PS: This only seems to be true when disk quotas are in place. So where to
get the per user disk usage?
-Oorspronkelijk bericht-
Van: galaxy-dev-boun...@lists.bx.psu.edu
[mailto:galaxy-dev-boun...@lists.bx.psu.edu] Namens Bossers, Alex
Verzonden: maandag 30 januari 2012 8:56
Aan: gala
Dear all,
There is currently no link between an user ssh connection on his own
account (own space on Unix) and the Galaxy connection.
How to run Galaxy on an Unix user account? How to link the data storage
system and the Unix user account (symlink?)?
The goal is to not need to copy or move da
Hi Greg,
Thanks for your answer.
I've deleted the row in the tool_shed_repository table, removed the installed
tool shed repository from disk, updated my Galaxy instance to 6629:cb458aca542e
from Galaxy central and restarted Galaxy server.
I am sorry to say but I do still have the same problem
Hi Nate,
Thanks for the info!
I'm trying to understand how the URL for DRMAA works but I don't
understand how we can set it so it uses a different machine.
Our Galaxy runner runs on machine A and the cluster is on machine B,
where do I put B in the URL?
In the wiki there is this example:
drm
Jim et al
Amanda has most of the scripts working now and will be putting them up on the
toolshed.
She will be in touch as soon as the scripts are validated a couple of times
with different datasets.
cheers...
Pat
On Dec 29, 2011, at 3:02 PM, Jim Johnson wrote:
>
> It is easiest to generate
This is great news -- thanks for letting us know, and for your hard work on this!RobOn Jan 29, 2012, at 9:46 AM, Jim Johnson wrote:
Pat,
That sounds great. Do one of you want to take ownership of the
toolshed repository?
At minimum, we should add developers to
I'd love to know answers to this question as well. So far, all I've done is
create two tools for copying files between Galaxy and a user's personal
directories using a rather dangerous setuid executable.
I have mulled over two possibilities for this problem. One is to run Galaxy as
root. The
Figured it out. It was an error introduced while resolving version control
conflicts.
--
Shantanu
On Jan 29, 2012, at 9:12 PM, Shantanu Pavgi wrote:
>
> I am getting following error with the latest galaxy-dist revision
> '26920e20157f' update. The Python version is 2.6.6.
>
> {{{
> gal
Hi Anne,
>From your paster log it looks like the repository is installed, but for
>whatever reason your shed_tool_conf.xml file cannot be updated. I've tried
>many things, but am not able to reproduce this. Can you answer the following?
Have you ever been able to install a tool from the tool
Hi Greg,
Please see below my inline answers to your questions.
On 30 Jan 2012, at 15:37, Greg Von Kuster wrote:
> Hi Anne,
>
> From your paster log it looks like the repository is installed, but for
> whatever reason your shed_tool_conf.xml file cannot be updated. I've tried
> many things, bu
On Jan 30, 2012, at 7:37 AM, Louise-Amélie Schmitt wrote:
> Hi Nate,
>
> Thanks for the info!
>
> I'm trying to understand how the URL for DRMAA works but I don't understand
> how we can set it so it uses a different machine.
> Our Galaxy runner runs on machine A and the cluster is on machine B
On Jan 17, 2012, at 5:51 PM, Carlos Borroto wrote:
> Hi,
>
> I tried a few more things. I see when I try to update a dataset in a
> library the "The resource could not be found" goes a way, although
> still nothing gets updated:
> ./update.py
> http://localhost:8080/api/libraries/f2db41e1fa331b3
On Jan 17, 2012, at 11:19 PM, Cory Spencer wrote:
>
> Hello all -
>
> I'm working on a tool for Galaxy that generates an output file. I am able to
> view the file without issue in Galaxy itself, but when I click on the
> "Download" icon, the History sidebar produces the following error messag
Hi Greg,
Sorry I forget to print everything. Here it is:
galaxy.util.shed_util DEBUG 2012-01-30 16:40:32,209 XXX shed_tool_conf_dict:
{'tool_path': '../shed_tools', 'config_filename': './shed_tool_conf.xml',
'config_elems': []}
galaxy.util.shed_util DEBUG 2012-01-30 16:40:32,210 XXX elem:
Ann
Hi Nate,
Thanks for the leads!
But setting DRMAA_LIBRARY_PATH means I'm in trouble since the libraries
are on machine B which is maintained by our IT dept. I cannot access
them from machine A.
Is it a desperate situation? Will it work if I have a copy of those libs
somewhere? :/
Best,
L-A
On Jan 30, 2012, at 12:07 PM, Louise-Amélie Schmitt wrote:
> Hi Nate,
>
> Thanks for the leads!
>
> But setting DRMAA_LIBRARY_PATH means I'm in trouble since the libraries are
> on machine B which is maintained by our IT dept. I cannot access them from
> machine A.
>
> Is it a desperate situa
On Jan 20, 2012, at 9:04 AM, Holger Klein wrote:
> Dear all,
>
> due to some work on the user management of our servers we had to rename
> the user galaxy runs as. Up to now we used ident as postgres
> authentication method, meaning that here postgres expects unix username
> "galaxy" to have perm
On Jan 23, 2012, at 6:07 PM, Jaime Frey wrote:
> Hello, everyone.
>
> I'm working on a Condor job-runner module for Galaxy that can provide better
> integration than the existing drmaa module. I'm sure I'll have many questions
> as I work on this module, but I have just a few to start with:
>
On Jan 24, 2012, at 4:16 PM, Lucilla Luzi wrote:
> ERRATA CORRIGE: sorry :(
>
> $ echo $PATH
> /System/Library/Frameworks/Python.framework/Versions/2.6/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/usr/X11/bin
>
> Original Message
> Subject: [galaxy-dev] Some eggs are o
On Jan 25, 2012, at 5:28 AM, Praveen Baskaran wrote:
> i have installed local instance of galaxy and have a small problem with
> samtools. when i try to convert sam file to bam, the result pane shows that
> the job is running (for several hours). but when check the galaxy log file,
> it shows t
Anne,
Thanks for all of your patience and help with this. You uncovered a problem
that is very nice to have corrected. The fix is included in change set
6634:ebf72cda61e7 on our central repository. This change set will allow you to
have section tags in your tool_conf.xml file that do not inc
On Jan 25, 2012, at 10:37 AM, Leandro Hermida wrote:
> Hello,
>
> In the latest galaxy-dist version when running the system cleanup commands in
> the documented order I get an error when running the purge_datasets.sh script:
>
> sh delete_userless_histories.sh
> sh purge_histories.sh
> sh purge
Hi all,
I'm working on integrating cummeRbund[1] into Galaxy. This is a very
helpful tool for analysis and visualization of cuffdiff output.
My problem is any text output from running R code, puts the galaxy
output in error state. Even if everything is working correctly and the
outputs are genera
I see following warning messages in galaxy logs after a job finishes up. Does
it mean something is misconfigured or a tool did not generate stdout and stderr
files?
{{{
galaxy.datatypes.metadata DEBUG 2012-01-30 11:52:07,345 loading metadata from
file for: HistoryDatasetAssociation 7
galaxy.j
Greg,
Thanks for your patience and help with this too!
I've upgraded to ebf72cda61e7, cleaned all up (db, tool_conf.xml and
shed_tool_conf.xml, file system) and restarted galaxy. The import of
tabular2html works without the version attribute in the section of the
tool_conf.xml file. After ins
Carlos,
You'll want to have your wrapper collect output to stderr and report only if
the tool fails. See the Cufflinks/compare/diff wrappers for examples of how
this can be done.
Good luck,
J.
On Jan 30, 2012, at 1:01 PM, Carlos Borroto wrote:
> Hi all,
>
> I'm working on integrating c
Hi Jeremy,
Thanks for your quick response.
I'll try switching from using 'tools/plotting/r_wrapper.sh' from
Galaxy distribution, to my own wrapper using python, so I can use your
advice.
I still wonder if this is the best way to run R's scripts? I would
have thought there would be a simpler opti
> I still wonder if this is the best way to run R's scripts? I would
> have thought there would be a simpler option. I wonder if
> "r_wrapper.sh" could be improved to absorb stderr messages, I would
> guess Bash has these capabilities.
Ah, this would be ideal. If you can get this to work, it woul
We just upgraded our Galaxy server last week to the one from change-set
b258de1e6cea.
We have several workflows that leverage the ability to select multiple input
files, that in turn launches an instance of the workflow per input file.
When I use these workflows, it now only runs a single insta
After some digging I just found an archived email from Dannon where it looks
like the problem I reported is fixed. In an email from Jan 8th entitled
“multiple file input not taken into account in workflows”, Dannon said it was
fixed in:
changeset 6368:52de9815a7c4.
If this is correct, please
Nope, you didn't miss anything, this was a regression introduced in
6185:07f3f601d645, later fixed in 6368:52de9815a7c4.
-Dannon
On Jan 30, 2012, at 2:20 PM, Dave Walton wrote:
> We just upgraded our Galaxy server last week to the one from change-set
> b258de1e6cea.
>
> We have several workfl
On Jan 30, 2012, at 1:46 PM, Lucilla Luzi wrote:
> Thank you Nate for your reply!! :)
>
> This is what I got.
>
> $ python ./scripts/get_platforms.py
> macosx-10.6-universal-ucs2
>
> (just FYI, I run this command from the galaxy-dist folder that has a path
> like this one:
> /Users/me/My_progr
On Jan 25, 2012, at 2:43 PM, Liisa Koski wrote:
> Hello,
> I am trying to upload BAM files (by pasting a URL) to my history(or
> DataLibrary) and get the following error. These are bam files which I had
> previously uploaded with no problems.
>
> Traceback (most recent call last):
> File "/d
On Jan 25, 2012, at 8:10 PM, Prashant Gupta wrote:
> Hi,
>
> I have installed the galaxy on production server. I have uploaded the files I
> require through ftp and now when I try to add it to the history, it gives me
> error "This link may not be followed from within Galaxy". However, I checke
On Jan 26, 2012, at 4:29 AM, Hans-Rudolf Hotz wrote:
>
>
> On 01/25/2012 08:20 PM, Kim, Hyunsoo wrote:
>> Hi again,
>>
>> I'm kind of lost here. Does "Data Library" allow regular users to upload
>> files directly to Galaxy from their remote work station, or does it allow
>> users to use files
On Jan 26, 2012, at 4:52 PM, Theodore Zeng wrote:
> Hi Guys,
>
> I have been trying to implement galaxy-dist on our new server for days. After
> adding a new tool into galaxy, a strange problem happened when I was testing
> some sample data.
>
> After clicking the execute button, new jobs were
On Jan 27, 2012, at 4:43 PM, Bossers, Alex wrote:
> Hi All,
>
> We are finally up-and-running again with the latest dist release. The
> previoous version was ok but already quite old.
>
> For our local public server at wur we are now encountering the awaited disk
> space issues. as had to
Hi Nate,
Thanks for your reply. I already sorted out the problem. The problem was
that I was accessing the galaxy instance directly, rather than going
through the proxy server (nginx). However, the galaxy universe_wsgi.ini
file was configured for the proxy server. Once I tried it through the proxy
Yeah, there is not currently a great solution to this problem. Some have
implemented a tools just like David's. You could also get around setuid with
sudo, although the security implications are probably the same.
I think the ideal system would be to start Galaxy as root, drop privileges, and
On Jan 30, 2012, at 1:04 PM, Shantanu Pavgi wrote:
>
> I see following warning messages in galaxy logs after a job finishes up. Does
> it mean something is misconfigured or a tool did not generate stdout and
> stderr files?
>
> {{{
> galaxy.datatypes.metadata DEBUG 2012-01-30 11:52:07,345 loa
Hi all,
I would like to add an AB 3500 Genetic Analyzer sequencer, a real time
500 Fasta machine and and Ion Torrent PGM to my external service types,
and manage all sequencing requests via galaxy.
Is there any guide about how to create the XMLs for new instruments in
the external_service_ty
I'm having a tough time keeping track of which data is which after analysis...
I can do a bunch of work customizing each tool and each workflow, renaming
results etc.
But I think it might be a lot easier to manage if step names were based on the
titles of the history items instead of "data 2" o
Hi all,
Do you have a working tool definition file for QIIME's
beta_diversity_through_plots.py script? We're investigating whether
replacing the Fast UniFrac website with this would be feasible, and
I'd like to see if you have something together before I try to write
one myself.
Thanks!
Greg
On S
Hello Alfonso,
Are you still having problems when the latest distribution from January
27? You may not have upgraded yet, but when you do, please retest and
let us know if issues persist.
http://wiki.g2.bx.psu.edu/DevNewsBriefs
Thanks!
Jen
Galaxy team
On 12/1/11 10:29 AM, Alfonso Núñez Sal
Hello all -
One of the Galaxy tools I've been developing generates HTML output which I'd
styled using a ... tag in the HTML header. After updating to
the latest Galaxy release earlier today, the , ...,
Nate,
Thanks I finally configured the reports and they work ok and are useful!
Are these reports public? How to limit these to admins only? There doesn't seem
to be any login or authentication feature.
For our dev server this not a problem but the reports are especially handy for
the production e
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