like the ampersand is. The following
download_by_url action should work:
action
type=download_by_urlhttp://downloads.sourceforge.net/project/transpose/transpose/transpose-2.0/2.0/transpose-2.0.zip/action
--Dave B.
On 09/30/2013 08:45 AM, Joachim Jacob | VIB | wrote:
Hi all,
Not fixed yet
Hi Ulf,
What I do:
1. make a history, doing the steps you want to do on one input file
2. create a workflow of that history
3. assemble all input files in one history
4. run the workflow and select the multiple input files to run the
workflow on.
5. Optionally: send the results to a new
Sorry, my answer doesn't fit your question. :-)
J
Joachim Jacob
Contact details: http://www.bits.vib.be/index.php/about/80-team
On 10/01/2013 03:08 PM, Joachim Jacob | VIB | wrote:
Hi Ulf,
What I do:
1. make a history, doing the steps you want to do on one input file
2. create a workflow
Hi all,
The download URL seems not to be accepted in tool_dependencies.xml. It
is an URL from sourceforge, the direct link to a package.
The error upon uploading the tool to my toolshed:
**
Metadata may have been defined for some items in revision
'5665a799775d'. Correct the
Hi Greg,
Sorry to dig up this unsolved thread from a few months back.
Recap of the bug: I have developed a small tool. I have put it in my
local Toolshed, and installed it. After applying some changes to the
tool, I 'hg push'ed the changes to my repository on my toolshed. I
uninstalled the
See attachment.
Joachim Jacob
Contact details: http://www.bits.vib.be/index.php/about/80-team
On 09/30/2013 02:15 PM, Peter Cock wrote:
On Mon, Sep 30, 2013 at 1:05 PM, Joachim Jacob | VIB |
joachim.ja...@vib.be wrote:
Hi Greg,
Sorry to dig up this unsolved thread from a few months back
://downloads.sourceforge.net/project/transpose/transpose/transpose-2.0/2.0/transpose-2.0.zip/action
--Dave B.
On 09/30/2013 08:45 AM, Joachim Jacob | VIB | wrote:
Hi all,
Not fixed yet. Somehow the download does not work: I have escaped the
ampersands and the hyphens. The download seems to have to proceed
from few posts here.
http://zfsonlinux.org/lists.html
cheers,
Simon
-Original Message-
From: galaxy-dev-boun...@lists.bx.psu.edu [mailto:galaxy-dev-
boun...@lists.bx.psu.edu] On Behalf Of Joachim Jacob | VIB |
Sent: Tuesday, 10 September 2013 10:29 p.m.
To: galaxy-dev@lists.bx.psu.edu
Hi Rui,
I should provide a 'sample metadata table', a tabular file with one
column the names of your samples, the other column the associated
metadata (e.g. type).
This is how I've done it in my DESeq2 wrapper. :-) Feel free to check
the interface at
require a search
step before creating a new repository to avoid accidental
duplication of effort? Or maybe a wiki page of wrappers
in progress?
(And maybe we should split this into a new thread)
Regards,
Peter
On Wed, Sep 11, 2013 at 8:59 AM, Joachim Jacob | VIB |
joachim.ja...@vib.be wrote
The latest code from the 'stable' branch of Galaxy is preferred. See the
news brief accompanying the update (release_2013.08.12) on
http://wiki.galaxyproject.org/DevNewsBriefs/2013_08_12
You need mercurial (http://mercurial.selenic.com/) for installing
Galaxy. Report bugs at
penalty. If you can
suffer the decreased space optimization, lzjb performs significantly better
than gzip. gzip-1 is a nice compromise between the default gzip level and
lzjb, as well.
--nate
On Sep 11, 2013, at 3:45 AM, Joachim Jacob | VIB | wrote:
Thank you all for the reactions.
Some details
OK, I would like to see that happen too :-)
I have been thinking about possible 'elegant' solutions to enable this
exporting. I am very enthousiastic about Bittorrent Sync, which could
perhaps be an efficient and secure way to export the histories
Hi all,
My issue: I have put a new version of a tool in our local toolshed (via
'hg push'). Now, going to the tool's page, still the old version of the
README is displayed. When browsing the repository, the new (last
uploaded) version is there. In addition, the tool's page show the latest
Hmm, now the tool's page is updated. Problem solved. Perhaps a browser
cache issue or something alike.
Joachim Jacob
Contact details: http://www.bits.vib.be/index.php/about/80-team
On 09/06/2013 10:22 AM, Joachim Jacob | VIB | wrote:
Hi all,
My issue: I have put a new version of a tool
Hi all,
Is it currently possible to export histories via the API? I have one
user who want to download and store her data. Total sizes of all her
histories combined is about ~700GB.
I think this is a typical API job: to list all her histories, start
'exporting to file' all of them, and
Hi all,
I have a problem that the mappings of an experiment suddenly don't show
up anymore in Trackster, only when I choose 'squish' as visualisation
format. 'Coverage' and 'dense' provide the expected output. So 'squish'
shows nothing. But 'Pack' shows only the names, without the bars.
Update: the 'dense' option does not work neither. So in summary: the
alignment can only be viewed in 'coverage' mode.
Thanks,
Joachim
Joachim Jacob
Contact details: http://www.bits.vib.be/index.php/about/80-team
On 09/05/2013 09:52 AM, Joachim Jacob | VIB | wrote:
Hi all,
I have a problem
Hi Adam,
I remembered having a hard time getting this to work. After it worked,
networkadmins decided to disallow ftp connections at our university due
to security concerns...
I do not remember the solution (...), but I can share my config files (I
am using apache instead of nginx):
This
Hi Peter,
I have used UGene before: it is a nice tool. I am not sure I have
understood your question. The easiest way to integrate your tool in
Galaxy, is that your tool can be driven by the command line (no GUI).
The tool and parameters should be configured by a tool config file, as
you
Hi all,
A Cheetah question: when I enter ; as a value in a text box of a tool
(stored in $exp), Cheetah prints this as X, and passed this string to
the tool.
How to disable this behaviour in Cheetah? I have tried to play with
#filter directives, but to no avail.
Thanks,
Joachim
--
Thanks both of you! Okay, so I was looking in the wrong direction. This
solved the issue.
Cheers,
Joachim
Joachim Jacob
Contact details: http://www.bits.vib.be/index.php/about/80-team
On 07/24/2013 11:13 AM, Björn Grüning wrote:
Hi Joachim,
try that one:
somebody of the
devteam grant me acces? Do I send the diff by email :-) ?
Cheers,
Joachim
Joachim Jacob
Contact details: http://www.bits.vib.be/index.php/about/80-team
On 07/24/2013 11:17 AM, Peter Cock wrote:
On Wed, Jul 24, 2013 at 9:40 AM, Joachim Jacob | VIB |
joachim.ja...@vib.be wrote:
Hi
Hmm, seems that collaborating on tools is kind of a burden... Three
places to notify this small change you say? (trello, galaxy-dev and
direct emailing to the authors.)
I have opted for Trello, card #1013
Cheers,
J
Joachim Jacob
Contact details: http://www.bits.vib.be/index.php/about/80-team
Oops, I was replying via theGalaxy Development List Archive
http://dev.list.galaxyproject.org/ interface, strange it has put the
reply off list...
So no functional test for my tool ( despite my enthousiasm :-) ), since
the repeat tags must be provided in the test.
Thanks,
Joachim.
Joachim
://www.bits.vib.be/index.php/about/80-team
On 07/16/2013 01:49 PM, Joachim Jacob | VIB | wrote:
Oops, I was replying via theGalaxy Development List Archive
http://dev.list.galaxyproject.org/ interface, strange it has put the
reply off list...
So no functional test for my tool ( despite my enthousiasm
I like your proposal. I don't think it is currently possible to add -
say - 5 repeat blocks at once. Feel free to add and describe your
suggested enhancement on Trello, so I can vote for it :-)
http://galaxyproject.org/trello
Cheers,
Joachim
Joachim Jacob
Contact details:
, Joachim Jacob | VIB | wrote:
Hi all,
I have developed a tool in our local Galaxy, and imported it in a
local toolshed. I next removed the 'dev' version of the tool in
Galaxy, and installed it now via het Tool Shed Manager.
I got an error that the dependencies could not be installed. If
figured
Hi all,
Before posting on Trello, perhaps someone can confirm that it is a bug:
1. In the admin menu, go to 'Manage installed tool shed repositories'
2. click on a tool that you have installed with dependencies (!)
3. In the top right 'repository actions', choose 'Manage tool dependencies'
4.
Hi all,
I have developed a tool in our local Galaxy, and imported it in a local
toolshed. I next removed the 'dev' version of the tool in Galaxy, and
installed it now via het Tool Shed Manager.
I got an error that the dependencies could not be installed. If figured
it out that it (needed to
Hi Daniel,
Make also sure you use correct firewall settings ('security groups') in
EC2. They are described the Galaxy wiki
(http://wiki.galaxyproject.org/CloudMan/AWS/GettingStarted?highlight=%28security%29|%28group%29),
but there are some small differences with the setting applied by
Dear all,
I updated to the latest Galaxy stable code, and updated the
datatypes_conf.xml.
Trackster displays an error after opening a saved view:
***
Error: The requested genome file
(/home/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/dm3.len) could not
be opened.
Hi Karen,
Can you first switch to the user under which Galaxy runs, and go to the
home directory of Galaxy: over there, run ./run.sh and watch which error
messages appear. This should give you more information. It is
recommended after a update to run Galaxy first like this.
Kind regards,
Hi all,
I am planning to launch a Galaxy Cloud Instance, to run for about one
month. But I believe I've read somewhere a new image of Galaxy on AWS is
being prepared right now.
Can somebody update me on the status? Perhaps it is smart to wait a few
days with launching through CloudLaunch
be due to an issue that
was fixed between 9320:47ddf167c9f1 and the current stable branch. I
would recommend updating to the most recent stable branch of
galaxy-central.
--Dave B.
On 5/29/13 09:30:37.000, Joachim Jacob | VIB | wrote:
Strange. When I just wget that link in a terminal, do
May 2013 11:52:54 AM CEST, Peter Cock wrote:
On Thu, May 30, 2013 at 10:30 AM, Joachim Jacob | VIB |
joachim.ja...@vib.be wrote:
Unfortunately, updating to the latest code (9320:47ddf167c9f1) does not
solve the problem.
In Trello, this card #584 was posted, mentioning installing compiled
binaries
file, while Safari displays it. This is the cause of the problem. Is
there a different URL to download blat that actually downloads it as an archive
os some kind?
Greg Von Kuster
On May 29, 2013, at 6:54 AM, Joachim Jacob | VIB | wrote:
Hi all,
I am building a wrapper around BLAT
it as an archive
os some kind?
Greg Von Kuster
On May 29, 2013, at 6:54 AM, Joachim Jacob | VIB | wrote:
Hi all,
I am building a wrapper around BLAT, and have put it locally in a toolshed.
However, the automatic installation of dependencies fails:
*
Tool dependency
changesets but they won't be activated when you update)
On Thu, May 16, 2013 at 11:08 AM, Joachim Jacob | VIB |
joachim.ja...@vib.be mailto:joachim.ja...@vib.be wrote:
OK. So I believe I can wait for the next stable release then. I
assume a do not want to go the default branch
Hi all,
I have fired up an cloud instance of Galaxy, 2 persistent nodes,
scalable up to 10. I have updated the code to the latest stable, after
issues with not being able to select multiple input for workflows (more
background:
It is most likely due to the cluster configuration, since on our
non-cluster production machine doesn't have this behaviour.
Cheers,
J
Joachim Jacob
Contact details: http://www.bits.vib.be/index.php/about/80-team
On 05/17/2013 10:16 AM, Joachim Jacob | VIB | wrote:
Hi all,
I have fired up
Hi all,
I have tried to fire up an Cloud instance of Galaxy following the wiki
page: http://wiki.galaxyproject.org/CloudMan
However, two attempts failed (Cloudman interface did not come up - I
could SSH into the machine). Next, I have tried the CloudLaunch
interface (added the link to the
Hi all,
I just found out that I cannot select multiple inputs in workflows
anymore in our local Galaxy. This option used to work on these workflows
in the past. I only get now a dropdown box, without the little icon at
the top of the input list to select multiple inputs.
I am a little
05:01 PM, Dannon Baker wrote:
Your instance isn't quite up-to-date enough for the fix -- it's around
9549:47ddf167c9f1 -central / 9452:94caae7433a7 grafted in -stable.
On Thu, May 16, 2013 at 10:56 AM, Joachim Jacob | VIB |
joachim.ja...@vib.be mailto:joachim.ja...@vib.be wrote:
Running
run_reports.sh dies silently.
Its last will in reports_webapp.log states:
Traceback (most recent call last):
File ./scripts/paster.py, line 33, in module
serve.run()
File /home/galaxy/galaxy-dist/lib/galaxy/util/pastescript/serve.py,
line 1056, in run
invoke(command, command_name,
Already reported in Trello
https://trello.com/c/o0S3klAF
Thanks for the fix!
Joachim Jacob
Rijvisschestraat 120, 9052 Zwijnaarde
Tel: +32 9 244.66.34
Bioinformatics Training and Services (BITS)
http://www.bits.vib.be
@bitsatvib
On 05/15/2013 03:19 PM, Joachim Jacob | VIB | wrote
Hi all,
Stupidly enough, I installed a tool shed repo under 'root' of the
toolbox. Yes, it was EMBOSS5.0 (btw, installation went flawless!).
1. From the admin menu, I choose to unactivate the repo (manage tool
shed repo's)
2. From the admin menu, I reinstalled the tool shed from Main Tool
,
Joachim
Joachim Jacob
Rijvisschestraat 120, 9052 Zwijnaarde
Tel: +32 9 244.66.34
Bioinformatics Training and Services (BITS)
http://www.bits.vib.be
@bitsatvib
On 03/28/2013 03:21 PM, Joachim Jacob | VIB | wrote:
OK, it seems to be a proxy error.
When the proxy does not receive data from the server
Hi Rob,
Indeed, I had/have some difficulties with setting temporary
directories. The problem was that FTP uploaded data was first copied to
TMPDIR prior to being put in the database directory.
My solution: I extended the /tmp partition to several GB's, by mounting
a bigger device over it.
Rijvisschestraat 120, 9052 Zwijnaarde
Tel: +32 9 244.66.34
Bioinformatics Training and Services (BITS)
http://www.bits.vib.be
@bitsatvib
On Tue 26 Mar 2013 03:45:43 PM CET, Assaf Gordon wrote:
Hello Joachim,
Joachim Jacob | VIB | wrote, On 03/26/2013 10:01 AM:
abrt was filling the root directory
and Services (BITS)
http://www.bits.vib.be
@bitsatvib
On 03/28/2013 02:58 PM, Joachim Jacob | VIB | wrote:
Hi Assaf,
After all, the problem appears not to be total size of the history,
but the size of the individual datasets.
Now, histories which contain big datasets (1GB) imported from Data
Rijvisschestraat 120, 9052 Zwijnaarde
Tel: +32 9 244.66.34
Bioinformatics Training and Services (BITS)
http://www.bits.vib.be
@bitsatvib
On 03/25/2013 05:18 PM, Assaf Gordon wrote:
Hello Joachim,
Couple of things to check:
On Mar 25, 2013, at 10:01 AM, Joachim Jacob | VIB | wrote:
Hi
OK (I see now I have posted twice the same error from the log - silly of
me, sorry).
First this: yes, the permissions in the data library are set so that
only I and one other person can access the data library (set by one
sharing role for both of us)
The entries in the job table related to
, 2013, at 9:47 AM, Joachim Jacob | VIB | wrote:
Hi all,
Since the last updata of Galaxy, I was not able anymore to view newly added
tracks to existing or newly created visualisations.
In the webhandler, I have traced down this error:
193.191.128.2 - - [14/Mar/2013:11:02:13 +0200] GET
/api
Hi all,
Exporting histories fails on our server: Reason: *Error reading from
remote server.
*When looking at the logs and the system:
tail /var/log/messages
Mar 19 15:52:47 galaxy abrt[25605]: Write error: No space left on device
Mar 19 15:52:49 galaxy abrt[25605]: Error writing
Hello,
I got an error on our local Galaxy using bam-to-sam. The BAM file is a
result of a Tophat version 1 run.
The error
Error sorting alignments from (/mnt/galaxydb/files/006/dataset_6733.dat),
error
An error occurred with this dataset:/Samtools Version: 0.1.18 (r982:295)
Error sorting
Hi all,
I make increasingly use of the Galaxy Reports tool. Until recently I
started it and shut it down again. Now I run it continuously. I have
noticed that a lot of the jobs listed in 'unfinished jobs' are actually
finished.
Any hint on how to clean up the database? Which table?
Hi all,
Installing htseq-count with dependencies fails on my system: htseq-count
installs four dependencies (numpy, picard, samtools, htseq) , of which
one fails (htseq), strangely enough.
The error is:
error: can't create or remove files in install directory
The following error occurred
Hi Hans,
OK, thanks: diving into the job table. Your question: why you consider
the job as being finished, and Galaxy thinks the job is still running
is the core issue that I need to find out. None of those jobs have
entries in the ps list.
Currently, I think that those jobs are still
Hi Lance,
[apologies for directly emailing to you and not through the galaxy-dev
list. I will post it on the dev list later on]
I am trying to install htseq-count, but it fails during the dependency
installation of htseq.
The error I get is:
error: can't create or remove files in install
Coraor wrote:
On Feb 11, 2013, at 7:48 AM, Joachim Jacob |VIB| wrote:
Hello all,
After a *reboot* of our Galaxy server, the environment variables are set
correctly.
However, after *restarting* the Galaxy process on a running server, by logging in as
Galaxy and running the init script on CentOS
Hi all,
Running ~/galaxy-dist/run_reports.sh brings up the Galaxy Reports
interface on poort 9001.
When clicking on 'Jobs per user' - picking a user - picking a month -
and clicking on 'State' in the bar at the top, clears the screen.
Thanks,
Joachim
--
Joachim Jacob
Rijvisschestraat
Hi Hagai,
Actually, using a workflow, you are able to select multiple input files,
and let the workflow run separately on all input files.
I would proceed by creating a data library for all your fastq files,
which you can upload via FTP, or via a system directory.
You can use a sample of
them to one.
On Tue, Feb 12, 2013 at 5:20 PM, Joachim Jacob |VIB|
joachim.ja...@vib.be mailto:joachim.ja...@vib.be wrote:
Hi Hagai,
Actually, using a workflow, you are able to select multiple input
files, and let the workflow run separately on all input files.
I would
://trello.com/card/show-roles-associated-with-data-libraries/506338ce32ae458f6d15e4b3/229
cheers
Joachim
Joachim Jacob
Rijvisschestraat 120, 9052 Zwijnaarde
Tel: +32 9 244.66.34
Bioinformatics Training and Services (BITS)
http://www.bits.vib.be
@bitsatvib
On 02/08/2013 04:29 PM, Joachim Jacob |VIB
Hello all,
After a *reboot* of our Galaxy server, the environment variables are set
correctly.
However, after *restarting* the Galaxy process on a running server, by
logging in as Galaxy and running the init script on CentOS as service
galaxyd restart, the environment variables seems to be
Bioinformatics Training and Services (BITS)
http://www.bits.vib.be
@bitsatvib
On 02/06/2013 12:08 PM, Peter Cock wrote:
On Wed, Feb 6, 2013 at 11:01 AM, Joachim Jacob |VIB|
joachim.ja...@vib.be wrote:
In risk of getting a discussion here: a long standing enhancement request is
to highlight the current
Hi all,
The data library I have created is only showing up partially.
I have made a data libray, via het Admin menu, with one folder in it. I
changed permissions, because I wanted it only to be visible to me. That
worked fine. Next I created plenty more folders in that data library.
Now,
In risk of getting a discussion here: a long standing enhancement
request is to highlight the current history item one is currently viewing.
Situation sketch: I often hide the history items panel to study results
(displayed in middle panel) into detail, and when I bring the history
item panel
On 02/06/2013 12:08 PM, Peter Cock wrote:
On Wed, Feb 6, 2013 at 11:01 AM, Joachim Jacob |VIB|
joachim.ja...@vib.be wrote:
In risk of getting a discussion here: a long standing enhancement request is
to highlight the current history item one is currently viewing.
Situation sketch: I often hide
Hi,
In the 'Admin' menu, reloading a tool's xml file does not update the
tool's interface.
Thanks for any assistance,
Joachim
--
Joachim Jacob
Rijvisschestraat 120, 9052 Zwijnaarde
Tel: +32 9 244.66.34
Bioinformatics Training and Services (BITS)
http://www.bits.vib.be
@bitsatvib
Unfortunately, no.
Joachim Jacob
Rijvisschestraat 120, 9052 Zwijnaarde
Tel: +32 9 244.66.34
Bioinformatics Training and Services (BITS)
http://www.bits.vib.be
@bitsatvib
On 01/30/2013 10:56 AM, Peter Cock wrote:
On Wed, Jan 30, 2013 at 9:54 AM, Joachim Jacob |VIB|
joachim.ja...@vib.be wrote
Thanks. Yes, I am running multiple webworkers. OK, nice to know what
causes this.
The toolshed option will be considered.
Joachim.
Joachim Jacob
Rijvisschestraat 120, 9052 Zwijnaarde
Tel: +32 9 244.66.34
Bioinformatics Training and Services (BITS)
http://www.bits.vib.be
@bitsatvib
On
Hi,
I have a similar - but not identical issue. The history panel is not
being updated: I have to restart Galaxy to see the updated panel.
It appears only to happen after an error relating to the history API of
Galaxy (it's a popup error, and I have closed it).
My apache config (thanks
Hi all,
After updating to the latest Galaxy dist-release (and moving our server
to a new location - but this can not be the reason I think), the status
of the jobs are not being updated. The box in the history stays grey.
After restarting Galaxy or the server, the correct status of the job
Hi,
Has the devteam a schedule of the order of the tools they plan to
migrate to the tool shed?
Thanks,
Joachim.
--
Joachim Jacob
Rijvisschestraat 120, 9052 Zwijnaarde
Tel: +32 9 244.66.34
Bioinformatics Training and Services (BITS)
http://www.bits.vib.be
@bitsatvib
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