date:20160620

Re: [galaxy-dev] Infinite recursion on conda dependency manager

2016-06-20 Thread Rathert , Philipp , Dr .

Hi Björn,



this is not working 



root@galaxy:/galaxy-central# export 
PATH=/galaxy-central/tool_deps/_conda/bin/:$PATH

root@galaxy:/galaxy-central# conda install -y -q conda=3.19.3

bash: conda: command not found



cheers,



Philipp



-Original message-
From: Björn Grüning 
Sent: Monday 20th June 2016 13:21
To: Rathert, Philipp, Dr. ; 
galaxy-dev@lists.galaxyproject.org
Cc: Björn Grüning 
Subject: Re: [galaxy-dev] Infinite recursion on conda dependency manager


Hi Philipp,

you are inside of the Docker container?

Can you do a:

export PATH=/galaxy-central/tool_deps/_conda/bin/:$PATH
conda install -y -q conda=3.19.3

Ciao,
Bjoern


Am 20.06.2016 um 13:01 schrieb Rathert, Philipp, Dr.:
> Dear all,
> 
> 
> 
> 
> 
>  I am trying to install bowtie as a dependency for bismarck. however, I am 
> getting the error posted below.
> 
> 
> 
> Maybe somebody has an idea how to fix this.
> 
> 
> 
> 
> 
> Thanks in advance,
> 
> 
> 
> philipp
> 
> 
> 
> 
> 
> In file included from SeqAn-1.1/seqan/basic.h:64:0,
>  from SeqAn-1.1/seqan/sequence.h:27,
>  from SeqAn-1.1/seqan/index.h:27,
>  from ebwt_build.cpp:5:
> SeqAn-1.1/seqan/basic/basic_holder.h: In function ‘void 
> seqan::setValue(seqan::Holder&, TValue&)’:
> SeqAn-1.1/seqan/basic/basic_holder.h:1001:59: warning: typedef ‘THolderType’ 
> locally defined but not used [-Wunused-local-typedefs]
>   typedef typename Value >::Type THolderType;
>ˆ
> SeqAn-1.1/seqan/basic/basic_holder.h: In function ‘typename 
> seqan::Reference >::Type 
> seqan::value(seqan::Holder&)’:
> SeqAn-1.1/seqan/basic/basic_holder.h:1027:59: warning: typedef ‘THolderType’ 
> locally defined but not used [-Wunused-local-typedefs]
>   typedef typename Value >::Type THolderType;
>ˆ
> SeqAn-1.1/seqan/basic/basic_holder.h: In function ‘void 
> seqan::assignValue(seqan::Holder&, const TSource&)’:
> SeqAn-1.1/seqan/basic/basic_holder.h:1051:59: warning: typedef ‘THostValue’ 
> locally defined but not used [-Wunused-local-typedefs]
>   typedef typename Value >::Type THostValue;
>ˆ
> In file included from SeqAn-1.1/seqan/sequence.h:38:0,
>  from SeqAn-1.1/seqan/index.h:27,
>  from ebwt_build.cpp:5:
> SeqAn-1.1/seqan/sequence/lexical.h: In function ‘void 
> seqan::compare_(seqan::Lexical&, TLeft&, TRight&)’:
> SeqAn-1.1/seqan/sequence/lexical.h:239:38: warning: typedef ‘TLeftValue’ 
> locally defined but not used [-Wunused-local-typedefs]
>   typedef typename Value::Type TLeftValue;
>   ˆ
> In file included from SeqAn-1.1/seqan/sequence.h:51:0,
>  from SeqAn-1.1/seqan/index.h:27,
>  from ebwt_build.cpp:5:
> SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void 
> seqan::assign(seqan::String&, const TSource&, 
> seqan::Tag)’:
> SeqAn-1.1/seqan/sequence/string_base.h:811:44: warning: typedef ‘TTarget’ 
> locally defined but not used [-Wunused-local-typedefs]
>   typedef String TTarget;
> ˆ
> SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void 
> seqan::assign(seqan::String&, const TSource&, TSize, 
> seqan::Tag)’:
> SeqAn-1.1/seqan/sequence/string_base.h:821:44: warning: typedef ‘TTarget’ 
> locally defined but not used [-Wunused-local-typedefs]
>   typedef String TTarget;
> ˆ
> SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void 
> seqan::assign(seqan::String&, const TSourceValue*, 
> seqan::Tag)’:
> SeqAn-1.1/seqan/sequence/string_base.h:834:44: warning: typedef ‘TTarget’ 
> locally defined but not used [-Wunused-local-typedefs]
>   typedef String TTarget;
> ˆ
> SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void 
> seqan::assign(seqan::String&, const TSourceValue*, TSize, 
> seqan::Tag)’:
> SeqAn-1.1/seqan/sequence/string_base.h:844:44: warning: typedef ‘TTarget’ 
> locally defined but not used [-Wunused-local-typedefs]
>   typedef String TTarget;
> ˆ
> SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void 
> seqan::append(seqan::String&, const TSource&, 
> seqan::Tag)’:
> SeqAn-1.1/seqan/sequence/string_base.h:1044:44: warning: typedef ‘TTarget’ 
> locally defined but not used [-Wunused-local-typedefs]
>   typedef String TTarget;
> ˆ
> SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void 
> seqan::append(seqan::String&, const TSource&, typename 
> seqan::Size >::Type, seqan::Tag)’:
> SeqAn-1.1/seqan/sequence/string_base.h:1056:44: warning: typedef ‘TTarget’ 
> locally defined but not used [-Wunused-local-typedefs]
>   typedef String TTarget;
> ˆ
> SeqAn-1.1/seqan/sequence/stri

Re: [galaxy-dev] Infinite recursion on conda dependency manager

2016-06-20 Thread Björn Grüning

Hi Philipp,

you are inside of the Docker container?

Can you do a:

export PATH=/galaxy-central/tool_deps/_conda/bin/:$PATH
conda install -y -q conda=3.19.3

Ciao,
Bjoern


Am 20.06.2016 um 13:01 schrieb Rathert, Philipp, Dr.:
> Dear all,
> 
> 
> 
> 
> 
>  I am trying to install bowtie as a dependency for bismarck. however, I am 
> getting the error posted below.
> 
> 
> 
> Maybe somebody has an idea how to fix this.
> 
> 
> 
> 
> 
> Thanks in advance,
> 
> 
> 
> philipp
> 
> 
> 
> 
> 
> In file included from SeqAn-1.1/seqan/basic.h:64:0,
>  from SeqAn-1.1/seqan/sequence.h:27,
>  from SeqAn-1.1/seqan/index.h:27,
>  from ebwt_build.cpp:5:
> SeqAn-1.1/seqan/basic/basic_holder.h: In function ‘void 
> seqan::setValue(seqan::Holder&, TValue&)’:
> SeqAn-1.1/seqan/basic/basic_holder.h:1001:59: warning: typedef ‘THolderType’ 
> locally defined but not used [-Wunused-local-typedefs]
>   typedef typename Value >::Type THolderType;
>^
> SeqAn-1.1/seqan/basic/basic_holder.h: In function ‘typename 
> seqan::Reference >::Type 
> seqan::value(seqan::Holder&)’:
> SeqAn-1.1/seqan/basic/basic_holder.h:1027:59: warning: typedef ‘THolderType’ 
> locally defined but not used [-Wunused-local-typedefs]
>   typedef typename Value >::Type THolderType;
>^
> SeqAn-1.1/seqan/basic/basic_holder.h: In function ‘void 
> seqan::assignValue(seqan::Holder&, const TSource&)’:
> SeqAn-1.1/seqan/basic/basic_holder.h:1051:59: warning: typedef ‘THostValue’ 
> locally defined but not used [-Wunused-local-typedefs]
>   typedef typename Value >::Type THostValue;
>^
> In file included from SeqAn-1.1/seqan/sequence.h:38:0,
>  from SeqAn-1.1/seqan/index.h:27,
>  from ebwt_build.cpp:5:
> SeqAn-1.1/seqan/sequence/lexical.h: In function ‘void 
> seqan::compare_(seqan::Lexical&, TLeft&, TRight&)’:
> SeqAn-1.1/seqan/sequence/lexical.h:239:38: warning: typedef ‘TLeftValue’ 
> locally defined but not used [-Wunused-local-typedefs]
>   typedef typename Value::Type TLeftValue;
>   ^
> In file included from SeqAn-1.1/seqan/sequence.h:51:0,
>  from SeqAn-1.1/seqan/index.h:27,
>  from ebwt_build.cpp:5:
> SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void 
> seqan::assign(seqan::String&, const TSource&, 
> seqan::Tag)’:
> SeqAn-1.1/seqan/sequence/string_base.h:811:44: warning: typedef ‘TTarget’ 
> locally defined but not used [-Wunused-local-typedefs]
>   typedef String TTarget;
> ^
> SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void 
> seqan::assign(seqan::String&, const TSource&, TSize, 
> seqan::Tag)’:
> SeqAn-1.1/seqan/sequence/string_base.h:821:44: warning: typedef ‘TTarget’ 
> locally defined but not used [-Wunused-local-typedefs]
>   typedef String TTarget;
> ^
> SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void 
> seqan::assign(seqan::String&, const TSourceValue*, 
> seqan::Tag)’:
> SeqAn-1.1/seqan/sequence/string_base.h:834:44: warning: typedef ‘TTarget’ 
> locally defined but not used [-Wunused-local-typedefs]
>   typedef String TTarget;
> ^
> SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void 
> seqan::assign(seqan::String&, const TSourceValue*, TSize, 
> seqan::Tag)’:
> SeqAn-1.1/seqan/sequence/string_base.h:844:44: warning: typedef ‘TTarget’ 
> locally defined but not used [-Wunused-local-typedefs]
>   typedef String TTarget;
> ^
> SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void 
> seqan::append(seqan::String&, const TSource&, 
> seqan::Tag)’:
> SeqAn-1.1/seqan/sequence/string_base.h:1044:44: warning: typedef ‘TTarget’ 
> locally defined but not used [-Wunused-local-typedefs]
>   typedef String TTarget;
> ^
> SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void 
> seqan::append(seqan::String&, const TSource&, typename 
> seqan::Size >::Type, seqan::Tag)’:
> SeqAn-1.1/seqan/sequence/string_base.h:1056:44: warning: typedef ‘TTarget’ 
> locally defined but not used [-Wunused-local-typedefs]
>   typedef String TTarget;
> ^
> SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void 
> seqan::append(seqan::String&, TSourceValue*, 
> seqan::Tag)’:
> SeqAn-1.1/seqan/sequence/string_base.h:1070:44: warning: typedef ‘TTarget’ 
> locally defined but not used [-Wunused-local-typedefs]
>   typedef String TTarget;
> ^
> SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void 
> seqan::append(seqan::String&, TSourceValue*, typename 
> seqan::Size >::Type, seqan::Tag)’:
> SeqAn-1.1/seqan/sequen

Re: [galaxy-dev] History is not up-to-date

2016-06-20 Thread Björn Grüning

Hi,

the image has the latest version, so you should be able to just repull
the image.

Cheers,
Bjoern

Am 20.06.2016 um 12:16 schrieb Nicola Soranzo:
> Hi Philipp,
> this has been fixed in the mean time on the release_16.04 branch of Galaxy, 
> see
> 
> https://github.com/galaxyproject/galaxy/pull/2506
> 
> Can you try to update your Galaxy server in the container and check if it's 
> working?
> 
> Cheers,
> Nicola
> 
> On 20/06/16 10:31, Rathert, Philipp, Dr. wrote:
>> RE: [galaxy-dev] History is not up-to-date
>>
>> Hi Carl,
>>
>>
>> it looks like the time is not correct.
>>
>>
>>  System Time: 2016-06-20T09:30:00.038328386Z
>>
>>  EventsListeners: 0
>>
>>  Init SHA1:
>>
>>  Init Path: /usr/local/bin/docker
>>
>>  Docker Root Dir: /mnt/sda1/var/lib/docker
>>
>> Labels:
>>
>>  provider=virtualbox
>>
>>
>> the clock on my mac says 11:25
>>
>>
>>
>> Is there an easy way to fix this or do I need to run galaxy in a new 
>> container? I run the container with -privileged=true, so it should be 
>> possible 
>> but so far I didn't find how...
>>
>>
>> Thanks for your help.
>>
>>
>> Cheers,
>>
>>
>> Philipp
>>
>>
>>
>>
>>
>> -Original message-
>> *From:* Philipp Rathert 
>> *Sent:* Wednesday 15th June 2016 9:07
>> *To:* 'Carl Eberhard' 
>> *Cc:* galaxy-dev@lists.galaxyproject.org
>> *Subject:* Re: [galaxy-dev] History is not up-to-date
>>
>> 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.
>> > > 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
>> HTT

Re: [galaxy-dev] History is not up-to-date

2016-06-20 Thread Rathert , Philipp , Dr .

Dear Nicola,



I am using the 16.04 release. did you implement changes in this one recently?



Cheers,



Philipp

-Original message-
From: Nicola Soranzo 
Sent: Monday 20th June 2016 12:16
To: Rathert, Philipp, Dr. ; 'Carl 
Eberhard' 
Cc: galaxy-dev@lists.galaxyproject.org
Subject: Re: [galaxy-dev] History is not up-to-date

 
 Hi Philipp,
 this has been fixed in the mean time on the release_16.04 branch of Galaxy, see
 
 https://github.com/galaxyproject/galaxy/pull/2506
 
 Can you try to update your Galaxy server in the container and check if it's 
working?
 
 Cheers,
 Nicola
 
 
On 20/06/16 10:31, Rathert, Philipp, Dr. wrote:
 
 

Hi Carl,
 

 


 

 

it looks like the time is not correct. 

 


 

 

 System Time: 2016-06-20T09:30:00.038328386Z

 

 EventsListeners: 0

 

 Init SHA1: 

 

 Init Path: /usr/local/bin/docker

 

 Docker Root Dir: /mnt/sda1/var/lib/docker

 

Labels:

 

 provider=virtualbox

 


 

 

the clock on my mac says 11:25

 


 

 


 

 

Is there an easy way to fix this or do I need to run galaxy in a new 
container? I run the container with -privileged=true, so it should be possible 
but so far I didn't find how...

 


 

 

Thanks for your help.

 


 

 

Cheers,

 


 

 

Philipp 

 


 

 


 

 


 

 


 

 -Original message-
 From: Philipp Rathert 
 Sent: Wednesday 15th June 2016 9:07
 To: 'Carl Eberhard' 
 Cc: galaxy-dev@lists.galaxyproject.org
 Subject: Re: [galaxy-dev] History is not up-to-date
 
 
 
 

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. 
 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
 => generate

Re: [galaxy-dev] History is not up-to-date

2016-06-20 Thread Rathert , Philipp , Dr .

Hi Carl,



it looks like the time is not correct. 



 System Time: 2016-06-20T09:30:00.038328386Z

 EventsListeners: 0

 Init SHA1: 

 Init Path: /usr/local/bin/docker

 Docker Root Dir: /mnt/sda1/var/lib/docker

Labels:

 provider=virtualbox



the clock on my mac says 11:25





Is there an easy way to fix this or do I need to run galaxy in a new 
container? I run the container with -privileged=true, so it should be possible 
but so far I didn't find how...



Thanks for your help.



Cheers,



Philipp 









-Original message-
From: Philipp Rathert 
Sent: Wednesday 15th June 2016 9:07
To: 'Carl Eberhard' 
Cc: galaxy-dev@lists.galaxyproject.org
Subject: Re: [galaxy-dev] History is not up-to-date

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

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Re: [galaxy-dev] History is not up-to-date

Re: [galaxy-dev] History is not up-to-date

Re: [galaxy-dev] History is not up-to-date

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