[galaxy-dev] fail to install pulsar on windows machine

2016-06-15 Thread Jun Fan 
Dear all,

  I used to utilize LWR on a windows machine to run windows-only tools. As 
recently I upgrade the Galaxy to the latest stable version 16_01, Galaxy 
indicated that no LwrJobRunner available. Therefore I had to install Pulsar. 
When I followed the instruction at 
https://pulsar.readthedocs.io/en/latest/install.html and failed.


1.   From PyPI option: after executing pulsar-config and two files app.yaml 
and server.ini being generated, the command pulsar returns the error saying 
'pulsar' is not recognized as an internal or external command, operable program 
or batch file.

2.   From Source option: it failed at run.bat step and got the main error 
message as "ImportError: No module named grp". My python is 2.7.11 and in the 
python shell, the command "import grp" gives the same error.

Any help is welcome

Best regards!
Jun
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Re: [galaxy-dev] Infinite recursion on conda dependency manager

2016-06-15 Thread Björn Grüning 
Hi Peter,

please install conda in version 3.19.3. Conda-4 has a bug when using
with --offline and --local.

conda install conda=3.19.3 should work.

https://github.com/galaxyproject/tools-iuc/blob/master/.travis.yml#L15

Thanks,
Bjoern

Am 15.06.2016 um 00:44 schrieb Peter van Heusden:
> Hi there
> 
> I've got a package in our lab conda channel (its still in testing phase)
> called goget. This is specified as a requirement for the build_ctb_gene
> tool like this:
> 
> 
>goget
> 
> 
> When the tool runs, I see infinite recursion on the conda side:
> 
> https://gist.github.com/pvanheus/c16a07a2c954741a311881cc7606df8d
> 
> Any ideas?
> 
> Thanks,
> Peter
> 
> 
> 
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Re: [galaxy-dev] History is not up-to-date

2016-06-15 Thread Philipp Rathert 
HI Carl,

 

I am travelling these days but will check on Monday. 

 

Thanks in advance.

 

Cheers,

 

Philipp 

 

From: Carl Eberhard [mailto:carlfeberh...@gmail.com] 
Sent: Tuesday, June 14, 2016 6:24 PM
To: Rathert, Philipp, Dr. 
Cc: galaxy-dev@lists.galaxyproject.org
Subject: Re: [galaxy-dev] History is not up-to-date

 

Hi, Phillip

 

Quick questions:

- is the time properly set on the computer where you've got Galaxy running in 
the browser?

- is the time in the docker container also correct?

 

>From you terminal output it looks like the update time might be the issue and 
>we can then take it from there. Thanks

 

 

On Tue, Jun 14, 2016 at 11:28 AM, Rathert, Philipp, Dr. 
mailto:philipp.rath...@ibc.uni-stuttgart.de> > wrote:

Dear All,

 

 

I have a problem with my histories. 

We are running the Docker galaxy stable version 16.04 and when I start a tool 
the history does not show that it is running. it is not specific for any tool 
but for all.

 

 

 

 



 

 

however, something is running in the back

 

129.69.102.30 - - [14/Jun/2016:12:57:21 +] "GET 
/api/histories/5114a2a207b7caff/contents?v=dev&q=update_time-ge&qv=2016-06-14T12%3A49%3A16.601Z
 HTTP/1.1" 200 - "http://129.69.102.42/"; "Mozilla/5.0 (Macintosh; Intel Mac OS 
X 10_11_3) AppleWebKit/601.4.4 (KHTML, like Gecko) Version/9.0.3 Safari/601.4.4"

[pid: 271|app: 0|req: 74/163] 129.69.102.30 () {44 vars in 964 bytes} [Tue Jun 
14 12:57:21 2016] GET 
/api/histories/5114a2a207b7caff/contents?v=dev&q=update_time-ge&qv=2016-06-14T12%3A49%3A16.601Z
 => generated 2511 bytes in 33 msecs (HTTP/1.1 200) 3 headers in 124 bytes (1 
switches on core 2)

129.69.102.30 - - [14/Jun/2016:12:57:25 +] "GET 
/api/histories/5114a2a207b7caff/contents?v=dev&q=update_time-ge&qv=2016-06-14T12%3A49%3A20.635Z
 HTTP/1.1" 200 - "http://129.69.102.42/"; "Mozilla/5.0 (Macintosh; Intel Mac OS 
X 10_11_3) AppleWebKit/601.4.4 (KHTML, like Gecko) Version/9.0.3 Safari/601.4.4"

[pid: 271|app: 0|req: 75/164] 129.69.102.30 () {44 vars in 964 bytes} [Tue Jun 
14 12:57:25 2016] GET 
/api/histories/5114a2a207b7caff/contents?v=dev&q=update_time-ge&qv=2016-06-14T12%3A49%3A20.635Z
 => generated 2511 bytes in 29 msecs (HTTP/1.1 200) 3 headers in 124 bytes (1 
switches on core 1)

129.69.102.30 - - [14/Jun/2016:12:57:29 +] "GET 
/api/histories/5114a2a207b7caff/contents?v=dev&q=update_time-ge&qv=2016-06-14T12%3A49%3A24.673Z
 HTTP/1.1" 200 - "http://129.69.102.42/"; "Mozilla/5.0 (Macintosh; Intel Mac OS 
X 10_11_3) AppleWebKit/601.4.4 (KHTML, like Gecko) Version/9.0.3 Safari/601.4.4"

[pid: 271|app: 0|req: 76/165] 129.69.102.30 () {44 vars in 964 bytes} [Tue Jun 
14 12:57:29 2016] GET 
/api/histories/5114a2a207b7caff/contents?v=dev&q=update_time-ge&qv=2016-06-14T12%3A49%3A24.673Z
 => generated 2112 bytes in 30 msecs (HTTP/1.1 200) 3 headers in 124 bytes (1 
switches on core 0)

129.69.102.30 - - [14/Jun/2016:12:57:33 +] "GET 
/api/histories/5114a2a207b7caff/contents?v=dev&q=update_time-ge&qv=2016-06-14T12%3A49%3A28.711Z
 HTTP/1.1" 200 - "http://129.69.102.42/"; "Mozilla/5.0 (Macintosh; Intel Mac OS 
X 10_11_3) AppleWebKit/601.4.4 (KHTML, like Gecko) Version/9.0.3 Safari/601.4.4"

[pid: 272|app: 0|req: 90/166] 129.69.102.30 () {44 vars in 964 bytes} [Tue Jun 
14 12:57:33 2016] GET 
/api/histories/5114a2a207b7caff/contents?v=dev&q=update_time-ge&qv=2016-06-14T12%3A49%3A28.711Z
 => generated 2112 bytes in 32 msecs (HTTP/1.1 200) 3 headers in 124 bytes (1 
switches on core 0)

129.69.102.30 - - [14/Jun/2016:12:57:37 +] "GET 
/api/histories/5114a2a207b7caff/contents?v=dev&q=update_time-ge&qv=2016-06-14T12%3A49%3A32.749Z
 HTTP/1.1" 200 - "http://129.69.102.42/"; "Mozilla/5.0 (Macintosh; Intel Mac OS 
X 10_11_3) AppleWebKit/601.4.4 (KHTML, like Gecko) Version/9.0.3 Safari/601.4.4"

[pid: 271|app: 0|req: 77/167] 129.69.102.30 () {44 vars in 964 bytes} [Tue Jun 
14 12:57:37 2016] GET 
/api/histories/5114a2a207b7caff/contents?v=dev&q=update_time-ge&qv=2016-06-14T12%3A49%3A32.749Z
 => generated 2112 bytes in 27 msecs (HTTP/1.1 200) 3 headers in 124 bytes (1 
switches on core 3)

 

 

 

I am not sure how to fix this and I am happy for any suggestion.

 

Cheers,

 

Philipp


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