Re: [galaxy-dev] How to display tool instead of html WWFSMD page at start-up?

[Jeremy Goecks]

Yes, this works on my local instance. Did you restart your Galaxy instance 
after adding the welcome_url setting?

On Jul 29, 2013, at 11:02 PM,  wrote:

> Yes I tried that but I still only see the default welcome.html page. Have you 
> got this to work?
> Thanks
> Neil
>  
> From: Jeremy Goecks [mailto:jeremy.goe...@emory.edu] 
> Sent: Tuesday, 30 July 2013 12:37 PM
> To: Burdett, Neil (ICT Centre, Herston - RBWH)
> Cc: ross.laza...@gmail.com; galaxy-dev@lists.bx.psu.edu
> Subject: Re: [galaxy-dev] How to display tool instead of html WWFSMD page at 
> start-up?
>  
> You'll need to add the setting further down in the config file, such as under 
> the 'UI Localization' section.
>  
> Best,
> J.
>  
> On Jul 29, 2013, at 8:49 PM,  wrote:
> 
> 
> Thanks Jeremy,
>   But this doesn’t seem to work.
>  
> If I add the welcome_url to the universe_wsgi.ini (is this the universe 
> config file you mentioned?) as shown below, I continue to get the 
> welcome.html page
>  
> #  Galaxy ---
> 
> # Configuration of the Galaxy application.
> 
> [app:main]
> filter-with = proxy-prefix
> cookie_path = /csiro
> 
> welcome_url = /tool_runner?tool_id=upload1
> 
> 
> 
> If I move the welcome_url higher up in the universe_wsgi.ini file I get an 
> error the last part is shown below:
>  
> File 
> "/home/galaxy/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.7.egg/paste/deploy/loadwsgi.py",
>  line 190, in invoke
> return filter(filtered)
>   File 
> "/home/galaxy/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.7.egg/paste/deploy/loadwsgi.py",
>  line 130, in filter_wrapper
> **context.local_conf)
>   File 
> "/home/galaxy/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.7.egg/paste/deploy/util/fixtypeerror.py",
>  line 57, in fix_call
> val = callable(*args, **kw)
> TypeError: make_prefix_middleware() got an unexpected keyword argument 
> 'welcome_url'
>  
> I can’t find anywhere in the code that has the test string “welcome_html” Any 
> ideas?
>  
> Thanks
> Neil
>  
> From: Jeremy Goecks [mailto:jeremy.goe...@emory.edu] 
> Sent: Tuesday, 30 July 2013 7:32 AM
> To: Ross
> Cc: Burdett, Neil (ICT Centre, Herston - RBWH); galaxy-dev@lists.bx.psu.edu
> Subject: Re: [galaxy-dev] How to display tool instead of html WWFSMD page at 
> start-up?
>  
> There's an undocumented setting in the universe config, welcome_url, that can 
> be used; if you point this as follows it will bring up the upload tool.
>  
> welcome_url = /tool_runner?tool_id=upload1
>  
> On Jul 29, 2013, at 3:28 AM, Ross wrote:
> 
> 
> 
> Neil,
> good news: the initial center panel renders static/welcome.html so easy to 
> change.
> bad news: AFAIK no way to show a (dynamic) default tool form instead - others 
> may know more..
>  
> 
> On Mon, Jul 29, 2013 at 5:03 PM,  wrote:
> Hi,
> When Galaxy is started the centre column displays the “Hello world! It’s 
> running ...” WWFSMD? Html Page. How can this be changed so that a tool i.e. 
> get data  tool is shown up on start-up with all its text boxes etc rather 
> than the default html file? Is this possible?
>  
> Thanks
> Neil
>  
>  
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>  

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[galaxy-dev] job_conf.xml about running Galaxy tools on a cluster.

[shenwiyn]

Hi everyone，
I am a newer in Galaxy. I installed my Galaxy with Torque2.5.0 . I used my 
job_conf.xml for a test ,my Galaxy seems to work with TORQUE by the interface 
of pbs_modoule ( _pbs.so)  successfully. 
In my test job_conf.xml , it seems that we should use collection of 
to specify bwa to run as 
multicorejobs4. But I do not sure wheather all the tools in Galaxy we should 
specify their destination (such as, regularjobs,longjobs), or all the tools 
would work with a default destination().,unless we specify them.
Could anyone give me some help please?
This is my test job_conf.xml:




























   
  scripts/drmaa_external_runner.py
  scripts/drmaa_external_killer.py
   scripts/external_chown_script.py
 


python
interactiveOrCluster








500
1
1
200
200
200
100






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[galaxy-dev] Defining $GALAXY_CPUS for use in tool wrappers

[Peter Cock]

Hello all,

Re:
http://lists.bx.psu.edu/pipermail/galaxy-dev/2012-June/010153.html
http://lists.bx.psu.edu/pipermail/galaxy-dev/2012-October/011557.html

Something I raised during the GCC2013, and we talked about
via Twitter as well was a Galaxy environment variable for use
within Tool Wrappers setting the number of threads/CPUs to
use.

The idea is that you can configure a default value, and then
override this per runner or per tool etc. James Taylor had
suggested calling this environment variable $GALAXY_CPUS
which seem fine to me (personally I'd say threads not CPUs
but I don't really mind). e.g.

my_tool --threads "\$GALAXY_CPUS"
--input "$input" --output "$output"

Everyone I spoke to about this seemed positive about the idea.

This would/should be integrated into the various cluster back
ends, for example for SGE/OGE the number of threads is
already configurable via the DRMAA settings and available
as the environment variable $NSLOTS for non-MPI jobs, so
my guess is all Galaxy needs to do is something like this:

$ hg diff
diff -r ce0d758bb995 lib/galaxy/jobs/runners/drmaa.py
--- a/lib/galaxy/jobs/runners/drmaa.py  Tue Jul 30 12:30:30 2013 +0100
+++ b/lib/galaxy/jobs/runners/drmaa.py  Tue Jul 30 16:10:40 2013 +0100
@@ -43,6 +43,7 @@
 #  - execute the command
 #  - take the command's exit code ($?) and write it to a file.
 drm_template = """#!/bin/sh
+export GALAXY_CPUS="$NSLOTS"
 GALAXY_LIB="%s"
 if [ "$GALAXY_LIB" != "None" ]; then
 if [ -n "$PYTHONPATH" ]; then

Is there an open Trello card for this?

Thanks,

Peter
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Re: [galaxy-dev] Number of outputs = number of inputs

[Shafer, Christina]

My question is related to this post 

 in the archive. As recommended, I referred to 
http://wiki.galaxyproject.org/Admin/Tools/Multiple%20Output%20Files#Number_of_Output_datasets_cannot_be_determined_until_tool_run
 for some guidance on how to achieve multiple output files, specifically one 
set of six files per number of times the  tag is called. The example 
provided isn't that informative, however, as it doesn't show what the 
example_tool.sh command script is doing so I can make my perl wrapper script do 
the same thing. If I have six files total, do I only specify one in the 
 tag and then have the remaining 5 named according to the scheme in 
the perl wrapper? Or is it Galaxy that does the naming of the remaining files 
automatically? Is there a perl equivalent to the "$__new_file_path__" variable 
that I can use, or is this the literal resolved file path (e.g. 
"/opt/galaxy/... etc)?

Right now, upon execution of my tool, if a user has two entries (so number of 
times  has executed is twice), my perl wrapper is called twice (good), 
but on the second call, Galaxy uses the same output filenames as the first run 
such that the first set of output files are all overwritten by the second 
execution (bad). How do I make sure that each  iteration results in a 
unique set of output files?

Thanks for your help!

Christina Shafer, Ph.D
Regenerative Biology Laboratory
Morgridge Institute for Research
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Re: [galaxy-dev] CloudMan Error

[Dannon Baker]

Yes, I tried it and everything appeared to load fine using the url
indicated above.  The data volume was mounted correctly, and it appears the
custom installation is in place though I would have no idea what it is or
does.

Did you install all the custom stuff originally?  If not, it may be useful
to talk to the person that did to find out if they're able to poke at it.
 That file that's indicated as missing (csamtools.so) is actually there if
you take a look, and I'd expect it should all work if initialized correctly.


On Tue, Jul 30, 2013 at 10:10 AM, Deniz Erezyilmaz wrote:

> HI - did you find anything with the share string? Thanks, Deniz
>
>
> On Fri, Jul 26, 2013 at 3:32 PM, Dannon Baker wrote:
>
>> Ahh, ok, I misunderstood and thought you were saying there was a
>> different error for the workaround.  Are you able to send me the share
>> string (directly if you want, feel free to drop the list) so that I might
>> take a look?  There should be no change at all in your instances from
>> before the new release when using the workaround.
>>
>>
>> On Fri, Jul 26, 2013 at 8:17 AM, Deniz Erezyilmaz wrote:
>>
>>> Dannon- the problems that I saw were with the workaround (see last
>>> post). The instance launches, but the program stops when it can't find
>>> something (module/dependencies).
>>>
>>> There were also some different steps in setting up the instance. I had
>>> to create my own key pair, whereas in the past I never had to do that. I
>>> guess that simply using the share string that Greg at Janelia created made
>>> this step automatic.
>>>
>>> The cluster was working well at the end of June. The problem arose
>>> suddenly Saturday June 29, when the share string would not load. Thanks
>>> again, Deniz
>>>
>>>
>>>
>>> On Thu, Jul 25, 2013 at 5:19 PM, Dannon Baker wrote:
>>>
 On Thu, Jul 25, 2013 at 4:47 PM, Deniz Erezyilmaz 
 wrote:

 The workaround doesn't seem to work
>

 Can you tell me what happens when you launch with the workaround
 mentioned previously (
 https://main.g2.bx.psu.edu/cloudlaunch?ami=ami-da58aab3&bucket_default=gxy-workshop)?


 This should launch the pre-migration AMI and Cloudman and shouldn't
 have any issues at all unless your cluster was already wonky.

 -Dannon

>>>
>>>
>>
>
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Re: [galaxy-dev] Defining $GALAXY_CPUS for use in tool wrappers

[James Taylor]

I would actually prefer we use $GALAXY_SLOTS.

--
James Taylor, Assistant Professor, Biology/CS, Emory University


On Tue, Jul 30, 2013 at 11:18 AM, Peter Cock  wrote:
> Hello all,
>
> Re:
> http://lists.bx.psu.edu/pipermail/galaxy-dev/2012-June/010153.html
> http://lists.bx.psu.edu/pipermail/galaxy-dev/2012-October/011557.html
>
> Something I raised during the GCC2013, and we talked about
> via Twitter as well was a Galaxy environment variable for use
> within Tool Wrappers setting the number of threads/CPUs to
> use.
>
> The idea is that you can configure a default value, and then
> override this per runner or per tool etc. James Taylor had
> suggested calling this environment variable $GALAXY_CPUS
> which seem fine to me (personally I'd say threads not CPUs
> but I don't really mind). e.g.
>
> my_tool --threads "\$GALAXY_CPUS"
> --input "$input" --output "$output"
>
> Everyone I spoke to about this seemed positive about the idea.
>
> This would/should be integrated into the various cluster back
> ends, for example for SGE/OGE the number of threads is
> already configurable via the DRMAA settings and available
> as the environment variable $NSLOTS for non-MPI jobs, so
> my guess is all Galaxy needs to do is something like this:
>
> $ hg diff
> diff -r ce0d758bb995 lib/galaxy/jobs/runners/drmaa.py
> --- a/lib/galaxy/jobs/runners/drmaa.py  Tue Jul 30 12:30:30 2013 +0100
> +++ b/lib/galaxy/jobs/runners/drmaa.py  Tue Jul 30 16:10:40 2013 +0100
> @@ -43,6 +43,7 @@
>  #  - execute the command
>  #  - take the command's exit code ($?) and write it to a file.
>  drm_template = """#!/bin/sh
> +export GALAXY_CPUS="$NSLOTS"
>  GALAXY_LIB="%s"
>  if [ "$GALAXY_LIB" != "None" ]; then
>  if [ -n "$PYTHONPATH" ]; then
>
> Is there an open Trello card for this?
>
> Thanks,
>
> Peter
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Re: [galaxy-dev] Number of outputs = number of inputs

[Peter Cock]

On Tue, Jul 30, 2013 at 4:29 PM, Shafer, Christina
 wrote:
> My question is related to this post in the archive. As recommended, I
> referred to
> http://wiki.galaxyproject.org/Admin/Tools/Multiple%20Output%20Files#Number_of_Output_datasets_cannot_be_determined_until_tool_run
> for some guidance on how to achieve multiple output files, specifically one
> set of six files per number of times the  tag is called. The example
> provided isn't that informative, however, as it doesn't show what the
> example_tool.sh command script is doing so I can make my perl wrapper script
> do the same thing. If I have six files total, do I only specify one in the
>  tag and then have the remaining 5 named according to the scheme in
> the perl wrapper? Or is it Galaxy that does the naming of the remaining
> files automatically? Is there a perl equivalent to the "$__new_file_path__"
> variable that I can use, or is this the literal resolved file path (e.g.
> "/opt/galaxy/... etc)?
>
> Right now, upon execution of my tool, if a user has two entries (so number
> of times  has executed is twice), my perl wrapper is called twice
> (good), but on the second call, Galaxy uses the same output filenames as the
> first run such that the first set of output files are all overwritten by the
> second execution (bad). How do I make sure that each  iteration
> results in a unique set of output files?

The normal expectation is the Galaxy wrapper calls the tool ONCE only,
with a more complex command line including multiple file names from
the repeat.

If I recall correctly from your last email, you are using a trick with semi
colons to embed multiple shell commands in the  tag, one
for each repetition of the  tag.

I suggest you rework your Perl script to be designed to be called once
for all the work,

Peter
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Re: [galaxy-dev] Defining $GALAXY_CPUS for use in tool wrappers

[Peter Cock]

On Tue, Jul 30, 2013 at 4:39 PM, James Taylor  wrote:
> I would actually prefer we use $GALAXY_SLOTS.
>

I like that too, CPUs is a bit of a fuzzy term with multiple cores,
and SLOTS has familiarity from the SGE terminology as well.

Peter
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Re: [galaxy-dev] Defining $GALAXY_CPUS for use in tool wrappers

[Nate Coraor]

On Jul 30, 2013, at 11:40 AM, Peter Cock wrote:

> On Tue, Jul 30, 2013 at 4:39 PM, James Taylor  wrote:
>> I would actually prefer we use $GALAXY_SLOTS.
>> 
> 
> I like that too, CPUs is a bit of a fuzzy term with multiple cores,
> and SLOTS has familiarity from the SGE terminology as well.

I started some work on this during a bit of free time at the GCC.  With some 
luck it may be finished in time for the September release.

--nate

> 
> Peter
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Re: [galaxy-dev] Defining $GALAXY_CPUS for use in tool wrappers

[Peter Cock]

On Tue, Jul 30, 2013 at 4:44 PM, Nate Coraor  wrote:
> On Jul 30, 2013, at 11:40 AM, Peter Cock wrote:
>
>> On Tue, Jul 30, 2013 at 4:39 PM, James Taylor  wrote:
>>> I would actually prefer we use $GALAXY_SLOTS.
>>>
>>
>> I like that too, CPUs is a bit of a fuzzy term with multiple cores,
>> and SLOTS has familiarity from the SGE terminology as well.
>
> I started some work on this during a bit of free time at the GCC.
> With some luck it may be finished in time for the September release.
>
> --nate

That's encouraging - is there a public branch of this yet?

Peter
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Re: [galaxy-dev] Defining $GALAXY_CPUS for use in tool wrappers

[Nate Coraor]

On Jul 30, 2013, at 11:47 AM, Peter Cock wrote:

> On Tue, Jul 30, 2013 at 4:44 PM, Nate Coraor  wrote:
>> On Jul 30, 2013, at 11:40 AM, Peter Cock wrote:
>> 
>>> On Tue, Jul 30, 2013 at 4:39 PM, James Taylor  wrote:
 I would actually prefer we use $GALAXY_SLOTS.
 
>>> 
>>> I like that too, CPUs is a bit of a fuzzy term with multiple cores,
>>> and SLOTS has familiarity from the SGE terminology as well.
>> 
>> I started some work on this during a bit of free time at the GCC.
>> With some luck it may be finished in time for the September release.
>> 
>> --nate
> 
> That's encouraging - is there a public branch of this yet?

No, nothing committable.

> 
> Peter


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[galaxy-dev] Local: BWA 0.5.9. SA Coordinate/Segmentation fault

[Moritz Juchler]

Hey,

1 I installed Galaxy locally.
2 I also have BWA installed and then used the
3 shed repository to get the bwa wrapper.
4 I have the reference genome

now I'm stuck with the calculate SA coordinate. Segmenation fault.
Google tells me that it could be a problem with
-space (I have 4GB left)
-the version I use. (I use 0.5.9 and did a succesful alignment with 0.7.5a,
but the tool shed says 0.5.9, hence *could I just change to the current
version* (without Galaxy knowing it), with which I did a succesful
alignment?)

Best
Moritz
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Re: [galaxy-dev] CloudMan Error

[Deniz Erezyilmaz]

Yes- I know that it loads in the workaround that you created, but it
doesn't run. The non-workaround version running fine until the last
Saturday of June. I know that Greg, who installed it, hasn't touched it in
months. Could this be related to the update that was recently completed?
That was supposed to be fixed last week. Is there any news? Thanks, Deniz


On Tue, Jul 30, 2013 at 11:35 AM, Dannon Baker wrote:

> Yes, I tried it and everything appeared to load fine using the url
> indicated above.  The data volume was mounted correctly, and it appears the
> custom installation is in place though I would have no idea what it is or
> does.
>
> Did you install all the custom stuff originally?  If not, it may be useful
> to talk to the person that did to find out if they're able to poke at it.
>  That file that's indicated as missing (csamtools.so) is actually there if
> you take a look, and I'd expect it should all work if initialized correctly.
>
>
> On Tue, Jul 30, 2013 at 10:10 AM, Deniz Erezyilmaz wrote:
>
>> HI - did you find anything with the share string? Thanks, Deniz
>>
>>
>> On Fri, Jul 26, 2013 at 3:32 PM, Dannon Baker wrote:
>>
>>> Ahh, ok, I misunderstood and thought you were saying there was a
>>> different error for the workaround.  Are you able to send me the share
>>> string (directly if you want, feel free to drop the list) so that I might
>>> take a look?  There should be no change at all in your instances from
>>> before the new release when using the workaround.
>>>
>>>
>>> On Fri, Jul 26, 2013 at 8:17 AM, Deniz Erezyilmaz wrote:
>>>
 Dannon- the problems that I saw were with the workaround (see last
 post). The instance launches, but the program stops when it can't find
 something (module/dependencies).

 There were also some different steps in setting up the instance. I had
 to create my own key pair, whereas in the past I never had to do that. I
 guess that simply using the share string that Greg at Janelia created made
 this step automatic.

 The cluster was working well at the end of June. The problem arose
 suddenly Saturday June 29, when the share string would not load. Thanks
 again, Deniz



 On Thu, Jul 25, 2013 at 5:19 PM, Dannon Baker 
 wrote:

> On Thu, Jul 25, 2013 at 4:47 PM, Deniz Erezyilmaz 
> wrote:
>
> The workaround doesn't seem to work
>>
>
> Can you tell me what happens when you launch with the workaround
> mentioned previously (
> https://main.g2.bx.psu.edu/cloudlaunch?ami=ami-da58aab3&bucket_default=gxy-workshop)?
>
>
> This should launch the pre-migration AMI and Cloudman and shouldn't
> have any issues at all unless your cluster was already wonky.
>
> -Dannon
>


>>>
>>
>
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Re: [galaxy-dev] CloudMan Error

[Deniz Erezyilmaz]

HI - did you find anything with the share string? Thanks, Deniz


On Fri, Jul 26, 2013 at 3:32 PM, Dannon Baker wrote:

> Ahh, ok, I misunderstood and thought you were saying there was a different
> error for the workaround.  Are you able to send me the share string
> (directly if you want, feel free to drop the list) so that I might take a
> look?  There should be no change at all in your instances from before the
> new release when using the workaround.
>
>
> On Fri, Jul 26, 2013 at 8:17 AM, Deniz Erezyilmaz wrote:
>
>> Dannon- the problems that I saw were with the workaround (see last post).
>> The instance launches, but the program stops when it can't find something
>> (module/dependencies).
>>
>> There were also some different steps in setting up the instance. I had to
>> create my own key pair, whereas in the past I never had to do that. I guess
>> that simply using the share string that Greg at Janelia created made this
>> step automatic.
>>
>> The cluster was working well at the end of June. The problem arose
>> suddenly Saturday June 29, when the share string would not load. Thanks
>> again, Deniz
>>
>>
>>
>> On Thu, Jul 25, 2013 at 5:19 PM, Dannon Baker wrote:
>>
>>> On Thu, Jul 25, 2013 at 4:47 PM, Deniz Erezyilmaz wrote:
>>>
>>> The workaround doesn't seem to work

>>>
>>> Can you tell me what happens when you launch with the workaround
>>> mentioned previously (
>>> https://main.g2.bx.psu.edu/cloudlaunch?ami=ami-da58aab3&bucket_default=gxy-workshop)?
>>>
>>>
>>> This should launch the pre-migration AMI and Cloudman and shouldn't have
>>> any issues at all unless your cluster was already wonky.
>>>
>>> -Dannon
>>>
>>
>>
>
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[galaxy-dev] lessc compiler error on blue_colors.ini

[Seth Sims]

Dear Galaxy devs,

I am attempting to create a style directory to match my school's look
and feel. I am mainly trying to get the development environment setup to do
this right now. My current problem is that when I attempt to compile the
standard blue_colors.ini which comes with galaxy I am receiving a syntax
error:

ParseError: Syntax Error on line 1 in
/srv/galaxy-dist/static/style/blue_colors.ini:1:10
1 base_text=#303030
2 base_bg_top=#FF

I have not edited that file at all. So the first question is, what version
of lessc is being used to compile the styles for the basic installation?
Also are there any pitfalls I should be aware of with this process.

- Seth
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[galaxy-dev] Running RabbitMQ listener requires a path update

[Ganote, Carrie L]

Hi list,

I ran into the following problem:
$ sh run_galaxy_listener.sh
Traceback (most recent call last):
  File "scripts/galaxy_messaging/server/amqp_consumer.py", line 33, in 
from galaxy.web.api.requests import RequestsAPIController
ImportError: No module named api.requests

Changed this line in scripts/galaxy_messaging/server/amqp_consumer.py:
from galaxy.webapps.galaxy.api.requests import RequestsAPIController

Just an artifact from the restructuring of Galaxy.
Hope this helps!

Sincerely,

Carrie Ganote
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[galaxy-dev] ActionInputError undefined

[Jim Johnson]

I was using the quotas api to update a quota amount and got the error:

galaxy.web.framework ERROR 2013-07-30 15:40:59,149 Uncaught exception in 
exposed API method:
Traceback (most recent call last):
  File "/Users/jj/gxt/gxt/lib/galaxy/web/framework/__init__.py", line 189, in 
decorator
rval = func( self, trans, *args, **kwargs)
  File "/Users/jj/gxt/gxt/lib/galaxy/web/framework/__init__.py", line 221, in 
decorator
return func( self, trans, *args, **kwargs )
  File "/Users/jj/gxt/gxt/lib/galaxy/webapps/galaxy/api/quotas.py", line 108, 
in update
except ActionInputError, e:
NameError: global name 'ActionInputError' is not defined

Was ActionInputError meant to be a class in lib/galaxy/exceptions/__init__.py  ?

diff -r 951e853b0bcd lib/galaxy/exceptions/__init__.py
--- a/lib/galaxy/exceptions/__init__.py Tue Jul 30 12:54:02 2013 -0400
+++ b/lib/galaxy/exceptions/__init__.py Tue Jul 30 16:38:50 2013 -0500
@@ -21,6 +21,9 @@
 class ItemOwnershipException( MessageException ):
 pass

+class ActionInputError( MessageException ):
+pass
+
 class ObjectNotFound( Exception ):
 """ Accessed object was not found """
 pass



--
James E. Johnson, Minnesota Supercomputing Institute, University of Minnesota
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[galaxy-dev] Appending _task_%d suffix to multi files

[Alex.Khassapov]

Hi guys,



We've been using Galaxy for a year now, we created our own Galaxy fork where we 
were making changes to adapt Galaxy to our requirements.  As we need "multiple 
file dataset" - we were using Johns' fork for that initially.



Now we are trying to use "The most updated version of the multiple file dataset 
stuff" https://bitbucket.org/msiappdev/galaxy-extras/ directly as we don't want 
to maintain our own version.



One of the problems we have - when we upload multiple files - their file names 
are changed (_task_%d suffix is added to their names).



On our branch we simply removed the code which does it, but now we wonder if it 
is possible to avoid this renaming somehow? I.e. make it configurable?



Is it really necessary to change the file names?



-Alex



-Original Message-
From: galaxy-dev-boun...@lists.bx.psu.edu 
[mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Jorrit Boekel
Sent: Thursday, 25 October 2012 8:35 PM
To: Peter Cock
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] the multi job splitter





I keep the files matched by keeping a _task_%d suffix to their names. So each 
task is matched with its correct counterpart with the same number.



cheers,

jorrit



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[galaxy-dev] Galaxy Proteomics mailing list

[Ira Cooke]

Dear All, 

The galaxy community now has a mailing list dedicated to proteomics.  If you're 
using galaxy to do proteomics, or if you are thinking of doing so then this 
list if for you. 

In case you missed it, there is also a proteomics wiki page at 
http://wiki.galaxyproject.org/Proteomics

To subscribe to the galaxy-proteomics list please add your email address to the 
list here:
  http://lists.bx.psu.edu/listinfo/galaxy-proteomics

See http://wiki.g2.bx.psu.edu/Mailing%20Lists for more information on this and 
other Galaxy mailing lists, including links to searchable archives of all 
Galaxy lists.

Many thanks to Dave C. and the Galaxy team for setting this up.

Thanks

Ira


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Re: [galaxy-dev] Build the Galaxy under Cluster

[shenwiyn]

Hi Carlos,
Thank you very much for your help.I use Galaxy with the torque2.5.0,pbs_python 
for a test.It seems to work successfully !




shenwiyn

From: Carlos Borroto
Date: 2013-07-10 01:49
To: shenwiyn
CC: galaxy-...@bx.psu.edu
Subject: Re: [galaxy-dev] Build the Galaxy under Cluster
Hi shenwyn,

This is a very generic question hard to answer. I can tell you I use
Galaxy with the torque 4.1.x branch, maui scheduler and pbs-drmaa. I
would suggest you take a look a this[1] wiki page. Please notice as it
is mentioned in that page, using libdrmaa.so from torque won't work, I
can confirm that.

[1]http://wiki.galaxyproject.org/Admin/Config/Performance/Cluster

Hope it helps,
Carlos


On Tue, Jul 2, 2013 at 5:50 AM, shenwiyn  wrote:
> Hi everyone,
> I want to install my local Galaxy under the Cluster with TORQUE.I have a
> question about how they work together successfully.In addition,after my
> local Galaxy and TORQUE install successfully,anything else should I do to
> the Cluster Galaxy?Thank you very much.
>
> 
> shenwiyn
>
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[galaxy-dev] shall us specify which tool run in cluster?

[shenwiyn]

Hi Thon Deboer ,
I am a newer in Galaxy.I installed my Galaxy with Torque2.5.0 ,and Galaxy uses 
the pbs_modoule to interface with TORQUE.But I have some question of the  
job_conf.xml :
1.)In your  job_conf.xml ,you use regularjobs,longjobs,shortjobs...to run 
different jobs ,how our Galaxy know which tool belongs to regularjobs or 
longjobs.And what is the meaning of "nativeSpecification"?
2.)Shall us use collection of to specify bwa ?Does it mean the bwa belong to 
multicorejobs4,and run in cluster?
3.)Does every tool need us to specify which job it belong to?
 I saw http://wiki.galaxyproject.org/Admin/Config/Jobs about this,but I am not 
sure above.Could you help me please?




shenwiyn

From: Thon Deboer
Date: 2013-07-18 14:31
To: galaxy-dev
Subject: [galaxy-dev] Jobs remain in queue until restart
Hi,
 
I have noticed that from time to time, the job queue seems to be “stuck” and 
can only be unstuck by restarting galaxy.
The jobs seem to be in the queue state and the python job handler processes are 
hardly ticking over and the cluster is empty.
 
When I restart, the startup procedure realizes all jobs are in the a “new 
state” and it then assigns a jobhandler after which the jobs start fine….
 
Any ideas?
 Torque 
 
Thon
 
P.S I am using the june version of galaxy and I DO set limits on my users in 
job_conf.xml as so: (Maybe it is related? Before it went into dormant mode, 
this user had started lots of jobs and may have hit the limit, but I assumed 
this limit was the number of running jobs at one time, right?)
 





















-V -q long.q -pe smp 1



-V -q long.q -pe smp 1



-V -q short.q -pe smp 1



-V -q long.q -pe smp 4

 

 


python
interactiveOrCluster









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