Re: [galaxy-dev] server datacache.g2.bx.psu.edu unreachable

[Sarah Maman]

Hi Nate,

We have made the connection to datacache thanks to a rsync but rsync 
failed to connect to datacache :



rsync rsync://datacache.galaxyproject.org
rsync: failed to connect to datacache.galaxyproject.org: Connection 
timed out (110)
rsync error: error in socket IO (code 10) at clientserver.c(124) 
[receiver=3.0.6]


rsync -avzP rsync://datacache.g2.bx.psu.edu/indexes/phiX .
rsync: failed to connect to datacache.g2.bx.psu.edu: Connection timed 
out (110)
rsync error: error in socket IO (code 10) at clientserver.c(124) 
[receiver=3.0.6]


Could you please help us ?
Thanks in advance,
Sarah


Nate Coraor a écrit :

Hi Sarah,

The connection to datacache should be made over rsync. Please (e.g. 
`rsync rsync://datacache.galaxyproject.org 
` on the command line). Does this 
work for you?


--nate

On Thu, Dec 4, 2014 at 8:56 AM, Sarah Maman 
mailto:sarah.ma...@toulouse.inra.fr>> 
wrote:


Hello,

The server datacache.g2.bx.psu.edu isn't reachable since 2/3 days,
so we can't access to banks provided by Galaxy Project
(https://wiki.galaxyproject.org/Admin/UseGalaxyRsync). Could you
please give us some informaiton to solve this problem?


The error message is the following :

/*En essayant d'accéder à l'URL http://datacache.g2.bx.psu.edu/
l'erreur suivante a été rencontrée :*/

/*La connexion 128.118.250.10 a échouée.*/

/*Le système a retourné : *//*(111) Connection refused
*/

/
/Thanks in advance for your help,
Sarah Maman




-- 
  --*--

Sarah Maman
INRA - GenPhySE - SIGENAE
http://www.sigenae.org/
Chemin de Borde-Rouge - CS 52 627 - 31326 Castanet Tolosan cedex
31326 Castanet-Tolosan cedex - FRANCE
Tel:   +33(0)5.61.28.57.08 
Fax:   +33(0)5.61.28.57.53  
 --*--



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--
 --*--
Sarah Maman
INRA - GenPhySE - SIGENAE
http://www.sigenae.org/
Chemin de Borde-Rouge - CS 52 627 - 31326 Castanet Tolosan cedex
31326 Castanet-Tolosan cedex - FRANCE
Tel:   +33(0)5.61.28.57.08
Fax:   +33(0)5.61.28.57.53 
--*--


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[galaxy-dev] When do tool tests run on main & test toolsheds?

[Peter Briggs]

Hello all

When do the tool tests run on the main and test toolsheds? In Greg's 
blog about the toolshed:


http://gregvonkuster.org/galaxy-tool-shed-certifying-repositories-install-test-framework/

it's implied that the tests run daily for both, but it doesn't look like 
any tests have run for tools that I've pushed to either toolshed over 
the last few days. I wondered if was because my tests are broken 
somehow, but the links to "Latest revision: missing tool tests" etc 
don't bring anything up either.


I'm interested because I'd like to check that the tests run on the test 
toolshed before I push the tool to the main toolshed - so any advice or 
suggestions appreciated.


Best wishes, Peter

--
Peter Briggs peter.bri...@manchester.ac.uk
Bioinformatics Core Facility University of Manchester
B.1083 Michael Smith Bldg Tel: (0161) 2751482
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Re: [galaxy-dev] When do tool tests run on main & test toolsheds?

[Peter Cock]

Hi Peter B,

Originally the tests were nightly, but due to the rising load
this was dropped to every two or three days. As far as I
know that is still the goal.

Unfortunately the tool shed test system seems to be somewhat
broken at the moment, see this thread starting last month:

http://dev.list.galaxyproject.org/Nothing-being-tested-on-Test-and-main-Tool-Shed-tc4665917.html

or,

https://lists.galaxyproject.org/pipermail/galaxy-dev/2014-November/020792.html
...
https://lists.galaxyproject.org/pipermail/galaxy-dev/2014-December/021078.html

Peter C

On Thu, Dec 11, 2014 at 12:56 PM, Peter Briggs
 wrote:
> Hello all
>
> When do the tool tests run on the main and test toolsheds? In Greg's blog
> about the toolshed:
>
> http://gregvonkuster.org/galaxy-tool-shed-certifying-repositories-install-test-framework/
>
> it's implied that the tests run daily for both, but it doesn't look like any
> tests have run for tools that I've pushed to either toolshed over the last
> few days. I wondered if was because my tests are broken somehow, but the
> links to "Latest revision: missing tool tests" etc don't bring anything up
> either.
>
> I'm interested because I'd like to check that the tests run on the test
> toolshed before I push the tool to the main toolshed - so any advice or
> suggestions appreciated.
>
> Best wishes, Peter
>
> --
> Peter Briggs peter.bri...@manchester.ac.uk
> Bioinformatics Core Facility University of Manchester
> B.1083 Michael Smith Bldg Tel: (0161) 2751482
> ___
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Re: [galaxy-dev] When do tool tests run on main & test toolsheds?

[Peter Briggs]

Hello Peter C

Thanks - I guess there are some issues still to resolve then. I'll watch 
these threads and wait until the framework is (hopefully) fixed before 
worrying about it again.


Best wishes

Peter

On 11/12/14 13:06, Peter Cock wrote:

Hi Peter B,

Originally the tests were nightly, but due to the rising load
this was dropped to every two or three days. As far as I
know that is still the goal.

Unfortunately the tool shed test system seems to be somewhat
broken at the moment, see this thread starting last month:

http://dev.list.galaxyproject.org/Nothing-being-tested-on-Test-and-main-Tool-Shed-tc4665917.html

or,

https://lists.galaxyproject.org/pipermail/galaxy-dev/2014-November/020792.html
...
https://lists.galaxyproject.org/pipermail/galaxy-dev/2014-December/021078.html

Peter C

On Thu, Dec 11, 2014 at 12:56 PM, Peter Briggs
 wrote:

Hello all

When do the tool tests run on the main and test toolsheds? In Greg's blog
about the toolshed:

http://gregvonkuster.org/galaxy-tool-shed-certifying-repositories-install-test-framework/

it's implied that the tests run daily for both, but it doesn't look like any
tests have run for tools that I've pushed to either toolshed over the last
few days. I wondered if was because my tests are broken somehow, but the
links to "Latest revision: missing tool tests" etc don't bring anything up
either.

I'm interested because I'd like to check that the tests run on the test
toolshed before I push the tool to the main toolshed - so any advice or
suggestions appreciated.

Best wishes, Peter

--
Peter Briggs peter.bri...@manchester.ac.uk
Bioinformatics Core Facility University of Manchester
B.1083 Michael Smith Bldg Tel: (0161) 2751482
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--
Peter Briggs peter.bri...@manchester.ac.uk
Bioinformatics Core Facility University of Manchester
B.1083 Michael Smith Bldg Tel: (0161) 2751482
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[galaxy-dev] "join" produces an import error

[Wang, Yu]

Hi, I am testing Basic Protocol 1 on my local galaxy instance. But Join didn't 
work. What did I do wrong?
I installed join from galaxy main tool shed, bx_python_0_7 was installed but 
with installation Status "missing tool dependencies".



 Thanks.
-
job id: 49
tool id: 
toolshed.g2.bx.psu.edu/repos/devteam/join/gops_join_1/1.0.0
tool version: 1.0.0
job pid or drm id: 46018
job tool version:
-
job command line:
python 
/home/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/join/de21bdbb8d28/join/gops_join.py/local/galaxy/database/files/000/dataset_45.dat
 /local/galaxy/database/files/000/dataset_46.dat 
/local/galaxy/database/files/000/dataset_50.dat -1 1,2,3,6 -2 1,2,3,6 -m 1 -f 
none
-
job stderr:
Traceback (most recent call last):
 File 
"/home/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/join/de21bdbb8d28/join/gops_join.py",
 line 13, in 
   from bx.intervals import *
ImportError: No module named bx.intervals

Cheers,
Yu

di29her
w...@lrz.de

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Re: [galaxy-dev] "join" produces an import error

[Peter Cock]

On Wed, Dec 10, 2014 at 4:31 PM, Wang, Yu  wrote:
> Hi, I am testing Basic Protocol 1 on my local galaxy instance. But Join
> didn't work. What did I do wrong?
> I installed join from galaxy main tool shed, bx_python_0_7 was installed but
> with installation Status "missing tool dependencies".
>
>...
> Traceback (most recent call last):
>  File
> "/home/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/join/de21bdbb8d28/join/gops_join.py",
> line 13, in 
>from bx.intervals import *
> ImportError: No module named bx.intervals

It looks like the automated installation of bx python failed somehow.

Looking at the package, it will attempt to install NumPy 1.7.1
https://toolshed.g2.bx.psu.edu/view/devteam/package_bx_python_0_7

Galaxy dev team, why isn't this declaring a dependency on:
https://toolshed.g2.bx.psu.edu/view/iuc/package_numpy_1_7

Peter
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[galaxy-dev] Assertion errors when starting Galaxy

[Lance Parsons]

After updating my local instance of Galaxy to latest_2014.10.06 I get a 
number of similar errors relating to DisplayApplications.


It seems that others have run into this problem as well (see 
http://dev.list.galaxyproject.org/Assertion-errors-when-starting-Galaxy-td4665805.html), 
but as of yet I haven't figured out the cause (or a workaround or 
solution).


An example is below:

galaxy.datatypes.registry ERROR 2014-12-11 10:57:01,183 Error loading 
display application (./display_applications/igv/vcf.xml): Filename and 
id attributes required for dynamic_links

Traceback (most recent call last):
  File "/data/galaxy-dev/galaxy-dev/lib/galaxy/datatypes/registry.py", 
line 576, in load_display_applications

display_app = DisplayApplication.from_file( config_path, self )
  File 
"/data/galaxy-dev/galaxy-dev/lib/galaxy/datatypes/display_applications/application.py", 
line 170, in from_file
return cls.from_elem( parse_xml( filename ).getroot(), 
datatypes_registry )
  File 
"/data/galaxy-dev/galaxy-dev/lib/galaxy/datatypes/display_applications/application.py", 
line 183, in from_elem
for link in DynamicDisplayApplicationBuilder( dynamic_links, rval, 
datatypes_registry.build_sites ):
  File 
"/data/galaxy-dev/galaxy-dev/lib/galaxy/datatypes/display_applications/application.py", 
line 91, in __init__
assert filename is not None, 'Filename and id attributes required 
for dynamic_links'

AssertionError: Filename and id attributes required for dynamic_links


Note: Cross posted on Galaxy Biostars site: 
https://biostar.usegalaxy.org/p/9944/


--
Lance Parsons - Scientific Programmer
134 Carl C. Icahn Laboratory
Lewis-Sigler Institute for Integrative Genomics
Princeton University

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