Re: [galaxy-dev] Send repeat parameter to code file for multiple select list

[Katherine Beaulieu]

On Fri, Sep 2, 2016 at 9:07 PM, Katherine Beaulieu <
katherine.beaulieu...@gmail.com> wrote:

> Hi Bjorn,
> Thank you for taking the time to reply to my question. I don't think this
> quite fits what I am trying to accomplish. I am trying to pass a set of
> metadata key value pairs, where the user can have as many key value pairs
> as they want, generated with a repeat parameter. I would need to pass the
> entire contents of the repeat parameter to the code file to generate a
> dynamic select list. Do you think this is possible? Perhaps I misread the
> file you have sent me a link to.
> Thanks,
> Katherine
>
> On Fri, Sep 2, 2016 at 6:12 PM, Björn Grüning 
> wrote:
>
>> Hi Katherine,
>>
>> have a look at this one using repeats:
>>
>> https://github.com/bgruening/galaxytools/blob/master/tools/d
>> eseq2/deseq_helper.py
>>
>> Ciao,
>> Bjoern
>>
>>
>> Am 01.09.2016 um 13:58 schrieb Katherine Beaulieu:
>> > Hello Galaxy Community,
>> > I was wondering if anyone had ever come across a situation where they
>> > have had to pass the contents of a repeat parameter to a code file in a
>> > Galaxy tool config? Is there any way to do this?
>> > Katherine
>> >
>> >
>> > ___
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>>
>
>
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Re: [galaxy-dev] Development/production instances updates management

[Ryan G]

We do exactly this.

We have a staging instance, and a production instance.   Both exist in a
single git repo as separate branches.  The main different for this is that
the staging and production config file point to different port and database
instances.

We also maintain a staging and production python environment to match.

Changes always flow from staging to production and follow the git branch
modeling from http://nvie.com/posts/a-successful-git-branching-model/

This has worked EXTREMELY well for us.



On Wed, Aug 31, 2016 at 3:00 AM, Mathieu Bahin <
mathieu.ba...@biologie.ens.fr> wrote:

> Hi all,
>
> First of all, I'm new to this list and already posted my question on
> biostar. Thanks to Hans-Rudolf for his answer but I'm not sure we have
> exactly the same constraints here and I send this message to try to get
> other answers and see what is the best solution for us.
>
> I'm trying to setup a good galaxy environment for a biology institute.
> To do so, I need to have a development and a production instances that
> are clones on the structure side. I'd like to update regularly these
> instances (following more or less galaxy main updates) and track them
> with git repos.
>
> I'm pretty sure lot of galaxy admins are trying to do that but I can't
> find the answer.
>
> My idea was to have a local git repo to save the development instance
> (not the data). When there is a new update, I git pull it from galaxy
> GitHub, compare what changed in the sample files and make the
> appropriate changes in the config files corresponding to these samples.
> Then I would git push towards the production instance. To do so, I need
> to have a proper .gitignore file (listing especially the data files). I
> saw that there is a .gitignore in the galaxy GitHub repo. It's probably
> relevant when I want to pull the updates but I'm not sure it is
> regarding the transfers between the development and production instances
> (for example, the config files have to be tracked I guess).
>
> Cheers,
> Mathieu
>
> --
> 
> ---
> | Mathieu Bahin
> | IE CNRS
> |
> | Institut de Biologie de l'Ecole Normale Supérieure (IBENS)
> | Biocomp team
> | 46 rue d'Ulm
> | 75230 PARIS CEDEX 05
> | 01.44.32.23.56
> 
> ---
>
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Re: [galaxy-dev] how to create users through Galaxy API?

[Björn Grüning]

Hi,

and here a script used by the Galaxy Docker project:

https://github.com/bgruening/docker-galaxy-stable/blob/master/galaxy/setup_postgresql.py

Cheers,
Bjoern

Am 30.08.2016 um 11:56 schrieb Peter Cock:
> Thanks Nicola & Peter B.,
> 
> I was hoping we could script new-user creation like this, and
> that someone else had already done this with the Galaxy API
> (and Bioblend). This looks great!
> 
> Thank you both,
> 
> Peter C.
> 
> On Tue, Aug 30, 2016 at 10:43 AM, Peter Briggs
>  wrote:
>> Hello Peter
>>
>> Following on from Nicola's suggestion: a while ago I had a go at writing
>> some command line tools using Bioblend to try and do some of my Galaxy admin
>> tasks via the API, including creating new user accounts so I'd also
>> recommend this route as much much easier than attempting to interact with
>> the API directly.
>>
>> The tools I wrote are here if you'd like to look at some an example of using
>> Bioblend for this, to get you started:
>>
>> https://github.com/pjbriggs/nebulizer/blob/master/nebulizer/users.py
>>
>> As long as the user that the API key belongs to is an admin user (or if
>> you're using a master API key) this works fine.
>>
>> HTH
>>
>> Best wishes
>>
>> Peter
>>
>>
>> On 29/08/16 17:37, Nicola Soranzo wrote:
>>>
>>> Hi Peter,
>>> why not use BioBlend?
>>>
>>>
>>> https://bioblend.readthedocs.io/en/latest/api_docs/galaxy/all.html#module-bioblend.galaxy.users
>>>
>>> Cheers,
>>> Nicola
>>>
>>>  Peter Cock ha scritto 
>>>
 Thanks Hans-Rudolf,

 Yes - you are right. The wiki does link there but it wasn't obvious to
 me.
 Reading the UserAPIController link source code suggests as long as
 I am authenticated as a Galaxy Admin, I could use this to create new
 user accounts:


 https://docs.galaxyproject.org/en/master/_modules/galaxy/webapps/galaxy/api/users.html#UserAPIController.create

 Thank looks very promising...

 Peter

 On Mon, Aug 29, 2016 at 4:36 PM, Hans-Rudolf Hotz  wrote:
>
> Hi Peter
>
> I guess it is here:
>
> https://docs.galaxyproject.org/en/master/api_doc.html
>
>
> Regards,  Hans-Rudolf
>
> On 08/29/2016 05:27 PM, Peter Cock wrote:
>>
>>
>> Hi Martin,
>>
>> I'd like to look into creating new users via the API (where we can
>> control the email address and username format for integration with our
>> cluster), and have the web-interface forbid users from
>> self-registration.
>>
>> The read-the-docs site you mentioned in this old email (below) doesn't
>> exist anymore, and the API wiki page doesn't seem to link to something
>> similar:
>>
>> https://wiki.galaxyproject.org/Admin/API
>>
>> Where is the official API documentation now?
>>
>> Thanks,
>>
>> Peter
>>
>> On Mon, Dec 30, 2013 at 4:34 AM, Martin Čech > > wrote:
>>
>> Hi,
>>
>> you specify username, password and email in the body (payload) of
>> the POST as Key:Value pairs.
>>
>> Code from the API method: (
>>
>>
>> https://galaxy-central.readthedocs.org/en/latest/_modules/galaxy/webapps/galaxy/api/users.html#UserAPIController.create
>>
>>
>> 
>> )
>>
>>
>>
>> username=payload['username']email=payload['email']password=payload['password']
>>
>> There are also other conditions that need to be fulfilled (e.g.
>> user
>> creation has to be turned on in the configuration) - you will find
>> these when you look at the source code of the method (because the
>> documentation is not perfect yet, sorry).
>>
>> M.
>>
>>
>>
>>
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>>
>
 ___
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Re: [galaxy-dev] Send repeat parameter to code file for multiple select list

[Björn Grüning]

Hi Katherine,

have a look at this one using repeats:

https://github.com/bgruening/galaxytools/blob/master/tools/deseq2/deseq_helper.py

Ciao,
Bjoern


Am 01.09.2016 um 13:58 schrieb Katherine Beaulieu:
> Hello Galaxy Community,
> I was wondering if anyone had ever come across a situation where they
> have had to pass the contents of a repeat parameter to a code file in a
> Galaxy tool config? Is there any way to do this?
> Katherine
> 
> 
> ___
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> 
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Re: [galaxy-dev] apache on ubuntu

[Bick Jochen]

Hi Ray,

I added two lines to the following file:
/etc/apache2/sites-available/000-default.conf
it now looks like this:


# The ServerName directive sets the request scheme, hostname and port 
that
# the server uses to identify itself. This is used when creating
# redirection URLs. In the context of virtual hosts, the ServerName
# specifies what hostname must appear in the request's Host: header to
# match this virtual host. For the default virtual host (this file) this
# value is not decisive as it is used as a last resort host regardless.
# However, you must set it for any further virtual host explicitly.
#ServerName www.example.com

ServerAdmin webmaster@localhost
DocumentRoot /var/www/html

# Available loglevels: trace8, ..., trace1, debug, info, notice, warn,
# error, crit, alert, emerg.
# It is also possible to configure the loglevel for particular
# modules, e.g.
#LogLevel info ssl:warn

ErrorLog ${APACHE_LOG_DIR}/error.log
CustomLog ${APACHE_LOG_DIR}/access.log combined

# For most configuration files from conf-available/, which are
# enabled or disabled at a global level, it is possible to
# include a line for only one particular virtual host. For example the
# following line enables the CGI configuration for this host only
# after it has been globally disabled with "a2disconf".
#Include conf-available/serve-cgi-bin.conf
RewriteEngine on
RewriteRule ^(.*) http://localhost:8080$1 [P]



# vim: syntax=apache ts=4 sw=4 sts=4 sr noet

but it does not have any effect. Here the error.log but there is no error:
[Fri Sep 02 15:28:21.677881 2016] [mpm_event:notice] [pid 6627:tid 
140049034254208] AH00493: SIGUSR1 received.  Doing graceful restart
[Fri Sep 02 15:28:21.688069 2016] [proxy_html:notice] [pid 6627:tid 
140049034254208] AH01425: I18n support in mod_proxy_html requires mod_xml2enc. 
Without it, non-ASCII characters in proxied pages are likely to display 
incorrectly.
[Fri Sep 02 15:28:21.689351 2016] [mpm_event:notice] [pid 6627:tid 
140049034254208] AH00489: Apache/2.4.18 (Ubuntu) OpenSSL/1.0.2g-fips configured 
-- resuming normal operations
[Fri Sep 02 15:28:21.689355 2016] [core:notice] [pid 6627:tid 140049034254208] 
AH00094: Command line: '/usr/sbin/apache2'


Cheers Jochen
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Re: [galaxy-dev] Testtoolshed status

[Martin Čech]

This has been fixed now, thanks Steve for the report and sorry for the
trouble.

Martin

On Fri, Sep 2, 2016 at 10:20 AM Dave Bouvier  wrote:

> Steve,
>
> Thank you for reporting this issue, we've determined a potential cause
> and are working to correct it.
>
> -
> Dave Bouvier
> http://galaxyproject.org
> http://usegalaxy.org
>
> On 09/02/2016 03:29 AM, Steve Cassidy wrote:
> > I’m getting a 500 response from the testtoolshed when I try to upload a
> > tool via planemo:
> >
> > ➜  alveo-galaxy-tools git:(master) ✗ planemo shed_update --shed_target
> > testtoolshed apitools
> > cd '/Users/steve/projects/alveo-galaxy-tools/apitools' && git rev-parse
> HEAD
> > cd '/Users/steve/projects/alveo-galaxy-tools/apitools' && git diff
> --quiet
> > Could not update alveoimport
> > Unexpected HTTP status code: 500: 
> >   Internal Server Error
> >   
> > Internal Server Error
> > The server has either erred or is incapable of performing
> > the requested operation.
> >
> > 
> > 
> > 
> > WSGI Server
> >   
> > 
> >
> > Repository metadata updated successfully for repository alveoimport.
> > Failed to update a repository.
> >
> > In addition, I just got a “Tool Shed could not be reached” message via
> > the web interface, so i’m wondering if something is up.
> >
> > Thanks,
> >
> > Steve
> > —
> > Department of Computing, Macquarie University
> > http://web.science.mq.edu.au/~cassidy
> >
> >
> >
> > ___
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> >
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> >
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Re: [galaxy-dev] apache on ubuntu

[Raymond Wan]

Hi Jochen,


On Fri, Sep 2, 2016 at 8:32 PM, Jochen Bick  wrote:
> yes exactly. So my problem is that I have no idea where to copy those
> settings. I have tutorial how it works on Centos but the file structure is
> different on Ubuntu.


Slightly different, but not too different.  If it's Apache then the
general format of its configuration files is probably the same.  Just
the path and how to restart the web server will differ.

I tried setting it up before but that was a long time ago.  But if not
me, perhaps someone else can help you if you post (a) what you have so
far in the configuration files and (b) what kind of errors you're
getting in your error logs.


> So I have my galaxy instance running on localhost:8080 (can also be moved to
> something else). If I run localhost or my local ip in a browser I see the
> apache also from a different PC in my network. So my idea is to redirect the
> apache or galaxy to my IP so that everyone in the network can see and use it
> (ssl encrypted if possible)


I would ignore SSL for the moment.  You should probably break up your
problem into smaller problems.

Try editing 000-default.conf.  Then throw the RewriteRules in the
aforementioned web page into that.  I think that page is actually
quite self-explanatory.  For example, this rule:

RewriteRule ^(.*) http://localhost:8080$1 [P]

would rewrite the URLs so that anyone accessing your site on port 80
would then get sent to port 8080.  If it's another server, then it
would then be something like this:

RewriteRule ^(.*) http://www.example.com:8080$1 [P]

Of course, you can change that to https, etc. but, again, move step by
step and see if you can get port 80 on localhost redirected to port
8080 on localhost first.

Ray
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Re: [galaxy-dev] Testtoolshed status

[Dave Bouvier]

Steve,

Thank you for reporting this issue, we've determined a potential cause 
and are working to correct it.


-
Dave Bouvier
http://galaxyproject.org
http://usegalaxy.org

On 09/02/2016 03:29 AM, Steve Cassidy wrote:

I’m getting a 500 response from the testtoolshed when I try to upload a
tool via planemo:

➜  alveo-galaxy-tools git:(master) ✗ planemo shed_update --shed_target
testtoolshed apitools
cd '/Users/steve/projects/alveo-galaxy-tools/apitools' && git rev-parse HEAD
cd '/Users/steve/projects/alveo-galaxy-tools/apitools' && git diff --quiet
Could not update alveoimport
Unexpected HTTP status code: 500: 
  Internal Server Error
  
Internal Server Error
The server has either erred or is incapable of performing
the requested operation.




WSGI Server
  


Repository metadata updated successfully for repository alveoimport.
Failed to update a repository.

In addition, I just got a “Tool Shed could not be reached” message via
the web interface, so i’m wondering if something is up.

Thanks,

Steve
—
Department of Computing, Macquarie University
http://web.science.mq.edu.au/~cassidy



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Re: [galaxy-dev] apache on ubuntu

[Jochen Bick]

Hi Ray,

yes exactly. So my problem is that I have no idea where to copy those 
settings. I have tutorial how it works on Centos but the file structure 
is different on Ubuntu.


So I have my galaxy instance running on localhost:8080 (can also be 
moved to something else). If I run localhost or my local ip in a browser 
I see the apache also from a different PC in my network. So my idea is 
to redirect the apache or galaxy to my IP so that everyone in the 
network can see and use it (ssl encrypted if possible)


Cheers Jochen

On 02.09.2016 06:02, Raymond Wan wrote:

Hi Jochen,

I presume you looked at this already:

https://wiki.galaxyproject.org/Admin/Config/ApacheProxy

Those instructions work for Ubuntu as well.  What do your Apache2
error logs says (in /var/log/apache2/)?  And what have you tried in
your configuration files?

And are you trying to forward port 80 to 8080, 443 to 8080 or something else?

Ray



On Fri, Sep 2, 2016 at 5:53 AM, Jochen Bick  wrote:

Hi,

I'm having trouble setting up the apache to redirect my local running galaxy
which runs on localhost:8080
I would like that people could have access inside the lab knowing my local
ip address. I read plenty of tutorials, can anyone help setting it up on
Ubuntu? The files I have to modify are located at:
/etc/apache2/sites-available/
000-default.conf and default-ssl.config ?

apache is up and running.

Cheers Jochen
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[galaxy-dev] Testtoolshed status

[Steve Cassidy]

I’m getting a 500 response from the testtoolshed when I try to upload a tool 
via planemo:

➜  alveo-galaxy-tools git:(master) ✗ planemo shed_update --shed_target 
testtoolshed apitools
cd '/Users/steve/projects/alveo-galaxy-tools/apitools' && git rev-parse HEAD
cd '/Users/steve/projects/alveo-galaxy-tools/apitools' && git diff --quiet
Could not update alveoimport
Unexpected HTTP status code: 500: 
  Internal Server Error
  
Internal Server Error
The server has either erred or is incapable of performing
the requested operation.




WSGI Server
  


Repository metadata updated successfully for repository alveoimport.
Failed to update a repository.

In addition, I just got a “Tool Shed could not be reached” message via the web 
interface, so i’m wondering if something is up.

Thanks,

Steve
—
Department of Computing, Macquarie University
http://web.science.mq.edu.au/~cassidy

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