Hi,
Thanks a lot for the answer. But I'm afraid that detail panel does not give
me the path to the dataset. Have you encountered this problem before?
Nilaksha
On Thu, Apr 3, 2014 at 12:26 PM, Hans-Rudolf Hotz h...@fmi.ch wrote:
Hi Nilaksha
Use the ! icon (View details) to get the full path
Hi,
Did anyone faced this issue ?. I struck here. Please suggest me.
Thanks,
JanakiRam
On Wed, Apr 2, 2014 at 3:10 PM, Janaki Rama Rao Gollapudi
janakiram.gollap...@india.semanticbits.com wrote:
Hi,
I have implemented a custom tool called 'barcode-parse' and uploaded this
custom to into
This might be due to different version of Galaxy. Is the Job
Command-Line listed? - Depending on the tool, you might find the path
there.
Hans-Rudolf
:Do you have the will also find the path in the job command
On 04/03/2014 09:03 AM, Nilaksha Neththikumara wrote:
Hi,
Thanks a lot for the
Hi Nilaksha,
unfortunately you only see the path if you are an admin. Can you get
admin right? Otherwise, maybe downloading via the API would an alternative.
Cheers,
Bjoern
Am 03.04.2014 09:03, schrieb Nilaksha Neththikumara:
Hi,
Thanks a lot for the answer. But I'm afraid that detail panel
No, It's not. Btw do you think this problem is causing due to the capacity
of the dataset.? have you experienced this before?
Thanking you,
Nilaksha
On Thu, Apr 3, 2014 at 12:43 PM, Hans-Rudolf Hotz h...@fmi.ch wrote:
This might be due to different version of Galaxy. Is the Job
Command-Line
This all seems to be fine, can you send me a tarball with both
repositories ...
Thanks,
Bjoern
Am 03.04.2014 09:05, schrieb Janaki Rama Rao Gollapudi:
Hi,
Did anyone faced this issue ?. I struck here. Please suggest me.
Thanks,
JanakiRam
On Wed, Apr 2, 2014 at 3:10 PM, Janaki Rama Rao
Hi,
Thanks for quick reply. Please find the attached .tar file of both the
repositories.
Thanks,
JanakiRam
On Thu, Apr 3, 2014 at 12:45 PM, Björn Grüning bjoern.gruen...@gmail.comwrote:
This all seems to be fine, can you send me a tarball with both
repositories ...
Thanks,
Bjoern
Am
Hi Bjoern,
I also exported both the repositories from local toolshed. Please find the
attached files.
Thanks,
JanakiRam
On Thu, Apr 3, 2014 at 12:50 PM, Janaki Rama Rao Gollapudi
janakiram.gollap...@india.semanticbits.com wrote:
Hi,
Thanks for quick reply. Please find the attached .tar
Hi Brad
I have a hacky shell script that I use to do rolling restarts of our
local server:
https://github.com/pjbriggs/galaxy-admin-utils/blob/master/rolling-restart.sh
Generally it works okay here but you would have to check how it fits
into your local setup. I can't guarantee that it's
Thanks for the tip. I got admin privileges by creating an admin account,
now I can see the full path. So that it basically means, we can't download
larger files directly through the browser window but only from tracing the
path and copying the file to some other place. Isn't it :)
On Thu, Apr
Hi Janaki,
can you try to remove this prior_installation_required completely?
Also why do you need a repository dependency, I think that is not needed or?
Cheers,
Bjoern
Am 03.04.2014 09:30, schrieb Janaki Rama Rao Gollapudi:
Hi Bjoern,
I also exported both the repositories from local
Hi Bjoern,
Please see my comments inline.
On Thu, Apr 3, 2014 at 3:14 PM, Björn Grüning bjoern.gruen...@gmail.comwrote:
Hi Janaki,
can you try to remove this prior_installation_required completely?
I didn't added 'prior_installation_required' in the
repository_dependencies.xml(as
Hi,
I just tested it in the test-toolshed and for me
'prior_installation_required' is not inserted. Which Galaxy version do
you use? Please note, that I'm not sure if that is really causing the
trouble you have seen.
If you remove the repository dependency everything is working as expected?
Am 03.04.2014 04:34, schrieb Wang, Xiaofei:
After SnpEff Databases Execute you still need to pick genome of
interest and run SnpEff Download. SnpEff Databases just downloads a
list of available genomes.
You mean SnpEff Download under Data Manager? But, there is no response when I
click on
Hi,
I am using latest checkout from
https://bitbucket.org/galaxy/galaxy-dist/(Just now I also updated my
local galaxy code base). Yes, without
repository dependency everything working fine.
Thanks,
JanakiRam
On Thu, Apr 3, 2014 at 3:39 PM, Björn Grüning bjoern.gruen...@gmail.comwrote:
Hi,
Hi JanakiRam,
I will take Greg into CC. He is the main Tool Shed developer, maybe we
spotted a bug in populating prior_installation_required in
repository_dependencies.xml file. He probably knows if that is supposed
to work.
Greg, to summarize our findings. It seems that if JanakiRam
Hi,
Bjoern, Yes the summary looks correct.
Greg, I have added tool_dependencies.xml to the same custom tool and
installed it successfully in my local galaxy. But If I add
repository_dependencies.xml to my custom tool and try to install the tool,
then galaxy showing an error message that the
Yes, if that is the behavior, that is definitely a bug. I'll take a look and
get back to you on this.
Thanks!
On Apr 3, 2014, at 7:35 AM, Björn Grüning bjoern.gruen...@gmail.com wrote:
Hi JanakiRam,
I will take Greg into CC. He is the main Tool Shed developer, maybe we
spotted a bug in
Hi Nilaksha,
You should be able to download a file of any size in your browser from Galaxy.
Can you try disabling the developer settings in your universe_wsgi.ini file and
see if that helps? Info for doing that is here:
Hi,
if you export workflows it can happen that your *.ga file contains
full-path informations to the chromosome len file.
For example try to export the mergeCols1 or the trimmer tool. The
field chromInfo will have a full path attached. I don't think that will
cause any harm, but it would be
Hello,
it is great you want to share tools with others through Galaxy, thank you!
We call added software a 'Galaxy tool'. You can start by reading the tool
basics in this page: https://wiki.galaxyproject.org/Admin/Tools and then
you can browse through wiki where the vast of information about
Hello Janaki and Björn,
This problematic behavior is a result of a bug in the repository export process
which has been fixed in the following changeset which is currently available in
the Galaxy central repo. Thanks very much for reporting this.
Thanks Greg, I will verify with new changes.
Thanks,
JanakiRam
On Thu, Apr 3, 2014 at 7:05 PM, Greg Von Kuster g...@bx.psu.edu wrote:
Hello Janaki and Björn,
This problematic behavior is a result of a bug in the repository export
process which has been fixed in the following changeset
Hi Luca,
Could you send your job_conf.xml please? Also, is there any chance that you
modified run.sh to set DRMAA_LIBRARY_PATH there (which would override what
you set on the command line)?
--nate
On Thu, Apr 3, 2014 at 9:17 AM, Luca Toldo lucato...@gmail.com wrote:
Dear All,
after having
I should have handled the import in the same commit, but did so in the
following changeset. It will eliminate the problematic
prior_installation_required=False attribute from the repository tag when a
capsule is being imported.
changeset: 12944:59bd7349a128
tag: tip
user:
1. click SnpEff Download
2. choose one genome from SnpEff Databases and install it
Yes, I need to wait a few minutes to get response. But, after these two steps,
I got an error again when I run the snpEff, here it is:
java.lang.RuntimeException: ERROR: Cannot read file
Dear there,
I am still stuck there for FASTQ Summary Statistics. Could you give me some
clues to fix it?
Thanks a lot!
Best,
Xiaofei
From: Wang, Xiaofei
Sent: Wednesday, April 02, 2014 11:21 AM
To: Daniel Blankenberg
Cc: Björn Grüning;
Hi John,
Thank you so much for this detailed explanation. Before I saw your email I went
ahead and manually made changes in the pbs.py script. I didn't follow your
mercurial commands and hope that is not a problem down the road (I guess I
could use the hg revert option then).This seemed to have
I saw from:
http://dev.list.galaxyproject.org/contributing-patches-to-toolshed-repos-td4663497.html
that B. Langhorst had submitted a change to the picard wrapper to support the
rna-seq metrics - has that patch made it into any of the repo's? I'm not
seeing it when I install the picard
Hi List,
I've noticed that the mechanisms for catching job termination signals don't
seem to apply to uploading jobs. I was having trouble with *any* jobs being
terminated until I pulled Nate's changeset 1298d3f from Galaxy central, but it
still doesn't work for uploads. It will remove them
Hi Xiaofei,
Can you provide some sample data that is causing the issue for you?
Thanks,
Dan
On Apr 3, 2014, at 11:46 AM, Wang, Xiaofei xfw...@ku.edu wrote:
Dear there,
I am still stuck there for FASTQ Summary Statistics. Could you give me some
clues to fix it?
Thanks a lot!
Best,
Oh, hooray, I figured it out.
what I did is to go to this folder /Users/pablocingolani/snpEff and download
the database by command again:
java -jar snpEff.jar download dm5.42
Thank you so much!
Best,
Xiaofei
_
From: galaxy-dev-boun...@lists.bx.psu.edu
Hi Brad,
can you please upvote that card?
https://trello.com/c/84df6nON
Thanks,
Bjoern
Am 03.04.2014 21:00, schrieb Brad Zeitner:
I saw from:
http://dev.list.galaxyproject.org/contributing-patches-to-toolshed-repos-td4663497.html
that B. Langhorst had submitted a change to the picard
Dear there,
When I run CloudMap EMS Variant Density Mapping workflow (takes VCF of
heterozygous and homozygous variants to subtract) (imported from uploaded file)
on local Galaxy instance, I got this
[X]
, when I wanted to edit the workflow. Also, I got this
The following tools are beinge
I have made a wrapper that has a tool that giving it an input file, gives
you two output files with known extension: .gem and .log
I call the tool with a python file, and I pass it the input file and the
two output file names for galaxy to show them, but when I look into de
database/files/000/ i
Hi Angelica,
It appears that you are attempting to directly name the output files.
Instead, use a variable naming method that permits Galaxy to actually
name the files accessed by the database, using output with data tags
to link any working files (with from_work_dir) and attach attributes
Hi Greg/Bjoern,
Thanks for all your help. I checkout the galaxy-central code
base(previously I am using galaxy-dist code base) and uploaded my custom
tool(with both tool and repository dependency) in to toolshed and also
installed custom tool from galaxy. The dependency tool also installed
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