the same workflow, then we would like to let the user fill
in field X only once in tool A
Hi Greg,
I made a tool for Galaxy which produces a normal XML output file and next to
that it also produces a HTML report with some quick summarized details for the
user.
I could solve this by using 2 output files, but I don't want to keep the
history as concise as possible. To I found the
Hi,
Is there more documentation on the topic of custom display applications?
I only found
http://wiki.g2.bx.psu.edu/Admin/Tools/External%20Display%20Applications%20Tutorial
which has a few examples, but these are incomplete. For example, they use some
variables like ${BASE_URL} and
Hi,
I have some questions about adding new custom tools to my Galaxy instance:
1-How can I reuse workflows?
a.Should I wrap a workflow as a tool?
b.Or can I just add a custom workflow as a workflow step in another
workflow?
2-I noticed that option 1.b above seems to copy
[mailto:p.j.a.c...@googlemail.com]
Sent: donderdag 13 oktober 2011 12:34
To: Lukasse, Pieter
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] Questions about reusing workflows
Hi Pieter,
You cannot currently embed on workflow within another, although that has been
suggested as a nice extension
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