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

[D K]

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. 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 03/01/2017 06:17 PM, D K wrote:
>> >>
>> >> Actually, when I click on the Shared Data-> Data Libraries link I get
>> >> only the Galaxy banner and a blank page, so I'm not even seeing the
>> data
>> >> libraries themselves.
>> >>
>> >> If I use the Admin link and then click Data libraries, I can see the
>> >> actual libraries. But when I try to enter one of the libraries with
>> lots
>> >> of files it hangs.
>> >>
>> >>
>> >> On Wed, Mar 1, 2017 at 9:03 AM, D K > >> > wrote:
>> >>
>> >> Hi Hans,
>> >>
>> >> I'm running 16.10. If I'm not mistaken, the old Data Library
>> >> interface is still accessible in 

Re: [galaxy-dev] Problem with installing tools using Conda

[John Chilton]

I've never seen anything like this before - I am sorry. Hopefully
someone else will have a more concrete idea.

Does that Conda executable work on the command line?

I'd try removing the whole Conda folder and rebuilding it. Is it
possible the install was corrupted at some point - maybe during
install?

The just released Galaxy 17.01 has much better logging of Conda
problems and a script that can be used outside of Galaxy to explicitly
setup Conda.

-John

On Thu, Mar 2, 2017 at 11:47 AM, Ashok Varadharajan  wrote:
> Dear Team,
>
> I have problem with the installation of tools using conda. I am getting
> following error message when i try to install tools from galaxy. I tried to
> install these tools manually with the same conda used by the galaxy and it
> worked. Can anyone help us to solve this issue ?
>
> Traceback (most recent call last):
>   File "//x/-/conda//bin/conda", line 4, in 
> from conda.cli.main import main
> ImportError: No module named conda.cli.main
> galaxy.tools.deps.resolvers.conda DEBUG 2017-03-02 17:35:49,759 Removing
> failed conda install of samtools, version '1.3.1'
> Traceback (most recent call last):
>   File "//x/-/conda//bin/conda", line 4, in 
> from conda.cli.main import main
> ImportError: No module named conda.cli.main
> galaxy.tools.deps.resolvers.conda DEBUG 2017-03-02 17:35:49,941 Removing
> failed conda install of samtools, version 'None'
> Traceback (most recent call last):
>   File "//x/-/conda//bin/conda", line 4, in 
> from conda.cli.main import main
> ImportError: No module named conda.cli.main
> galaxy.tools.deps.resolvers.conda DEBUG 2017-03-02 17:35:50,142 Removing
> failed conda install of bwa, version '0.7.15'
> Traceback (most recent call last):
>   File "//x/-/conda//bin/conda", line 4, in 
> from conda.cli.main import main
> ImportError: No module named conda.cli.main
>
> We are running galaxy-16.07 behind the proxy using nginx, uwsgi and
> supervisor in scientific linux 7. Below are the details of galaxy.ini and
> supervisor configuration.
>
>
> ### galaxy.ini
>
> conda_prefix = //x/-/conda/
> #conda_exec =
> conda_debug = False
> conda_ensure_channels = r,bioconda,iuc
> #conda_auto_install = False
> #conda_verbose_install_check=False
> conda_auto_init = True
>
> ### supervisor
>
> [supervisord]
>
> [program:galaxy_web]
> command = $GALAXY_PATH/.venv/bin/uwsgi --virtualenv
> $GALAXY_PATH/.venv --ini-paste $GALAXY_PATH/config/galaxy.ini --logdate
> --master --processes 3 --threads 6 --logto
> $GALAXY_PATH/logs/galaxy.uwsgi.log --socket 127.0.0.1:4001 --pythonpath lib
> --stats 127.0.0.1:9191
> directory   = $GALAXY_PATH
> umask   = 022
> autostart   = true
> autorestart = true
> startsecs   = 20
> user= galaxy
> environment =
> PATH=$GALAXY_PATH/.venv/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin,PYTHONHOME=$GALAXY_PATH/.venv,DRMAA_LIBRARY_PATH=/usr/local/lib/libdrmaa.so
> numprocs = 1
> stoplight = INT
> startretries= 15
> process_name= web%(process_num)s
>
> [program:handler]
> command = $GALAXY_PATH/.venv/bin/python ./lib/galaxy/main.py -c
> $GALAXY_PATH/config/galaxy.ini --server-name=handler%(process_num)s
> --log-file=$GALAXY_PATH/logs/
>>galaxy_handler%(process_num)s.log
> directory   = $GALAXY_PATH
> process_name= handler%(process_num)s
> numprocs = 3
> umask   = 022
> autostart   = true
> autorestart = true
> startsecs   = 20
> user= galaxy
> environment =
> PATH=$GALAXY_PATH/.venv/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin,PYTHONHOME=$GALAXY_PATH/.venv,DRMAA_LIBRARY_PATH=/usr/local/lib/libdrmaa.so
> startretries= 15
>
> --
> Thanks and Regards,
> Ashok Vardharajan
>
>
> ___
> 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] Shared Data Library, large number of files

[D K]

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. 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 03/01/2017 06:17 PM, D K wrote:
>> >>
>> >> Actually, when I click on the Shared Data-> Data Libraries link I get
>> >> only the Galaxy banner and a blank page, so I'm not even seeing the
>> data
>> >> libraries themselves.
>> >>
>> >> If I use the Admin link and then click Data libraries, I can see the
>> >> actual libraries. But when I try to enter one of the libraries with
>> lots
>> >> of files it hangs.
>> >>
>> >>
>> >> On Wed, Mar 1, 2017 at 9:03 AM, D K > >> > wrote:
>> >>
>> >> Hi Hans,
>> >>
>> >> I'm running 16.10. If I'm not mistaken, the old Data Library
>> >> interface is still accessible in the Admin menu isn't it? I have
>> the
>> >> same issue when navigating to a Data Library either from the Admin
>> >> or Shared Data links. I also tried this in 16.07 with the same
>> >> result.  If it makes a difference, I'm using PostgreSQL and Apache.
>> >>
>> >> Dwight
>> >>
>> >>
>> >>
>> >> On Tue, Feb 28, 2017 at 11:47 PM, Hans-Rudolf Hotz > >> > wrote:
>> >>
>> >> Hi Daniel
>> >>
>> >> Just double checking which version of galaxy are you running?
>> In
>> >> other words: are you still using the old Data Library
>> interface?
>> >> (if I remember correctly, the old UI was deprecated in 15.10)
>> >> We had similar issues with the old UI.
>> >>
>> >> The new one works fine and is very fast. E.g. we have a 'MISEQ'
>> >> folder with more than 100 sub folders and a 

[galaxy-dev] Problem with installing tools using Conda

[Ashok Varadharajan]

Dear Team,

I have problem with the installation of tools using conda. I am getting
following error message when i try to install tools from galaxy. I tried to
install these tools manually with the same conda used by the galaxy and it
worked. Can anyone help us to solve this issue ?

Traceback (most recent call last):
  File "//x/-/conda//bin/conda", line 4, in 
from conda.cli.main import main
ImportError: No module named conda.cli.main
galaxy.tools.deps.resolvers.conda DEBUG 2017-03-02 17:35:49,759 Removing
failed conda install of samtools, version '1.3.1'
Traceback (most recent call last):
  File "//x/-/conda//bin/conda", line 4, in 
from conda.cli.main import main
ImportError: No module named conda.cli.main
galaxy.tools.deps.resolvers.conda DEBUG 2017-03-02 17:35:49,941 Removing
failed conda install of samtools, version 'None'
Traceback (most recent call last):
  File "//x/-/conda//bin/conda", line 4, in 
from conda.cli.main import main
ImportError: No module named conda.cli.main
galaxy.tools.deps.resolvers.conda DEBUG 2017-03-02 17:35:50,142 Removing
failed conda install of bwa, version '0.7.15'
Traceback (most recent call last):
  File "//x/-/conda//bin/conda", line 4, in 
from conda.cli.main import main
ImportError: No module named conda.cli.main

We are running galaxy-16.07 behind the proxy using nginx, uwsgi and
supervisor in scientific linux 7. Below are the details of galaxy.ini and
supervisor configuration.


*### galaxy.ini *

conda_prefix = //x/-/conda/
#conda_exec =
conda_debug = False
conda_ensure_channels = r,bioconda,iuc
#conda_auto_install = False
#conda_verbose_install_check=False
conda_auto_init = True

*### supervisor*

[supervisord]

[program:galaxy_web]
command = $GALAXY_PATH/.venv/bin/uwsgi --virtualenv
$GALAXY_PATH/.venv --ini-paste $GALAXY_PATH/config/galaxy.ini --logdate
--master --processes 3 --threads 6 --logto
$GALAXY_PATH/logs/galaxy.uwsgi.log --socket 127.0.0.1:4001 --pythonpath lib
--stats 127.0.0.1:9191
directory   = $GALAXY_PATH
umask   = 022
autostart   = true
autorestart = true
startsecs   = 20
user= galaxy
environment =
PATH=$GALAXY_PATH/.venv/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin,PYTHONHOME=$GALAXY_PATH/.venv,DRMAA_LIBRARY_PATH=/usr/local/lib/libdrmaa.so
numprocs = 1
stoplight = INT
startretries= 15
process_name= web%(process_num)s

[program:handler]
command = $GALAXY_PATH/.venv/bin/python ./lib/galaxy/main.py -c
$GALAXY_PATH/config/galaxy.ini --server-name=handler%(process_num)s
--log-file=$GALAXY_PATH/logs/
>galaxy_handler%(process_num)s.log
directory   = $GALAXY_PATH
process_name= handler%(process_num)s
numprocs = 3
umask   = 022
autostart   = true
autorestart = true
startsecs   = 20
user= galaxy
environment =
PATH=$GALAXY_PATH/.venv/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin,PYTHONHOME=$GALAXY_PATH/.venv,DRMAA_LIBRARY_PATH=/usr/local/lib/libdrmaa.so
startretries= 15

-- 
*Thanks and Regards,*
*Ashok Vardharajan*
___
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]

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 03/01/2017 06:17 PM, D K wrote:
> >>
> >> Actually, when I click on the Shared Data-> Data Libraries link I get
> >> only the Galaxy banner and a blank page, so I'm not even seeing the data
> >> libraries themselves.
> >>
> >> If I use the Admin link and then click Data libraries, I can see the
> >> actual libraries. But when I try to enter one of the libraries with lots
> >> of files it hangs.
> >>
> >>
> >> On Wed, Mar 1, 2017 at 9:03 AM, D K  >> > wrote:
> >>
> >> Hi Hans,
> >>
> >> I'm running 16.10. If I'm not mistaken, the old Data Library
> >> interface is still accessible in the Admin menu isn't it? I have the
> >> same issue when navigating to a Data Library either from the Admin
> >> or Shared Data links. I also tried this in 16.07 with the same
> >> result.  If it makes a difference, I'm using PostgreSQL and Apache.
> >>
> >> Dwight
> >>
> >>
> >>
> >> On Tue, Feb 28, 2017 at 11:47 PM, Hans-Rudolf Hotz  >> > wrote:
> >>
> >> Hi Daniel
> >>
> >> Just double checking which version of galaxy are you running? In
> >> other words: are you still using the old Data Library interface?
> >> (if I remember correctly, the old UI was deprecated in 15.10)
> >> We had similar issues with the old UI.
> >>
> >> The new one works fine and is very fast. E.g. we have a 'MISEQ'
> >> folder with more than 100 sub folders and a HISEQ folder with
> >> more than 600 sub folders. Each containing up to 100plus fastq
> >> and text files.
> >>
> >> Regards, Hans-Rudolf
> >>
> >>
> >>
> >> On 03/01/2017 12:13 AM, D K wrote:
> >>
> >> Hi,
> >>
> >> I've noticed that the more files / folders (think hundreds
> >> of folders
> >> each with 20+ fastq files) I add to a Shared Data Library,
> >> the longer
> >> and longer it takes to initially navigate the folder
> >> structure (after
> >> clicking on the specific Shared Data Library). Just opening
> >> up the
> >> Shared Data Library can take several minutes and often the
> >> browser times
> >> out. Is there a way to speed this up?
> >>
> >> If it's relevant, when I add shared data, it's linked rather
> >> than copied
> >> into Galaxy. Any 

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

[Devon Ryan]

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 03/01/2017 06:17 PM, D K wrote:
>>
>> Actually, when I click on the Shared Data-> Data Libraries link I get
>> only the Galaxy banner and a blank page, so I'm not even seeing the data
>> libraries themselves.
>>
>> If I use the Admin link and then click Data libraries, I can see the
>> actual libraries. But when I try to enter one of the libraries with lots
>> of files it hangs.
>>
>>
>> On Wed, Mar 1, 2017 at 9:03 AM, D K > > wrote:
>>
>> Hi Hans,
>>
>> I'm running 16.10. If I'm not mistaken, the old Data Library
>> interface is still accessible in the Admin menu isn't it? I have the
>> same issue when navigating to a Data Library either from the Admin
>> or Shared Data links. I also tried this in 16.07 with the same
>> result.  If it makes a difference, I'm using PostgreSQL and Apache.
>>
>> Dwight
>>
>>
>>
>> On Tue, Feb 28, 2017 at 11:47 PM, Hans-Rudolf Hotz > > wrote:
>>
>> Hi Daniel
>>
>> Just double checking which version of galaxy are you running? In
>> other words: are you still using the old Data Library interface?
>> (if I remember correctly, the old UI was deprecated in 15.10)
>> We had similar issues with the old UI.
>>
>> The new one works fine and is very fast. E.g. we have a 'MISEQ'
>> folder with more than 100 sub folders and a HISEQ folder with
>> more than 600 sub folders. Each containing up to 100plus fastq
>> and text files.
>>
>> Regards, Hans-Rudolf
>>
>>
>>
>> On 03/01/2017 12:13 AM, D K wrote:
>>
>> Hi,
>>
>> I've noticed that the more files / folders (think hundreds
>> of folders
>> each with 20+ fastq files) I add to a Shared Data Library,
>> the longer
>> and longer it takes to initially navigate the folder
>> structure (after
>> clicking on the specific Shared Data Library). Just opening
>> up the
>> Shared Data Library can take several minutes and often the
>> browser times
>> out. Is there a way to speed this up?
>>
>> If it's relevant, when I add shared data, it's linked rather
>> than copied
>> into Galaxy. Any suggestions would be greatly appreciated
>>
>> Thanks!
>>
>>
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>>
>>
>>
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