Re: [galaxy-dev] bacterial genomes missing?

[Jennifer Jackson]

Hello,

Yes, this was noticed but it took a few days to track down and correct 
the problem. As of this afternoon, the genome builds list was restored 
to the original content plus a few new additions.


If you notice any genome missing that was previously present, we would 
definitely like to know.


Very sorry for the inconvenience!

Best,

Jen
Galaxy team

On 3/6/12 2:14 PM, Langhorst, Brad wrote:

Hi Dan:

When I look at builds.txt I see only the eukaryotic genomes...

the canary that triggered my investigation was eschColi_K12.

It used to be present, but is now not in builds.txt
it is present in ucsc_build_sites.txt


When i go to the xml at ucsc's test server
http://genome-test.cse.ucsc.edu/cgi-bin/das/dsn
i don't see eschColi_K12

I've looked in my backups and I find that the builds.txt from 3 weeks
ago did have eschColi_K12 (and many other now missing items).

I think we'll have to fetch these from the other sites now...


Brad



On Mar 6, 2012, at 4:59 PM, Daniel Blankenberg wrote:


Hi Brad,

I just ran the updateucsc.sh script and it seemed to work correctly.
Can you be more specific as to which builds you are missing and could
you try running the script again and if it doesn't work, copy the log
output here?


Thanks for using Galaxy,

Dan


On Mar 6, 2012, at 12:15 PM, Langhorst, Brad wrote:


It seems that the bacterial genomes that used to come from ucsc via
update_ucsc.sh are now gone...

Has anybody else observed this? Fixed it?

Brad
--
Brad Langhorst
langho...@neb.com 
978-380-7564




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--
Brad Langhorst
langho...@neb.com 
978-380-7564






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--
Jennifer Jackson
http://usegalaxy.org
http://galaxyproject.org/wiki/Support
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[galaxy-dev] Error when installing toolshed tool

[Anthonius deBoer]

I'm getting this error when I try to install the NGS Java toolkit toolshed...Version information for the tools included in the java_genomics_toolkit
 repository is missing.  Reset all of this repository's metadata in the 
tool shed, then set the installed tool versions from the installed 
repository's Repository Actions menu.  Installed 1 repository and all tools were loaded into tool panel section NGS: Toolkit:Installed repositories: java_genomics_toolkit.Any idea why the version number stuff is not correctly inserted in the database?Bug?ThanksThon
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[galaxy-dev] How to configure "Get Data | get microbial data"

[JIE CHEN]

Dear all,

I have spent several days trying to make "get microbial data" to work in my
local Galaxy instance, but failed.

What i did is:
1. cd /galaxy-dist/tool-data/
2. nano microbial_data
3. uncomment the lines starting with "ORG", "CHR" or "DATA"

After that, i restarted Galaxy and can see the options on the web. However,
it cannot work yet. I am pretty sure that is because the URLs are not
properly specified and i don't have a local mirror of all the related files
yet. Can anyone help and tell me where and how to download the files? And
how can i continue to make it work?

(In addition, i find some information under the link
http://gmod.827538.n3.nabble.com/Setting-up-microbial-data-loc-given-a-mirror-of-NCBI-FTP-site-td2120728.html#a2122753.
But still cannot figure out how to do it)

THANKS A LOT!!!


Cheers,
Tyler
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Re: [galaxy-dev] postgres

[Dannon Baker]

Yes, see the table 'job'.  You may or may not find this helpful, but here's a 
big database schema from our wiki:

http://wiki.g2.bx.psu.edu/DataModel?action=AttachFile&do=view&target=galaxy_schema.png

-Dannon


On Mar 9, 2012, at 8:00 AM, christin weinberg wrote:

> Hi,
> 
> thanks for the answer.  I have one more question. Is there one main table (in 
> the database), which creates one key for one job and this key is allocated 
> over other tables?
> 
> Thank you!
> 
> Best,
> Christin
> 
> Am 08.03.2012 16:40, schrieb Björn Grüning:
>> Hi Christin,
>> 
>>> I would like to clarify whether we have understood something about the
>>> database correctly. Is is right that all calculations with galaxy are
>>> stored as a link in the database. And the data are stored somewhereelse?
>> Yes, kind of :)
>> 
>>> Is it possible to store the data only in the database?
>> No and its advisable to do so. Galaxy operates on files and they can be
>> huge. It does not make much sense to store such data in a database.
>> 
>> Best,
>> Bjoern
>> 
>>> For some advice, I am very grateful.
>>> 
>>> Best regards,
>>> Christin
>>> 
> 
> 
> -- 
> 
> Christin Weinberg
> Institute for Applied Computer Science (IACS)
> FH Stralsund - University of Applied Sciences
> 
> Phone: +49 3831 456948
> E-Mail : christin.weinb...@fh-stralsund.de
> 
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Re: [galaxy-dev] postgres

[christin weinberg]

Hi,

thanks for the answer.  I have one more question. Is there one main 
table (in the database), which creates one key for one job and this key 
is allocated over other tables?


Thank you!

Best,
Christin

Am 08.03.2012 16:40, schrieb Björn Grüning:

Hi Christin,


I would like to clarify whether we have understood something about the
database correctly. Is is right that all calculations with galaxy are
stored as a link in the database. And the data are stored somewhereelse?

Yes, kind of :)


Is it possible to store the data only in the database?

No and its advisable to do so. Galaxy operates on files and they can be
huge. It does not make much sense to store such data in a database.

Best,
Bjoern


For some advice, I am very grateful.

Best regards,
Christin




--

Christin Weinberg
Institute for Applied Computer Science (IACS)
FH Stralsund - University of Applied Sciences

Phone: +49 3831 456948
E-Mail : christin.weinb...@fh-stralsund.de

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[galaxy-dev] Production environment and Apache's sendfile

[Yuri D'Elia]

Hi everyone. I've set up a galaxy production environment and it seems to be 
working.
I've identified a couple of issues though:

If I enable apache_xsendfile, the little "eye" icon ("Display data in browser") 
on each dataset stops working. I get the following instead:

The requested URL /datasets/7e93e3cf926fb2b3/display/ was not found on this 
server

My document root is not the same as the galaxy root (as suggested). Everything 
else seems to work. Is this a bug?

Second question:

I want to rotate the galaxy log file (as specified with paster.py serve 
--log-file. I can't find a way to reopen the logfile in galaxy without taking 
down the whole service, or a way to redirect the log to a pipe together while 
using --daemon.

I cannot let the file grow forever.
Any suggestions?

Right now I've setup logrotate to "copytruncate" the log (the log is opened in 
append anyway), but it's not a very nice solution. Does "paster" support some 
standard signal such as SIGUSR1 to re-open log files?

Thanks.

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[galaxy-dev] Display galaxy variable

[Sarah Maman]

Hello,

In a Galaxy tool, I would like to display a pre-completed path in the 
xml inputbox, inside the tool.xml file.
Consequently, I would like to add a variable in an  
tag , like this :


test.sh $in $out

  

...
and in test.sh : $out is defined to be ${trans.user.username}

Do you have any idea to display  ${trans.user.username} variable in 
order to  be shown in galaxy interface (gui) thanks to xml file ?


I achieve to display ${trans.user.username} in 
/templates/root/tool_menu.mako but not in the xml file.


Thanks in advance,
Sarah
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[galaxy-dev] Tool and dynamic

[Yuri D'Elia]

Hi everyone. I'm writing a tool that can take a parameter with a dynamic list 
of values.

The tool XML file looks like this:


  
XYZ
ZYX
ZXY
  
  

  ...

  


I would like to generate the inner  elements dynamically by calling an 
external utility in response to the first parameter ("outer"), or at least some 
piece of python code.

I know I can use  to load this from an external file, but that's not 
enough. I tried to use , but I'm afraid I wasn't able to generate the 
list of options dynamically (by using the first conditional when selected). I 
couldn't find a tool that uses  to this end.

Does anybody have any suggestion?

I was thinking of adding a new attribute to , like . Would you accept such a patch to galaxy?

Thanks.

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Re: [galaxy-dev] Welcome.html page

[Hans-Rudolf Hotz]

On 03/09/2012 01:04 AM, Huayan Gao wrote:

Dear Hans,

I emptied cache and it is not showing up the changes. I changed a computer and 
tried again. No luck.

Yes, I killed the process and restart the server, no luck.

It should be pretty straight forward but it just did not come out as I expected.

Any ideas?



first (wild) guess: you have two galaxy servers (ie galaxy directories). 
you change the file in one, but in the web browser, you are looking at a 
different installation.


so just double checking: what happens when you delete (ie re-name or 
move to a different location):


  ~/galaxy_dist/static/welcome.html
  ~/galaxy_dist/tool_conf.xml
  ~/galaxy_dist/tool_conf.xml.sample

and restart the server? the missing "tool_conf.xml" should cause the 
start-up to fail



Regards, Hans


Best,
Huayan


On 8 Mar, 2012, at 10:52 PM, Hans-Rudolf Hotz wrote:


Hi Huayan


I got a silly question for you. My galaxy is running now but I'd like
to customize it.
I've changed the welcome.html page but the galaxy mirror site is
showing the old one. Do I need to change some other files or other
configurations?


Are you sure the page is not cached locally?


Also, I add   in tool_conf.xml file but it does not show up
either. Is there another file I need to change too?



I assume you mean "label", have you restarted your galaxy server?


I hope this helps
Regards, Hans






Best,
Huayan
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