Re: [galaxy-dev] Shared Data Library, large number of files

[Martin Čech]

The code at L120 does not exist in 16.07. It was broken in 16.10 and fixed
for 17.01. I made a PR to backport the fix to 16.10:
https://github.com/galaxyproject/galaxy/pull/3728

You shouldn't be seeing the 'Cannot read property 'masthead' of
undefined' error in 16.07 and it should be fixed in 16.10 after that PR is
merged. 17.01 or dev shouldn't have this problem already.

Please let me know how this works for you.

Thanks,

Martin



On Wed, Mar 8, 2017 at 3:09 PM D K  wrote:

> Hi Martin,
>
> I've pasted the file you requested here:
>
> http://collabedit.com/xcx5b
>
> Thanks!
>
> On Wed, Mar 8, 2017 at 11:04 AM, Martin Čech  wrote:
>
> Can you please share your '/client/galaxy/scripts/layout/menu.js' file
> with me? (e.g. using https://gist.github.com or similar).
>
> thanks
>
> M.
>
>
> On Wed, Mar 8, 2017 at 1:34 PM D K  wrote:
>
> Hi Martin,
>
> I've tried this on both v16.07 and v16.10
>
> D
>
>
>
> On Wed, Mar 8, 2017 at 10:29 AM, Martin Čech  wrote:
>
> Daniel:
>
> what version is your Galaxy?
>
> Martin
>
> On Wed, Mar 8, 2017 at 12:40 PM D K  wrote:
>
> I've copied and pasted the javascript error below. Any help would be
> greatly appreciated. Thanks!
>
> Uncaught TypeError: Cannot read property 'masthead' of undefined
> at n. (menu.js:120)
> at Function.each (jquery.js:370)
> at HTMLDocument. (menu.js:117)
> at l (jquery.js:3232)
> at Object.add [as done] (jquery.js:3291)
> at t.fn.init.vt.fn.ready (jquery.js:3542)
> at callback (menu.js:116)
> at Object.t.success (backbone.js:1051)
> at l (jquery.js:3232)
> at Object.fireWith [as resolveWith] (jquery.js:3362)
>
>
> On Thu, Mar 2, 2017 at 10:43 AM, D K  wrote:
>
> Hi Martin,
>
> I do get a javascript error, I've attached a screenshot of the relevant
> window. I also tried logging in as a non-admin user and had the same issue.
> In this Galaxy instance are 5 data libraries, each with about 150
> individual folders, and each folder has a variable number of fastq.gz files.
>
> Thanks!
>
> On Thu, Mar 2, 2017 at 10:13 AM, Martin Čech  wrote:
>
> Daniel:
>
> Could you please open browser console and look for javascript errors on
> the page that fails to load for you? Additionally I assume you are an admin
> when trying this (admins load all of the instance's libraries) could you
> try loading the library list as a normal user? How many libraries do you
> have on the instance?
>
> Thanks
>
> Martin
>
> On Thu, Mar 2, 2017 at 12:38 PM D K  wrote:
>
> Hi Martin / Hans / Devon,
>
> I can confirm that I am using the new UI from the top menu. Right now when
> I click on the link I often do not even get the list of libraries whereas
> when I click on the admin Data Library link I at least see the list of
> libraries (although I can't open any of them since they are so large). I've
> tried refreshing the page, deleting the cookies for the session and using
> Incognito mode, using chrome and firefox both from a linux and windows
> machine and can confirm this behavior on all systems. However, occasionally
> when clicking the Shared Data Library link from the top I do get a list of
> libraries and can navigate them, but this has only happened once during my
> tests and I cannot replicate this behavior.
>
> Thanks for the assistance!
>
> On Thu, Mar 2, 2017 at 5:47 AM, Martin Čech  wrote:
>
> Hi all,
>
> *Devon* is correct -the old data library UI under Admin menu is still in
> place (because it has some features perceived as important to some admins).
> However majority of users and most of the admins are using the interface
> under 'Shared Data' I hope and the old UI is deprecated since 15.10 (
> https://docs.galaxyproject.org/en/master/releases/15.10_announce.html). I
> created a PR to adjust the label in the admin interface to make this clear:
> https://github.com/galaxyproject/galaxy/pull/3694
>
> The old UI is very slow for large libraries but the new UI under Shared
> Data/Data Libraries in the top menu shouldn't have this kind of issues for
> hundreds of folders/datasets that are mentioned here.
>
> *Daniel* are you using the new UI form the top menu? If so are you
> experiencing this only with a specific folder full of linked datasets or
> does it occur for any folder with many datasets in it?
>
> Martin
>
>
>
> On Thu, Mar 2, 2017 at 3:49 AM Devon Ryan  wrote:
>
> I observe the same thing on 16.07. As an example, I'm just opened a
> data library under Admin->Data->Data Libraries and this took about a
> minute and a half. It looks like this is related to the quantity of
> data in this folder. The associated entry in the uwsgi log is as
> follows:
>
> [pid: 357|app: 0|req: 2059/5647] 10.1.6.77 () {44 vars in 1220 bytes}
> [Thu Mar  2 08:40:19 2017] GET
>
> 

Re: [galaxy-dev] Shared Data Library, large number of files

[D K]

Hi Martin,

I've pasted the file you requested here:

http://collabedit.com/xcx5b

Thanks!

On Wed, Mar 8, 2017 at 11:04 AM, Martin Čech  wrote:

> Can you please share your '/client/galaxy/scripts/layout/menu.js' file
> with me? (e.g. using https://gist.github.com or similar).
>
> thanks
>
> M.
>
>
> On Wed, Mar 8, 2017 at 1:34 PM D K  wrote:
>
>> Hi Martin,
>>
>> I've tried this on both v16.07 and v16.10
>>
>> D
>>
>>
>>
>> On Wed, Mar 8, 2017 at 10:29 AM, Martin Čech  wrote:
>>
>> Daniel:
>>
>> what version is your Galaxy?
>>
>> Martin
>>
>> On Wed, Mar 8, 2017 at 12:40 PM D K  wrote:
>>
>> I've copied and pasted the javascript error below. Any help would be
>> greatly appreciated. Thanks!
>>
>> Uncaught TypeError: Cannot read property 'masthead' of undefined
>> at n. (menu.js:120)
>> at Function.each (jquery.js:370)
>> at HTMLDocument. (menu.js:117)
>> at l (jquery.js:3232)
>> at Object.add [as done] (jquery.js:3291)
>> at t.fn.init.vt.fn.ready (jquery.js:3542)
>> at callback (menu.js:116)
>> at Object.t.success (backbone.js:1051)
>> at l (jquery.js:3232)
>> at Object.fireWith [as resolveWith] (jquery.js:3362)
>>
>>
>> On Thu, Mar 2, 2017 at 10:43 AM, D K  wrote:
>>
>> Hi Martin,
>>
>> I do get a javascript error, I've attached a screenshot of the relevant
>> window. I also tried logging in as a non-admin user and had the same issue.
>> In this Galaxy instance are 5 data libraries, each with about 150
>> individual folders, and each folder has a variable number of fastq.gz files.
>>
>> Thanks!
>>
>> On Thu, Mar 2, 2017 at 10:13 AM, Martin Čech  wrote:
>>
>> Daniel:
>>
>> Could you please open browser console and look for javascript errors on
>> the page that fails to load for you? Additionally I assume you are an admin
>> when trying this (admins load all of the instance's libraries) could you
>> try loading the library list as a normal user? How many libraries do you
>> have on the instance?
>>
>> Thanks
>>
>> Martin
>>
>> On Thu, Mar 2, 2017 at 12:38 PM D K  wrote:
>>
>> Hi Martin / Hans / Devon,
>>
>> I can confirm that I am using the new UI from the top menu. Right now
>> when I click on the link I often do not even get the list of libraries
>> whereas when I click on the admin Data Library link I at least see the list
>> of libraries (although I can't open any of them since they are so large).
>> I've tried refreshing the page, deleting the cookies for the session and
>> using Incognito mode, using chrome and firefox both from a linux and
>> windows machine and can confirm this behavior on all systems. However,
>> occasionally when clicking the Shared Data Library link from the top I do
>> get a list of libraries and can navigate them, but this has only happened
>> once during my tests and I cannot replicate this behavior.
>>
>> Thanks for the assistance!
>>
>> On Thu, Mar 2, 2017 at 5:47 AM, Martin Čech  wrote:
>>
>> Hi all,
>>
>> *Devon* is correct -the old data library UI under Admin menu is still in
>> place (because it has some features perceived as important to some admins).
>> However majority of users and most of the admins are using the interface
>> under 'Shared Data' I hope and the old UI is deprecated since 15.10 (
>> https://docs.galaxyproject.org/en/master/releases/15.10_announce.html).
>> I created a PR to adjust the label in the admin interface to make this
>> clear: https://github.com/galaxyproject/galaxy/pull/3694
>>
>> The old UI is very slow for large libraries but the new UI under Shared
>> Data/Data Libraries in the top menu shouldn't have this kind of issues for
>> hundreds of folders/datasets that are mentioned here.
>>
>> *Daniel* are you using the new UI form the top menu? If so are you
>> experiencing this only with a specific folder full of linked datasets or
>> does it occur for any folder with many datasets in it?
>>
>> Martin
>>
>>
>>
>> On Thu, Mar 2, 2017 at 3:49 AM Devon Ryan  wrote:
>>
>> I observe the same thing on 16.07. As an example, I'm just opened a
>> data library under Admin->Data->Data Libraries and this took about a
>> minute and a half. It looks like this is related to the quantity of
>> data in this folder. The associated entry in the uwsgi log is as
>> follows:
>>
>> [pid: 357|app: 0|req: 2059/5647] 10.1.6.77 () {44 vars in 1220 bytes}
>> [Thu Mar  2 08:40:19 2017] GET
>> /library_common/browse_library?sort=name=All=All
>> deleted=False=library_admin=browse=355326571f7132ff
>> => generated 21761790 bytes in 108644 msecs (HTTP/1.1 200) 2 headers
>> in 73 bytes (14 switches on core 2)
>>
>> So this library is causing ~21 megs of data to be returned to the
>> browser, which I presume is the source of the issue.
>>
>> As an aside, the old data library API is still in use in the admin
>> section until at least 16.07. 

Re: [galaxy-dev] DeepTools installation error

[Devon Ryan]

The documentation here is quite good: 
https://docs.galaxyproject.org/en/master/admin/conda_faq.html


As an aside, the dockerized version of Galaxy 
(https://github.com/bgruening/docker-galaxy-stable) from Björn Gruening 
makes this convenient.


Devon


On 03/08/2017 08:55 PM, Md. Rezaul Karim wrote:

Hi Devon,

I'm also experiencing similar issues. Could you please briefly explain 
how to use Condo with Galaxy?


Is there any other versions where Conda is integrated apart from the 
regular Galaxy distributions?


On Mar 8, 2017 7:38 PM, "Devon Ryan" > wrote:


Hi Timo,

Use conda for dependency resolution in Galaxy and make your life
easier :)

Devon

On 03/08/2017 06:31 PM, Timo Janßen wrote:

Hi all,

trying to install the deeptools_suite from the toolshed I only get the
following error:

"500 Internal Server Error

nginx/1.11.10"

This happens as well for the dependencies, e.g. deeptools_bigwig_compare.

I am currently using Galaxy 16.10 with nginx proxy.

Also the installation of the dependency
package_python_2_7_matplotlib_1_4 fails because of a missing dependency:

"Error installing tool dependency python version 2.7.10: Unable to
locate required tool shed repository named package_python_2_7_10 owned
by iuc with revision 80931fb5f433."

Has anyone seen these problems before and knows a solution?

Best regards,
Timo Janßen

___
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-- 
Devon Ryan, PhD

Bioinformatician / Data manager
Bioinformatics Core Facility
Max Planck Institute for Immunobiology and Epigenetics
Email:dprya...@gmail.com 

___ Please
keep all replies on the list by using "reply all" in your mail
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lists, please use the interface at:
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 To search Galaxy mailing lists
use the unified search at:
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--
Devon Ryan, PhD
Bioinformatician / Data manager
Bioinformatics Core Facility
Max Planck Institute for Immunobiology and Epigenetics
Email: dprya...@gmail.com
___
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and other Galaxy lists, please use the interface at:
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Re: [galaxy-dev] DeepTools installation error

[Md. Rezaul Karim]

Hi Devon,

I'm also experiencing similar issues. Could you please briefly explain how
to use Condo with Galaxy?

Is there any other versions where Conda is integrated apart from the
regular Galaxy distributions?

On Mar 8, 2017 7:38 PM, "Devon Ryan"  wrote:

> Hi Timo,
>
> Use conda for dependency resolution in Galaxy and make your life easier :)
> Devon
>
> On 03/08/2017 06:31 PM, Timo Janßen wrote:
>
> Hi all,
>
> trying to install the deeptools_suite from the toolshed I only get the
> following error:
>
> "500 Internal Server Error
>
> nginx/1.11.10"
>
> This happens as well for the dependencies, e.g. deeptools_bigwig_compare.
>
> I am currently using Galaxy 16.10 with nginx proxy.
>
> Also the installation of the dependency
> package_python_2_7_matplotlib_1_4 fails because of a missing dependency:
>
> "Error installing tool dependency python version 2.7.10: Unable to
> locate required tool shed repository named package_python_2_7_10 owned
> by iuc with revision 80931fb5f433."
>
> Has anyone seen these problems before and knows a solution?
>
> Best regards,
> Timo Janßen
>
>
>
>
> ___
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
>   https://lists.galaxyproject.org/
>
> To search Galaxy mailing lists use the unified search at:
>   http://galaxyproject.org/search/mailinglists/
>
>
> --
> Devon Ryan, PhD
> Bioinformatician / Data manager
> Bioinformatics Core Facility
> Max Planck Institute for Immunobiology and Epigenetics
> Email: dprya...@gmail.com
>
>
> ___
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
>   https://lists.galaxyproject.org/
>
> To search Galaxy mailing lists use the unified search at:
>   http://galaxyproject.org/search/mailinglists/
>
___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/

Re: [galaxy-dev] DeepTools installation error

[Devon Ryan]

Hi Timo,

Use conda for dependency resolution in Galaxy and make your life easier :)

Devon

On 03/08/2017 06:31 PM, Timo Janßen wrote:

Hi all,

trying to install the deeptools_suite from the toolshed I only get the
following error:

"500 Internal Server Error

nginx/1.11.10"

This happens as well for the dependencies, e.g. deeptools_bigwig_compare.

I am currently using Galaxy 16.10 with nginx proxy.

Also the installation of the dependency
package_python_2_7_matplotlib_1_4 fails because of a missing dependency:

"Error installing tool dependency python version 2.7.10: Unable to
locate required tool shed repository named package_python_2_7_10 owned
by iuc with revision 80931fb5f433."

Has anyone seen these problems before and knows a solution?

Best regards,
Timo Janßen



___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
   https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
   http://galaxyproject.org/search/mailinglists/


--
Devon Ryan, PhD
Bioinformatician / Data manager
Bioinformatics Core Facility
Max Planck Institute for Immunobiology and Epigenetics
Email: dprya...@gmail.com

___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/

Re: [galaxy-dev] Shared Data Library, large number of files

[Martin Čech]

Can you please share your '/client/galaxy/scripts/layout/menu.js' file with
me? (e.g. using https://gist.github.com or similar).

thanks

M.

On Wed, Mar 8, 2017 at 1:34 PM D K  wrote:

> Hi Martin,
>
> I've tried this on both v16.07 and v16.10
>
> D
>
>
>
> On Wed, Mar 8, 2017 at 10:29 AM, Martin Čech  wrote:
>
> Daniel:
>
> what version is your Galaxy?
>
> Martin
>
> On Wed, Mar 8, 2017 at 12:40 PM D K  wrote:
>
> I've copied and pasted the javascript error below. Any help would be
> greatly appreciated. Thanks!
>
> Uncaught TypeError: Cannot read property 'masthead' of undefined
> at n. (menu.js:120)
> at Function.each (jquery.js:370)
> at HTMLDocument. (menu.js:117)
> at l (jquery.js:3232)
> at Object.add [as done] (jquery.js:3291)
> at t.fn.init.vt.fn.ready (jquery.js:3542)
> at callback (menu.js:116)
> at Object.t.success (backbone.js:1051)
> at l (jquery.js:3232)
> at Object.fireWith [as resolveWith] (jquery.js:3362)
>
>
> On Thu, Mar 2, 2017 at 10:43 AM, D K  wrote:
>
> Hi Martin,
>
> I do get a javascript error, I've attached a screenshot of the relevant
> window. I also tried logging in as a non-admin user and had the same issue.
> In this Galaxy instance are 5 data libraries, each with about 150
> individual folders, and each folder has a variable number of fastq.gz files.
>
> Thanks!
>
> On Thu, Mar 2, 2017 at 10:13 AM, Martin Čech  wrote:
>
> Daniel:
>
> Could you please open browser console and look for javascript errors on
> the page that fails to load for you? Additionally I assume you are an admin
> when trying this (admins load all of the instance's libraries) could you
> try loading the library list as a normal user? How many libraries do you
> have on the instance?
>
> Thanks
>
> Martin
>
> On Thu, Mar 2, 2017 at 12:38 PM D K  wrote:
>
> Hi Martin / Hans / Devon,
>
> I can confirm that I am using the new UI from the top menu. Right now when
> I click on the link I often do not even get the list of libraries whereas
> when I click on the admin Data Library link I at least see the list of
> libraries (although I can't open any of them since they are so large). I've
> tried refreshing the page, deleting the cookies for the session and using
> Incognito mode, using chrome and firefox both from a linux and windows
> machine and can confirm this behavior on all systems. However, occasionally
> when clicking the Shared Data Library link from the top I do get a list of
> libraries and can navigate them, but this has only happened once during my
> tests and I cannot replicate this behavior.
>
> Thanks for the assistance!
>
> On Thu, Mar 2, 2017 at 5:47 AM, Martin Čech  wrote:
>
> Hi all,
>
> *Devon* is correct -the old data library UI under Admin menu is still in
> place (because it has some features perceived as important to some admins).
> However majority of users and most of the admins are using the interface
> under 'Shared Data' I hope and the old UI is deprecated since 15.10 (
> https://docs.galaxyproject.org/en/master/releases/15.10_announce.html). I
> created a PR to adjust the label in the admin interface to make this clear:
> https://github.com/galaxyproject/galaxy/pull/3694
>
> The old UI is very slow for large libraries but the new UI under Shared
> Data/Data Libraries in the top menu shouldn't have this kind of issues for
> hundreds of folders/datasets that are mentioned here.
>
> *Daniel* are you using the new UI form the top menu? If so are you
> experiencing this only with a specific folder full of linked datasets or
> does it occur for any folder with many datasets in it?
>
> Martin
>
>
>
> On Thu, Mar 2, 2017 at 3:49 AM Devon Ryan  wrote:
>
> I observe the same thing on 16.07. As an example, I'm just opened a
> data library under Admin->Data->Data Libraries and this took about a
> minute and a half. It looks like this is related to the quantity of
> data in this folder. The associated entry in the uwsgi log is as
> follows:
>
> [pid: 357|app: 0|req: 2059/5647] 10.1.6.77 () {44 vars in 1220 bytes}
> [Thu Mar  2 08:40:19 2017] GET
>
> /library_common/browse_library?sort=name=All=All=False=library_admin=browse=355326571f7132ff
> => generated 21761790 bytes in 108644 msecs (HTTP/1.1 200) 2 headers
> in 73 bytes (14 switches on core 2)
>
> So this library is causing ~21 megs of data to be returned to the
> browser, which I presume is the source of the issue.
>
> As an aside, the old data library API is still in use in the admin
> section until at least 16.07. Perhaps this has been changed since
> then, I hadn't planed to update our system until the end of the month.
> For what it's worth, opening the same library via "shared data" takes
> ~100 msec.
>
> Devon
> --
> Devon Ryan, Ph.D.
> Email: dpr...@dpryan.com
> Data Manager/Bioinformatician
> Max Planck Institute 

Re: [galaxy-dev] Shared Data Library, large number of files

[Martin Čech]

Daniel:

what version is your Galaxy?

Martin

On Wed, Mar 8, 2017 at 12:40 PM D K  wrote:

> I've copied and pasted the javascript error below. Any help would be
> greatly appreciated. Thanks!
>
> Uncaught TypeError: Cannot read property 'masthead' of undefined
> at n. (menu.js:120)
> at Function.each (jquery.js:370)
> at HTMLDocument. (menu.js:117)
> at l (jquery.js:3232)
> at Object.add [as done] (jquery.js:3291)
> at t.fn.init.vt.fn.ready (jquery.js:3542)
> at callback (menu.js:116)
> at Object.t.success (backbone.js:1051)
> at l (jquery.js:3232)
> at Object.fireWith [as resolveWith] (jquery.js:3362)
>
>
> On Thu, Mar 2, 2017 at 10:43 AM, D K  wrote:
>
> Hi Martin,
>
> I do get a javascript error, I've attached a screenshot of the relevant
> window. I also tried logging in as a non-admin user and had the same issue.
> In this Galaxy instance are 5 data libraries, each with about 150
> individual folders, and each folder has a variable number of fastq.gz files.
>
> Thanks!
>
> On Thu, Mar 2, 2017 at 10:13 AM, Martin Čech  wrote:
>
> Daniel:
>
> Could you please open browser console and look for javascript errors on
> the page that fails to load for you? Additionally I assume you are an admin
> when trying this (admins load all of the instance's libraries) could you
> try loading the library list as a normal user? How many libraries do you
> have on the instance?
>
> Thanks
>
> Martin
>
> On Thu, Mar 2, 2017 at 12:38 PM D K  wrote:
>
> Hi Martin / Hans / Devon,
>
> I can confirm that I am using the new UI from the top menu. Right now when
> I click on the link I often do not even get the list of libraries whereas
> when I click on the admin Data Library link I at least see the list of
> libraries (although I can't open any of them since they are so large). I've
> tried refreshing the page, deleting the cookies for the session and using
> Incognito mode, using chrome and firefox both from a linux and windows
> machine and can confirm this behavior on all systems. However, occasionally
> when clicking the Shared Data Library link from the top I do get a list of
> libraries and can navigate them, but this has only happened once during my
> tests and I cannot replicate this behavior.
>
> Thanks for the assistance!
>
> On Thu, Mar 2, 2017 at 5:47 AM, Martin Čech  wrote:
>
> Hi all,
>
> *Devon* is correct -the old data library UI under Admin menu is still in
> place (because it has some features perceived as important to some admins).
> However majority of users and most of the admins are using the interface
> under 'Shared Data' I hope and the old UI is deprecated since 15.10 (
> https://docs.galaxyproject.org/en/master/releases/15.10_announce.html). I
> created a PR to adjust the label in the admin interface to make this clear:
> https://github.com/galaxyproject/galaxy/pull/3694
>
> The old UI is very slow for large libraries but the new UI under Shared
> Data/Data Libraries in the top menu shouldn't have this kind of issues for
> hundreds of folders/datasets that are mentioned here.
>
> *Daniel* are you using the new UI form the top menu? If so are you
> experiencing this only with a specific folder full of linked datasets or
> does it occur for any folder with many datasets in it?
>
> Martin
>
>
>
> On Thu, Mar 2, 2017 at 3:49 AM Devon Ryan  wrote:
>
> I observe the same thing on 16.07. As an example, I'm just opened a
> data library under Admin->Data->Data Libraries and this took about a
> minute and a half. It looks like this is related to the quantity of
> data in this folder. The associated entry in the uwsgi log is as
> follows:
>
> [pid: 357|app: 0|req: 2059/5647] 10.1.6.77 () {44 vars in 1220 bytes}
> [Thu Mar  2 08:40:19 2017] GET
>
> /library_common/browse_library?sort=name=All=All=False=library_admin=browse=355326571f7132ff
> => generated 21761790 bytes in 108644 msecs (HTTP/1.1 200) 2 headers
> in 73 bytes (14 switches on core 2)
>
> So this library is causing ~21 megs of data to be returned to the
> browser, which I presume is the source of the issue.
>
> As an aside, the old data library API is still in use in the admin
> section until at least 16.07. Perhaps this has been changed since
> then, I hadn't planed to update our system until the end of the month.
> For what it's worth, opening the same library via "shared data" takes
> ~100 msec.
>
> Devon
> --
> Devon Ryan, Ph.D.
> Email: dpr...@dpryan.com
> Data Manager/Bioinformatician
> Max Planck Institute of Immunobiology and Epigenetics
> Stübeweg 51
> 79108 Freiburg
> Germany
>
>
> On Thu, Mar 2, 2017 at 8:30 AM, Hans-Rudolf Hotz  wrote:
> >
> > this sounds more like a browser issue to me
> > which browser do you use? what happens when you use a different browser?
> and
> > what happens when you just reload the page
> >
> >
> > Hans-Rudolf
> >
> > On 

[galaxy-dev] Fwd: [Bosc] BOSC 2017: Call for Abstracts

[Peter Cock]

Dear all,

Recent BOSC meetings have had a strong Galaxy presence, so please do
consider submitting an abstract and/or attending BOSC 2017 in Prague.

Thank you,

Peter

Dr. Peter Cock,
Bioinformatician at The James Hutton Institute;
Open Bioinformatics Foundation, board of directors, treasurer;
BOSC 2017 organising committee member.

-- Forwarded message --
From: Nomi Harris 
Date: Mon, Mar 6, 2017 at 6:50 PM
Subject: [Bosc] BOSC 2017: Call for Abstracts
To: bosc-annou...@mailman.open-bio.org, bosc-review...@open-bio.org
Cc: Nomi Harris , BOSC 2017 Organizing Committee <
b...@open-bio.org>


*Call for Abstracts for the 18th Annual Bioinformatics Open Source
Conference (BOSC 2017)*
An ISMB/ECCB Community of Special Interest (COSI)

Dates: July 22-23, 2017
Location: Prague, Czech Republic
Web site: http://www.open-bio.org/wiki/BOSC_2017
Email: b...@open-bio.org
BOSC announcements mailing list: http://lists.open-bio.
org/mailman/listinfo/bosc-announce
Twitter: @OBF_BOSC

*Important Dates*

   - Call for one-page abstracts
    opens: March 6,
   2017
   - Abstract submission
    deadline: April
   13, 2017
   - Travel fellowship
   
application
   deadline: April 15, 2017
   - Authors notified: May 10, 2017
   - Codefest 2017 : July
   21-22, Prague
   - BOSC 2017 : July 22-23,
   Prague  (days 1 and 2 of ISMB/ECCB)
   - ISMB/ECCB 2017 : July 21-25, Prague

*About BOSC*
Since 2000, the yearly Bioinformatics Open Source Conference (BOSC) has
provided a forum for developers and users to interact and share research
results and ideas in open source bioinformatics. BOSC’s broad spectrum of
topics includes practical techniques for solving bioinformatics problems;
software development practices; standards and ontologies; approaches that
promote open science and sharing of data, results and software; and ways to
grow open source communities while promoting diversity within them.

In the past, BOSC has taken place the two days before ISMB as a Special
Interest Group (SIG). This year, ISMB is trying a new structure: the SIGs
(now called COSIs) are integrated into the main ISMB meeting. BOSC will
take place the first two full days of ISMB (July 22-23). Attendees will
have the option to register for the full ISMB/ECCB meeting (July 21-25) or
for just two days (there is no single-day registration option this year). A
limited number of partial travel fellowships will be granted to some
accepted speakers who would not otherwise be able to attend BOSC--please
see https://github.com/OBF/obf-docs/blob/master/Travel_fellowships.md for
more information.

We encourage you to submit one-page abstracts on any topic of relevance to
open source bioinformatics and open science. After review, some abstracts
will be selected for lightning talks, longer talks, and/or posters.
Abstract submission instructions and a link to the EasyChair portal can be
found on https://www.open-bio.org/wiki/BOSC_Abstract_Submission

*Session topics include:*

   - Open Science and Reproducible Research
   - Open Biomedical Data
   - Citizen/Participatory Science
   - Standards and Interoperability
   - Data Science
   - Workflows
   - Visualization
   - Medical and Translational Bioinformatics
   - Developer Tools and Libraries
   - Bioinformatics Open Source Project Progress Reports

*Sponsorship*
We gratefully accept sponsorships from relevant private companies. These
sponsorships enable us to offer free registration to some BOSC speakers to
help increase diversity at our meeting. Sponsors in 2016 included
Curoverse, the company behind the open source platform Arvados. Please
contact us if you are interested in being a sponsor of BOSC 2017!

Thank you,
  BOSC 2017 Organizing Committee:   Nomi Harris (chair), Brad Chapman,
Peter Cock, Christopher Fields, Bastian Greshake, Karsten Hokamp, Hilmar
Lapp, Mónica Muñoz-Torres, Heather Wiencko

P.S. Don't forget to submit your BOSC abstract by April 13 at
https://www.open-bio.org/wiki/BOSC_Abstract_Submission!

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Re: [galaxy-dev] Shared Data Library, large number of files

[D K]

I've copied and pasted the javascript error below. Any help would be
greatly appreciated. Thanks!

Uncaught TypeError: Cannot read property 'masthead' of undefined
> at n. (menu.js:120)
> at Function.each (jquery.js:370)
> at HTMLDocument. (menu.js:117)
> at l (jquery.js:3232)
> at Object.add [as done] (jquery.js:3291)
> at t.fn.init.vt.fn.ready (jquery.js:3542)
> at callback (menu.js:116)
> at Object.t.success (backbone.js:1051)
> at l (jquery.js:3232)
> at Object.fireWith [as resolveWith] (jquery.js:3362)


On Thu, Mar 2, 2017 at 10:43 AM, D K  wrote:

> Hi Martin,
>
> I do get a javascript error, I've attached a screenshot of the relevant
> window. I also tried logging in as a non-admin user and had the same issue.
> In this Galaxy instance are 5 data libraries, each with about 150
> individual folders, and each folder has a variable number of fastq.gz files.
>
> Thanks!
>
> On Thu, Mar 2, 2017 at 10:13 AM, Martin Čech  wrote:
>
>> Daniel:
>>
>> Could you please open browser console and look for javascript errors on
>> the page that fails to load for you? Additionally I assume you are an admin
>> when trying this (admins load all of the instance's libraries) could you
>> try loading the library list as a normal user? How many libraries do you
>> have on the instance?
>>
>> Thanks
>>
>> Martin
>>
>> On Thu, Mar 2, 2017 at 12:38 PM D K  wrote:
>>
>>> Hi Martin / Hans / Devon,
>>>
>>> I can confirm that I am using the new UI from the top menu. Right now
>>> when I click on the link I often do not even get the list of libraries
>>> whereas when I click on the admin Data Library link I at least see the list
>>> of libraries (although I can't open any of them since they are so large).
>>> I've tried refreshing the page, deleting the cookies for the session and
>>> using Incognito mode, using chrome and firefox both from a linux and
>>> windows machine and can confirm this behavior on all systems. However,
>>> occasionally when clicking the Shared Data Library link from the top I do
>>> get a list of libraries and can navigate them, but this has only happened
>>> once during my tests and I cannot replicate this behavior.
>>>
>>> Thanks for the assistance!
>>>
>>> On Thu, Mar 2, 2017 at 5:47 AM, Martin Čech  wrote:
>>>
>>> Hi all,
>>>
>>> *Devon* is correct -the old data library UI under Admin menu is still
>>> in place (because it has some features perceived as important to some
>>> admins). However majority of users and most of the admins are using the
>>> interface under 'Shared Data' I hope and the old UI is deprecated since
>>> 15.10 (https://docs.galaxyproject.org/en/master/releases/15.10_ann
>>> ounce.html). I created a PR to adjust the label in the admin interface
>>> to make this clear: https://github.com/galaxyproject/galaxy/pull/3694
>>>
>>> The old UI is very slow for large libraries but the new UI under Shared
>>> Data/Data Libraries in the top menu shouldn't have this kind of issues for
>>> hundreds of folders/datasets that are mentioned here.
>>>
>>> *Daniel* are you using the new UI form the top menu? If so are you
>>> experiencing this only with a specific folder full of linked datasets or
>>> does it occur for any folder with many datasets in it?
>>>
>>> Martin
>>>
>>>
>>>
>>> On Thu, Mar 2, 2017 at 3:49 AM Devon Ryan  wrote:
>>>
>>> I observe the same thing on 16.07. As an example, I'm just opened a
>>> data library under Admin->Data->Data Libraries and this took about a
>>> minute and a half. It looks like this is related to the quantity of
>>> data in this folder. The associated entry in the uwsgi log is as
>>> follows:
>>>
>>> [pid: 357|app: 0|req: 2059/5647] 10.1.6.77 () {44 vars in 1220 bytes}
>>> [Thu Mar  2 08:40:19 2017] GET
>>> /library_common/browse_library?sort=name=All&
>>> f-name=All=False=library_admin=browse=
>>> 355326571f7132ff
>>> => generated 21761790 bytes in 108644 msecs (HTTP/1.1 200) 2 headers
>>> in 73 bytes (14 switches on core 2)
>>>
>>> So this library is causing ~21 megs of data to be returned to the
>>> browser, which I presume is the source of the issue.
>>>
>>> As an aside, the old data library API is still in use in the admin
>>> section until at least 16.07. Perhaps this has been changed since
>>> then, I hadn't planed to update our system until the end of the month.
>>> For what it's worth, opening the same library via "shared data" takes
>>> ~100 msec.
>>>
>>> Devon
>>> --
>>> Devon Ryan, Ph.D.
>>> Email: dpr...@dpryan.com
>>> Data Manager/Bioinformatician
>>> Max Planck Institute of Immunobiology and Epigenetics
>>> Stübeweg 51
>>> 79108 Freiburg
>>> Germany
>>>
>>>
>>> On Thu, Mar 2, 2017 at 8:30 AM, Hans-Rudolf Hotz  wrote:
>>> >
>>> > this sounds more like a browser issue to me
>>> > which browser do you use? what happens when you use a different
>>> browser? and
>>> > what happens when you 

[galaxy-dev] DeepTools installation error

[Timo Janßen]

Hi all,

trying to install the deeptools_suite from the toolshed I only get the
following error:

"500 Internal Server Error

nginx/1.11.10"

This happens as well for the dependencies, e.g. deeptools_bigwig_compare.

I am currently using Galaxy 16.10 with nginx proxy.

Also the installation of the dependency
package_python_2_7_matplotlib_1_4 fails because of a missing dependency:

"Error installing tool dependency python version 2.7.10: Unable to
locate required tool shed repository named package_python_2_7_10 owned
by iuc with revision 80931fb5f433."

Has anyone seen these problems before and knows a solution?

Best regards,
Timo Janßen

-- 

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Re: [galaxy-dev] Rg: Galaxy Version

[Li, Haiqing]

Check lib/galaxy/version.py

Bests,

Haiqing

From: galaxy-dev [mailto:galaxy-dev-boun...@lists.galaxyproject.org] On Behalf 
Of Anamika Singh
Sent: Wednesday, March 08, 2017 2:37 AM
To: galaxy-dev@lists.galaxyproject.org
Subject: [galaxy-dev] Rg: Galaxy Version

Dear galaxy team,
I am using galaxy platform (old version) in Linux OS which was not installed by 
me. I would like to know 'how to check what is the galaxy version installed 
currently in my system.

Regards

--
Anamika


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Re: [galaxy-dev] Rg: Galaxy Version

[Peter Cock]

Thanks Martin & Eugen,

That's much easier (although Anamika will likely need to check if
their Galaxy was setup using hg or git anyway for updating it).

I'm not sure when it was introduced, but its been a while as even
the older Galaxy instance in my example under hg gives:

{"version_major": "15.05"}

Regards,

Peter


On Wed, Mar 8, 2017 at 2:06 PM, Martin Čech  wrote:
> Hi Anamika,
>
> adding a detail to Peter's excellent answer:
>
> For newer versions of Galaxy (while it is running) you can go to the url
> `your.galaxy.com/api/version` to learn the release of Galaxy you have.
>
> Thanks for using Galaxy,
>
> Martin
>
> On Wed, Mar 8, 2017 at 7:39 AM Peter Cock  wrote:
>>
>> Galaxy was originally distributed via the mercurial (hg) version
>> control system, later the git version control system.
>>
>> Try this (which will work on a very old Galaxy using hg),
>>
>> $ hg log | head
>> changeset:   17125:e837a68e8d14
>> tag: tip
>> parent:  17121:7a4e3a661a76
>> parent:  17124:46a4ef8850b5
>> user:Nate Coraor 
>> date:Fri May 15 15:21:34 2015 -0400
>> summary: Merge stable to default
>> ...
>>
>> If that fails, try this which will work on a Galaxy distributed with git:
>>
>> $ git log | head
>> commit cbd527b9a4671c7abe9a22cf69e869b5d2de858a
>> Merge: 33dec01 d0f39ce
>> Author: Nicola Soranzo 
>> Date:   Wed Dec 7 20:35:40 2016 +
>>
>> Merge branch 'release_16.10' into dev
>>
>> Conflicts:
>> static/scripts/bundled/analysis.bundled.js
>> static/scripts/bundled/analysis.bundled.js.map
>> ...
>>
>>
>> If it isn't clear from the commit message, you can then match those
>> commits
>> to the relevant repository and hopefully work it out, here those were:
>>
>> https://bitbucket.org/galaxy/galaxy-central/commits/e837a68e8d14
>>
>> and
>>
>>
>> https://github.com/galaxyproject/galaxy/commits/cbd527b9a4671c7abe9a22cf69e869b5d2de858a
>>
>> If neither git nor hg work, then perhaps your Galaxy was installed via a
>> different route - and that will likely complicate updating it.
>>
>> Peter
>>
>>
>> On Wed, Mar 8, 2017 at 10:36 AM, Anamika Singh 
>> wrote:
>> > Dear galaxy team,
>> >
>> > I am using galaxy platform (old version) in Linux OS which was not
>> > installed
>> > by me. I would like to know 'how to check what is the galaxy version
>> > installed currently in my system.
>> >
>> > Regards
>> >
>> > --
>> > Anamika
>> >
>> > ___
>> > Please keep all replies on the list by using "reply all"
>> > in your mail client.  To manage your subscriptions to this
>> > and other Galaxy lists, please use the interface at:
>> >   https://lists.galaxyproject.org/
>> >
>> > To search Galaxy mailing lists use the unified search at:
>> >   http://galaxyproject.org/search/mailinglists/
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[galaxy-dev] tool problems (data_manager_fetch_ncbi_taxonomy & ggplot2)

[Matthias Bernt]

Dear mailing list,

I'm experimenting with the tools available at the Tool Shed and ran into 
problems with two of the tools.


1. data_manager_fetch_ncbi_taxonomy

If I run the data manager I get an error in the browser: "Uncaught 
exception in exposed API method"


The terminal shows the following stack trace:

Traceback (most recent call last):
  File "/home/berntm/galaxy/lib/galaxy/web/framework/decorators.py", 
line 282, in decorator

rval = func( self, trans, *args, **kwargs )
  File "/home/berntm/galaxy/lib/galaxy/webapps/galaxy/api/tools.py", 
line 98, in build

return tool.to_json(trans, kwd.get('inputs', kwd))
  File "/home/berntm/galaxy/lib/galaxy/tools/__init__.py", line 1853, 
in to_json

tools = self.app.toolbox.get_loaded_tools_by_lineage( self.id )
  File "/home/berntm/galaxy/lib/galaxy/tools/toolbox/base.py", line 
492, in get_loaded_tools_by_lineage

tool_lineage = self._lineage_map.get( tool_id )
  File 
"/home/berntm/galaxy/lib/galaxy/tools/toolbox/lineages/factory.py", line 
38, in get

lineage = ToolShedLineage.from_tool_id( self.app, tool_id )
  File 
"/home/berntm/galaxy/lib/galaxy/tools/toolbox/lineages/tool_shed.py", 
line 70, in from_tool_id

return ToolShedLineage( app, tool_version )
  File 
"/home/berntm/galaxy/lib/galaxy/tools/toolbox/lineages/tool_shed.py", 
line 53, in __init__

self.tool_version_id = tool_version.id
  File 
"/home/berntm/galaxy/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/attributes.py", 
line 237, in __get__

return self.impl.get(instance_state(instance), dict_)
  File 
"/home/berntm/galaxy/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/attributes.py", 
line 578, in get

value = state._load_expired(state, passive)
  File 
"/home/berntm/galaxy/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/state.py", 
line 474, in _load_expired

self.manager.deferred_scalar_loader(self, toload)
  File 
"/home/berntm/galaxy/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/loading.py", 
line 610, in load_scalar_attributes

(state_str(state)))
DetachedInstanceError: Instance  is not 
bound to a Session; attribute refresh operation cannot proceed


Any ideas whats going on - and how to fix this?

2. The second tool is ggplot2_2_2_1. Here mingchen0919 is listed as 
owner in the Tool Shed -- so I do not know if this mailing list is the 
correct address. If not: how do I find contact information to the owner 
of a tool in the ToolShed?


Otherwise, the problem is missing dependencies:

In package_fontconfig_2_11_1 (which is a dependency of ggplot) I get

"""
configure: error: in 
`/home/berntm/galaxy/database/tmp/tmp-toolshed-mtdBsL0ig/fontconfig-2.11.1':
configure: error: The pkg-config script could not be found or is too 
old.  Make sure it

is in your PATH or set the PKG_CONFIG environment variable to the full
path to pkg-config.

Alternatively, you may set the environment variables FREETYPE_CFLAGS
and FREETYPE_LIBS to avoid the need to call pkg-config.
See the pkg-config man page for more details.

To get pkg-config, see .
See `config.log' for more details
"""

Is pkg-config supposed to be installed on the computer running galaxy? 
Or should this be installed within galaxy?


In addition on the terminal the following error appears after the 
pkg-config error:


"""
Exception happened during processing of request from ('127.0.0.1', 42534)
Traceback (most recent call last):
  File 
"/home/berntm/galaxy/.venv/local/lib/python2.7/site-packages/paste/httpserver.py", 
line 1085, in process_request_in_thread

self.finish_request(request, client_address)
  File "/usr/lib/python2.7/SocketServer.py", line 331, in finish_request
self.RequestHandlerClass(request, client_address, self)
  File "/usr/lib/python2.7/SocketServer.py", line 654, in __init__
self.finish()
  File "/usr/lib/python2.7/SocketServer.py", line 713, in finish
self.wfile.close()
  File "/usr/lib/python2.7/socket.py", line 283, in close
self.flush()
  File "/usr/lib/python2.7/socket.py", line 307, in flush
self._sock.sendall(view[write_offset:write_offset+buffer_size])
error: [Errno 32] Broken pipe
"""

Thank you very much for your help.

Best regards,
Matthias


--

---
Matthias Bernt
Bioinformatics Service
Molekulare Systembiologie (MOLSYB)
Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/
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Re: [galaxy-dev] Rg: Galaxy Version

[Rempel, Eugen]

Dear Anamika,

you can check the version in your browser using the link

$link_to_your_galaxy/api/version.

Example for the usegalaxy.org:

https://usegalaxy.org/api/version

Best,

Eugen


On 08 Mar 2017, at 11:36, Anamika Singh 
> wrote:

Dear galaxy team,

I am using galaxy platform (old version) in Linux OS which was not installed by 
me. I would like to know 'how to check what is the galaxy version installed 
currently in my system.

Regards

--
Anamika
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Re: [galaxy-dev] Search Tool Shed

[Martin Čech]

Hi Matthias,

it is supposed to open an iframe in the right panel with view of MTS
categories for browsing. Do you see a warning icon in the right of your
browser's URL bar? I think I saw this before when there was https/https
mismatch. How does your config/tool_sheds_conf.xml look like? Do you see
any errors/warnings in the browser's JS console?

Martin



On Wed, Mar 8, 2017 at 9:56 AM Matthias Bernt  wrote:

> Dear mailing list,
>
> What is the expected behavior if I click in the Admin area under "Search
> Tool Shed" on the "Galaxy Main Tool Shed" button (or any of the Browse
> .. or Search .. actions that are available via the black triangle submenu)?
>
> I remember that a new tab with the corresponding Tool Shed page opened
> in the browser.
>
> This is currently not happening in my installation. What could be the
> problem? As a work around I can trigger the Browse action via right
> click and "open link in new tab".
>
> As far as I can see this is not a JavaScript problem.
>
> Best,
> Matthias
>
>
>
> --
>
> ---
> Matthias Bernt
> Bioinformatics Service
> Molekulare Systembiologie (MOLSYB)
> Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/
> Helmholtz Centre for Environmental Research GmbH - UFZ
> Permoserstraße 15, 04318 Leipzig, Germany
> Phone +49 341 235 482296 <+49%20341%20235482296>,
> m.be...@ufz.de, www.ufz.de
>
> Sitz der Gesellschaft/Registered Office: Leipzig
> Registergericht/Registration Office: Amtsgericht Leipzig
> Handelsregister Nr./Trade Register Nr.: B 4703
> Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board:
> MinDirig Wilfried Kraus
> Wissenschaftlicher Geschäftsführer/Scientific Managing Director:
> Prof. Dr. Dr. h.c. Georg Teutsch
> Administrative Geschäftsführerin/ Administrative Managing Director:
> Prof. Dr. Heike Graßmann
> ---
>
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>
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[galaxy-dev] Search Tool Shed

[Matthias Bernt]

Dear mailing list,

What is the expected behavior if I click in the Admin area under "Search 
Tool Shed" on the "Galaxy Main Tool Shed" button (or any of the Browse 
.. or Search .. actions that are available via the black triangle submenu)?


I remember that a new tab with the corresponding Tool Shed page opened 
in the browser.


This is currently not happening in my installation. What could be the 
problem? As a work around I can trigger the Browse action via right 
click and "open link in new tab".


As far as I can see this is not a JavaScript problem.

Best,
Matthias



--

---
Matthias Bernt
Bioinformatics Service
Molekulare Systembiologie (MOLSYB)
Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/
Helmholtz Centre for Environmental Research GmbH - UFZ
Permoserstraße 15, 04318 Leipzig, Germany
Phone +49 341 235 482296,
m.be...@ufz.de, www.ufz.de

Sitz der Gesellschaft/Registered Office: Leipzig
Registergericht/Registration Office: Amtsgericht Leipzig
Handelsregister Nr./Trade Register Nr.: B 4703
Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board: 
MinDirig Wilfried Kraus

Wissenschaftlicher Geschäftsführer/Scientific Managing Director:
Prof. Dr. Dr. h.c. Georg Teutsch
Administrative Geschäftsführerin/ Administrative Managing Director:
Prof. Dr. Heike Graßmann
---



smime.p7s
Description: S/MIME Cryptographic Signature
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[galaxy-dev] Rg: Galaxy Version

[Anamika Singh]

Dear galaxy team,

I am using galaxy platform (old version) in Linux OS which was not
installed by me. I would like to know 'how to check what is the galaxy
version installed currently in my system.

Regards

-- 
Anamika
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