date:20160801

Re: [galaxy-dev] Returning BLAST datatypes and DB loc files to Galaxy core?

2016-08-01 Thread Peter Cock

Hi Gildas,

When datatypes were moved to the Tool Shed, I
think the idea was to eventually have only a core
set of topic-neutral datatypes (plain text, tabular,
etc) in Galaxy itself. That does seem sensible.

I'm not quite sure why policy has returned to a
larger centralised set - but limitations of the
ToolShed like dependencies (for Python code
imported directly into Galaxy), lack of versioning
of datatypes, and better control of namespaces
are likely part of this. I missed GCC2017 sadly.

Even with a large set of datatypes included with
Galaxy, it should be easy to hide/disable lots
(e.g. for an image analysis Galaxy you would
not want any of the sequence file formats).

Peter

P.S. Good point about EDAM, its been raised
on the BLAST datatypes pull request:
https://github.com/galaxyproject/galaxy/pull/2696

On Mon, Aug 1, 2016 at 9:27 PM, Gildas Le Corguillé
 wrote:
> Hi all,
>
> If indeed, datatypes return within the Galaxy distribution, can we imagine
> propose different datatypes_conf.xml?
>
> Galaxy isn’t anymore dedicated to NGS purpose. It is use also for
> metabolomics, proteomics, …
>
> So it could be great to propose 1 "common" list of datatypes (text, tabular,
> png, pdf, …) and n specific datatypes lists for the n scientific areas to
> reduce this huge list of datatypes proposed to the users.
> Maybe this selection should be based on edam ontology. As you know they are
> almost already annotated with edam_format and edam_data
>
>
> Gildas
>
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[galaxy-dev] Connecting LDAP with Galaxy

2016-08-01 Thread Yip, Miu ki

Hi,

I’m trying to configure a new instance of Galaxy and I want to use LDAP for 
user authentication. I have taken a look at this wiki page: 
https://wiki.galaxyproject.org/Admin/Config/ExternalUserAuth

I followed the instructions and when I looked into the auth_conf.xml file, I 
was unsure of what exactly Galaxy is looking for when trying to connect with 
LDAP. Are there specific options that I must give it? May I ask how Galaxy uses 
LDAP to authenticate users?

Thank you,
Miuki Yip
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Re: [galaxy-dev] Returning BLAST datatypes and DB loc files to Galaxy core?

2016-08-01 Thread Gildas Le Corguillé

Hi all,

If indeed, datatypes return within the Galaxy distribution, can we imagine 
propose different datatypes_conf.xml?

Galaxy isn’t anymore dedicated to NGS purpose. It is use also for metabolomics, 
proteomics, … 

So it could be great to propose 1 "common" list of datatypes (text, tabular, 
png, pdf, …) and n specific datatypes lists for the n scientific areas to 
reduce this huge list of datatypes proposed to the users.
Maybe this selection should be based on edam ontology. As you know they are 
almost already annotated with edam_format and edam_data


Gildas

-
Gildas Le Corguillé - Bioinformatician/Bioanalyste

Plateform ABiMS (Analyses and Bioinformatics for Marine Science)
http://abims.sb-roscoff.fr 

Member of the Workflow4Metabolomics project
http://workflow4metabolomics.org 

Station Biologique de Roscoff - UPMC/CNRS - FR2424
Place Georges Teissier 29680 Roscoff FRANCE
tel: +33 2 98 29 23 81
--



> Le 1 août 2016 à 18:41, Peter Cock  a écrit :
> 
> I have a work-in-progress branch and pull request here,
> https://github.com/peterjc/galaxy/tree/blast_datatypes
> https://github.com/galaxyproject/galaxy/pull/2696
> 
> The Galaxy TravisCI tests looked fine.
> 
> Peter
> 
> On Mon, Aug 1, 2016 at 11:18 AM, Peter Cock  wrote:
>> Dear all,
>> 
>> I ran this past the IUC first, and the only comments were
>> positive.
>> 
>> Although I wasn't at GCC2017 to discuss this in person,
>> I understand that the Galaxy Team now encourages
>> widely used datatypes to be included in the main Galaxy
>> repository, rather than distributed via the Tool Shed.
>> 
>> To that end, would a pull request returning the BLAST
>> datatypes and associated database *.loc files be welcome?
>> 
>> These are currently on my GitHub repository here:
>> https://github.com/peterjc/galaxy_blast/
>> 
>> And the datatypes are distributed via the Tool Shed here:
>> http://toolshed.g2.bx.psu.edu/view/devteam/blast_datatypes
>> 
>> Assuming this happens, we would need to phase out the
>> tool shed version (but it will still be needed while older
>> Galaxy instances are still running).
>> 
>> Are there any pitfalls to worry about if the datatypes are
>> already there with Galaxy and the tool shed version is
>> installed on top? Or the tool shed version was installed
>> but then Galaxy was updated to include the version
>> bundled with Galaxy?
>> 
>> Thanks,
>> 
>> Peter
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Re: [galaxy-dev] Returning BLAST datatypes and DB loc files to Galaxy core?

2016-08-01 Thread Peter Cock

I have a work-in-progress branch and pull request here,
https://github.com/peterjc/galaxy/tree/blast_datatypes
https://github.com/galaxyproject/galaxy/pull/2696

The Galaxy TravisCI tests looked fine.

Peter

On Mon, Aug 1, 2016 at 11:18 AM, Peter Cock  wrote:
> Dear all,
>
> I ran this past the IUC first, and the only comments were
> positive.
>
> Although I wasn't at GCC2017 to discuss this in person,
> I understand that the Galaxy Team now encourages
> widely used datatypes to be included in the main Galaxy
> repository, rather than distributed via the Tool Shed.
>
> To that end, would a pull request returning the BLAST
> datatypes and associated database *.loc files be welcome?
>
> These are currently on my GitHub repository here:
> https://github.com/peterjc/galaxy_blast/
>
> And the datatypes are distributed via the Tool Shed here:
> http://toolshed.g2.bx.psu.edu/view/devteam/blast_datatypes
>
> Assuming this happens, we would need to phase out the
> tool shed version (but it will still be needed while older
> Galaxy instances are still running).
>
> Are there any pitfalls to worry about if the datatypes are
> already there with Galaxy and the tool shed version is
> installed on top? Or the tool shed version was installed
> but then Galaxy was updated to include the version
> bundled with Galaxy?
>
> Thanks,
>
> Peter
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Re: [galaxy-dev] Remote user auth and API

2016-08-01 Thread Sarah DIEHL

Hi Nicola,

thanks a lot for the help! Yes, it's a self-signed certificate, I didn't bother 
with letsencrypt yet ;-).

So now the error turned to

ConnectionError: GET: error 401: b'\n\n401 Authorization 
Required\n\nAuthorization Required\nThis 
server could not verify that you\nare authorized to access the 
document\nrequested.  Either you supplied the wrong\ncredentials (e.g., bad 
password), or your\nbrowser doesn\'t understand how to supply\nthe credentials 
required.\n\n', 0 attempts left: None

which is what I expected, since apache now wants the authentication through 
LDAP.

So anybody know what the right settings are to get both the dataset import and 
the API working with external user auth over apache and LDAP?

Thanks,
Sarah


Sarah Diehl
HPC System Administrator

UNIVERSITÉ DU LUXEMBOURG

LUXEMBOURG CENTRE FOR SYSTEMS BIOMEDICINE
Campus Belval | Biotech II
6, avenue du Swing
L-4371 Belvaux
T +352 46 66 44 5360
sarah.di...@uni.lu 
http://lcsb.uni.lu
-
This message is confidential and may contain privileged information. It is 
intended for the named recipient only. If you receive it in error please notify 
me and permanently delete the original message and any copies.
-


From: Nicola Soranzo 
mailto:nicola.sora...@gmail.com>> on behalf of Nicola 
Soranzo mailto:nsora...@tiscali.it>>
Date: Monday 1 August 2016 12:58
To: Sarah DIEHL mailto:sarah.di...@uni.lu>>, 
"galaxy-dev@lists.galaxyproject.org" 
mailto:galaxy-dev@lists.galaxyproject.org>>
Subject: Re: [galaxy-dev] Remote user auth and API

Hi Sarah!
I guess that your problem is with an untrusted certificate, you can get one for 
free at https://letsencrypt.org/

You can disable certificate verification in bioblend as in the example below:

import bioblend.galaxy
gi = bioblend.galaxy.GalaxyInstance(url=my_server, key=my_key)
gi.verify = False

Cheers,
Nicola

On 01/08/16 09:08, Sarah DIEHL wrote:
Dear all,

since the recent update to 16.04 I get the following error when trying to 
import a file from a user directory to a data library:

AssertionError: use_remote_user is set but HTTP_REMOTE_USER header was not 
provided

I use apache as a proxy and use an LDAP server for authentication. In order to 
get the API to work previously the apache had to be set to not check 
authentication for the requests to /api. In the logs I can see that the dataset 
import is an request to the API, so since the auth is not checked then, there 
is also no REMOTE_USER header set.

What is the recommended way to solve this issue with the current Galaxy 
version? I disabled the special settings for /api and the dataset import works 
now.

I tried to check the API with an old test script based on bioblend, but I now 
get the following error:

ConnectionError: [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed 
(_ssl.c:645), 0 attempts left: None

Previously I could disable it with

import requests
requests.packages.urllib3.disable_warnings()

but that doesn't seem to work anymore (switched to Python 3 now). Since 
bioblend wraps all the requests methods, I cannot apply any of the common 
solutions I found online (e.g. set verify=False).

Any help to solve these issues is highly appreciated :-).

Best regards,
Sarah




Sarah Diehl
HPC System Administrator

UNIVERSITÉ DU LUXEMBOURG

LUXEMBOURG CENTRE FOR SYSTEMS BIOMEDICINE
Campus Belval | Biotech II
6, avenue du Swing
L-4371 Belvaux
T +352 46 66 44 5360
sarah.di...@uni.lu 
http://lcsb.uni.lu
-
This message is confidential and may contain privileged information. It is 
intended for the named recipient only. If you receive it in error please notify 
me and permanently delete the original message and any copies.
-




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Re: [galaxy-dev] Remote user auth and API

2016-08-01 Thread Nicola Soranzo


Hi Sarah!
I guess that your problem is with an untrusted certificate, you can get 
one for free at https://letsencrypt.org/


You can disable certificate verification in bioblend as in the example 
below:


import bioblend.galaxy
gi = bioblend.galaxy.GalaxyInstance(url=my_server, key=my_key)
gi.verify = False

Cheers,
Nicola

On 01/08/16 09:08, Sarah DIEHL wrote:

Dear all,

since the recent update to 16.04 I get the following error when trying 
to import a file from a user directory to a data library:


AssertionError: use_remote_user is set but HTTP_REMOTE_USER header was 
not provided


I use apache as a proxy and use an LDAP server for authentication. In 
order to get the API to work previously the apache had to be set to 
not check authentication for the requests to /api. In the logs I can 
see that the dataset import is an request to the API, so since the 
auth is not checked then, there is also no REMOTE_USER header set.


What is the recommended way to solve this issue with the current 
Galaxy version? I disabled the special settings for /api and the 
dataset import works now.


I tried to check the API with an old test script based on bioblend, 
but I now get the following error:


ConnectionError: [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify 
failed (_ssl.c:645), 0 attempts left: None


Previously I could disable it with

import requests
requests.packages.urllib3.disable_warnings()

but that doesn't seem to work anymore (switched to Python 3 now). 
Since bioblend wraps all the requests methods, I cannot apply any of 
the common solutions I found online (e.g. set verify=False).


Any help to solve these issues is highly appreciated :-).

Best regards,
Sarah




Sarah Diehl
HPC System Administrator
UNIVERSITÉ DU LUXEMBOURG
LUXEMBOURG CENTRE FOR SYSTEMS BIOMEDICINE
Campus Belval | Biotech II
6, avenue du Swing
L-4371 Belvaux
T +352 46 66 44 5360
sarah.di...@uni.lu http://lcsb.uni.lu 


-
This message is confidential and may contain privileged information. 
It is intended for the named recipient only. If you receive it in 
error please notify me and permanently delete the original message and 
any copies.

-



___
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in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
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[galaxy-dev] Fwd: Returning BLAST datatypes and DB loc files to Galaxy core?

2016-08-01 Thread Peter Cock

Dear all,

I ran this past the IUC first, and the only comments were
positive.

Although I wasn't at GCC2017 to discuss this in person,
I understand that the Galaxy Team now encourages
widely used datatypes to be included in the main Galaxy
repository, rather than distributed via the Tool Shed.

To that end, would a pull request returning the BLAST
datatypes and associated database *.loc files be welcome?

These are currently on my GitHub repository here:
https://github.com/peterjc/galaxy_blast/

And the datatypes are distributed via the Tool Shed here:
http://toolshed.g2.bx.psu.edu/view/devteam/blast_datatypes

Assuming this happens, we would need to phase out the
tool shed version (but it will still be needed while older
Galaxy instances are still running).

Are there any pitfalls to worry about if the datatypes are
already there with Galaxy and the tool shed version is
installed on top? Or the tool shed version was installed
but then Galaxy was updated to include the version
bundled with Galaxy?

Thanks,

Peter
___
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/

[galaxy-dev] Remote user auth and API

2016-08-01 Thread Sarah DIEHL

Dear all,

since the recent update to 16.04 I get the following error when trying to 
import a file from a user directory to a data library:

AssertionError: use_remote_user is set but HTTP_REMOTE_USER header was not 
provided

I use apache as a proxy and use an LDAP server for authentication. In order to 
get the API to work previously the apache had to be set to not check 
authentication for the requests to /api. In the logs I can see that the dataset 
import is an request to the API, so since the auth is not checked then, there 
is also no REMOTE_USER header set.

What is the recommended way to solve this issue with the current Galaxy 
version? I disabled the special settings for /api and the dataset import works 
now.

I tried to check the API with an old test script based on bioblend, but I now 
get the following error:

ConnectionError: [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed 
(_ssl.c:645), 0 attempts left: None

Previously I could disable it with

import requests
requests.packages.urllib3.disable_warnings()

but that doesn't seem to work anymore (switched to Python 3 now). Since 
bioblend wraps all the requests methods, I cannot apply any of the common 
solutions I found online (e.g. set verify=False).

Any help to solve these issues is highly appreciated :-).

Best regards,
Sarah




Sarah Diehl
HPC System Administrator

UNIVERSITÉ DU LUXEMBOURG

LUXEMBOURG CENTRE FOR SYSTEMS BIOMEDICINE
Campus Belval | Biotech II
6, avenue du Swing
L-4371 Belvaux
T +352 46 66 44 5360
sarah.di...@uni.lu 
http://lcsb.uni.lu
-
This message is confidential and may contain privileged information. It is 
intended for the named recipient only. If you receive it in error please notify 
me and permanently delete the original message and any copies.
-

___
Please keep all replies on the list by using "reply all"
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and other Galaxy lists, please use the interface at:
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[galaxy-dev] run-as-user and Galaxy 16.04

2016-08-01 Thread Peter van Heusden

Hi there

Does anyone have the run-as-user support working with Galaxy 16.04? If so,
could you describe your config?

Thanks,
Peter
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Re: [galaxy-dev] Returning BLAST datatypes and DB loc files to Galaxy core?

[galaxy-dev] Connecting LDAP with Galaxy

Re: [galaxy-dev] Returning BLAST datatypes and DB loc files to Galaxy core?

Re: [galaxy-dev] Returning BLAST datatypes and DB loc files to Galaxy core?

Re: [galaxy-dev] Remote user auth and API

Re: [galaxy-dev] Remote user auth and API

[galaxy-dev] Fwd: Returning BLAST datatypes and DB loc files to Galaxy core?

[galaxy-dev] Remote user auth and API

[galaxy-dev] run-as-user and Galaxy 16.04

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