[galaxy-dev] Please help fix toolshed repository: trtr

2016-03-14 Thread Lance Parsons 
I was helping someone with their toolshed repository and we ran into an 
issue, there is an old folder "myTools" in the repository that we cannot 
delete. It has a second copy of the tool (inadvertently). However, when 
we upload a new version with Planemo, the directory remains. Attempts to 
delete it via the toolshed web interface result in internal server 
errors. Can an admin take a look?


https://toolshed.g2.bx.psu.edu/view/mrvollger/trtr/13cad5d36301


--
Lance Parsons - Scientific Programmer
Carl C. Icahn Laboratory - Room 136
Lewis-Sigler Institute for Integrative Genomics
Princeton University

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[galaxy-dev] Cloudman & AWS IAM_PROFILE support?

2016-03-14 Thread Ryan G 
Hi - Does Cloudman support IAM_PROFILES?   We run our instances within a
VPC and assign an IAM_PROFILE to the ec2 instances so that they have access
to resouces.   Does Cloudman have this support?
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Re: [galaxy-dev] Galaxy tools for docking protein-compounds.

2016-03-14 Thread Léo Biscassi 
Hi, thanks for the reply.
About the branch model, ok! I'll follow the model presented.
About the error in planemo functional tests, the problem is that the
content of example output is not the same of output file of test. This is
shown by the command diff performed on planemo test.
Today, I'll create a pull request in your repository for that we can fix
the problem.
Thank for the helps.

I'm excited about this.

Best regards,



On Thu, Mar 10, 2016 at 5:51 PM Björn Grüning 
wrote:

>
>
> Am 10.03.2016 um 21:30 schrieb Léo Biscassi:
> > Hi folks,
> > I have make somes alterations on my tools to adjust of according with
> > best pratices of development of tools presented in [1] [2]. The
> > repository of tools was changed for [3].
> > I was testing the tool of docking [4] with the command planemo t, but as
> > the algorithm used is heuristic, the output files not have the same
> > content that as output files example and planemo tests fails. Any
> > suggestion to solve this problem?
>
> Is there anything in the file that is the same? Filesize? Some lines
> that are everytime the same (no matter where in the file)?
>
> You could create a PR and I will review it and give you feedback.
> Cheers,
> Bjoern
>
>
> > [1]
> >
> https://galaxy-iuc-standards.readthedocs.org/en/latest/best_practices.html
> > [2] https://planemo.readthedocs.org/en/latest/
> > [3] https://github.com/leobiscassi/autodock_vina_tools
> > [4]
> >
> https://github.com/leobiscassi/autodock_vina_tools/tree/docking/tools/docking
> >
> > Att.
> >
> > On Sat, Jan 30, 2016 at 3:44 PM Léo Biscassi  > > wrote:
> >
> > Hi Bjorn, the branch model of ChemicalToolBoX is the same presented
> > in [1]? Could guide me about it?
> >
> > [1] https://github.com/galaxyproject/galaxy/blob/dev/CONTRIBUTING.md
> >
> > Att.
> >
> > On Mon, Dec 28, 2015 at 5:04 PM Léo Biscassi  > > wrote:
> >
> > Ok, thanks!
> >
> > Best regards,
> >
> > On Mon, Dec 28, 2015 at 5:36 PM Björn Grüning
> > >
> > wrote:
> >
> >
> >
> > Am 28.12.2015 um 20:33 schrieb Léo Biscassi:
> > > Hi,
> > > Thanks all your attention.
> > > Although my project is functional prototype, its current
> > version is able to
> > > integrate with projects. In fact, I was looking for
> > projects like
> > > ChemicalToolBoX because I would like to develop my tools
> > under project that
> > > has more options. In this way, ChemicalToolBoX is a great
> > opportunity for
> > > me.
> > > Can you update the trello card with my project? Is it
> > necessary for your
> > > organization?
> >
> > I added you :) So you have all right to modify cards.
> > Let me know if you need help with Tool development or git.
> >
> > This is exciting!
> > Cheers,
> > Bjoern
> >
> > > Best regards,
> > >
> > > On Mon, Dec 28, 2015 at 5:12 PM Björn Grüning
> >  >>
> > > wrote:
> > >
> > >>
> > >>
> > >> Am 28.12.2015 um 20:06 schrieb Léo Biscassi:
> > >>> Hi,
> > >>>
> > >>> I've found this Trello card (
> > >>> https://trello.com/c/2eIu6SBa/49-autodock-integration).
> > Do you have more
> > >>> information about it?
> > >>
> > >> Afaik we can not use his work as it was done for some
> > company and he
> > >> moved on ... so this is unfortunately no option afaik.
> > >>
> > >>
> > >>
> > >>> best,
> > >>>
> > >>> On Mon, Dec 28, 2015 at 4:33 PM Björn Grüning
> >  >
> > >>>
> > >>> wrote:
> > >>>
> >  Hi,
> > 
> >  yes we had some idea, but nothing materialised so far.
> > We started with
> >  the visualisation, because this was more fun :)
> > 
> >  Have a look at this board for more ideas:
> >  https://trello.com/b/t9Wr8lSY/chemicaltoolbox
> > 
> >  Ciao,
> >  Bjoern
> > 
> > 
> >  Am 28.12.2015 um 19:29 schrieb Léo Biscassi:
> > > Hi Bjorn, thanks for reply.
> > > Would be great idea join forces in this project. How
> >

[galaxy-dev] Mapping users to slurm

2016-03-14 Thread Pardo Diaz, Alfonso 
Hello,

I have connected my galaxy to a Slurm cluster via DRMAA. Galaxy can send jobs 
to the cluster without problems. But then I configure galaxy to use “real 
users” I got this error:

"User myu...@mydomain.es is not mapped to any real 
user, and not permitted to start jobs”


Could you help me?

Tanks!!

This is my job_con.xml:



   
   
   /opt/slurm-drmaa/lib/libdrmaa.so
   
   
   
   
   
   
   
   /opt/galaxy/scripts/drmaa_external_runner.py
   /opt/galaxy/scripts/drmaa_external_killer.py
   /opt/galaxy/scripts/external_chown_script.py
   
   


this is my auth_conf.xml:



   ldap
   
True
   False
ldap://ldap.ceta-ciemat.es
   True
   False
((mail={email})(uid={username}))
uid,mail,dn
   ou=xx,dc=x,dc=x
{dn}
   {password}
   {uid}
   {mail}
   True

   
   

   
   localdb
   
   
   true
   
   



And this is my galaxy.ini:

[server:main]
port = 8080
host = 0.0.0.0
use_threadpool = True
threadpool_kill_thread_limit = 10800

[filter:gzip]
[filter:proxy-prefix]
prefix = /galaxy
[app:main]
paste.app_factory = galaxy.web.buildapp:app_factory
database_connection = postgres://:xx@x/galaxy_project
database_engine_option_server_side_cursors = True
database_engine_option_strategy = threadlocal
new_file_path = database/tmp
tool_config_file = config/tool_conf.xml,config/shed_tool_conf.xml
tool_dependency_dir = dependency_dir
cluster_files_directory = database/pbs
smtp_server = localhost
use_nglims = False
nglims_config_file = tool-data/nglims.yaml
debug = true
use_interactive = True
require_login = True
allow_user_creation = False
allow_user_deletion = True
allow_user_impersonation = True
allow_user_dataset_purge = True
new_user_dataset_access_role_default_private = True
auth_config_file = config/auth_conf.xml
enable_quotas = True
expose_dataset_path = False
job_config_file = config/job_conf.xml
enable_job_recovery = True
outputs_to_working_directory = True
drmaa_external_runjob_script = scripts/drmaa_external_runner.py
drmaa_external_killjob_script = scripts/drmaa_external_killer.py
external_chown_script = scripts/external_chown_script.py


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Re: [galaxy-dev] Scaling tools: data available?

2016-03-14 Thread Eric Rasche 
Hi Peter,

The vision I had was a cron script admins could install which would send
thr past day/week's collectl/memory/parameter/dataset size logs to GRT.

Again, the GRT side stalled when I hit issues with collectl locally. If you
have time/energy to work on that we should chat :-) Otherwise I plan to
find time for it before GCC, minus the collectl stuff, just capturing
runtimes as a start.

Ciao,
Eric
14. mar. 2016 1.09 p.m. skrev "Peter van Heusden" :

> Hi Eric
>
> I'm having a look at the GRT. We're collecting metrics on our local Galaxy
> server, I'm just trying to understand how you envision these metrics
> getting into the GRT?
>
> Peter
>
> On 22 February 2016 at 07:31, Eric Rasche  wrote:
>
>> Hi peter,
>>
>> I've been working on this in the past but got caught up in other
>> projects. There's work for a server-side component here (maybe 50% done),
>> the client side stuff could all be done through collectl but I was having
>> issues actually collecting collectl data that had put the project on hold
>> temporarily.
>>
>> https://github.com/erasche/galactic-radio-telescope
>>
>> I'd be very, very interested in finishing this project up.
>>
>> Cheers,
>> Eric
>>
>>
>> On 02/21/2016 11:13 PM, Peter van Heusden wrote:
>>
>> Hi there
>>
>> We're researching the resource (CPU time and memory) requirements for RNA
>> STAR at the moment. Specifically, we'd like to build up a database of input
>> size to resource usage so that we can use this to feed a dynamic
>> destination mapper (currently our STAR configuration uses a thumbsuck for
>> RAM and CPU requirements that is not optimal but works in many cases).
>>
>> Has anyone collected these metrics before? And more generally, is anyone
>> collecting metrics for a range of bioinformatics tools? A database like
>> this could be very useful!
>>
>> Thanks!
>> Peter
>>
>>
>> ___
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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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>>   http://galaxyproject.org/search/mailinglists/
>>
>>
>> --
>> --
>> Eric Rasche
>> Programmer II
>>
>> Center for Phage Technology
>> Rm 312A, BioBio
>> Texas A University
>> College Station, TX 77843
>> 404-692-2048
>> e...@tamu.edu
>> Not responding quickly enough?
>> 
>>
>
>
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Re: [galaxy-dev] Scaling tools: data available?

2016-03-14 Thread Peter van Heusden 
Hi Eric

I'm having a look at the GRT. We're collecting metrics on our local Galaxy
server, I'm just trying to understand how you envision these metrics
getting into the GRT?

Peter

On 22 February 2016 at 07:31, Eric Rasche  wrote:

> Hi peter,
>
> I've been working on this in the past but got caught up in other projects.
> There's work for a server-side component here (maybe 50% done), the client
> side stuff could all be done through collectl but I was having issues
> actually collecting collectl data that had put the project on hold
> temporarily.
>
> https://github.com/erasche/galactic-radio-telescope
>
> I'd be very, very interested in finishing this project up.
>
> Cheers,
> Eric
>
>
> On 02/21/2016 11:13 PM, Peter van Heusden wrote:
>
> Hi there
>
> We're researching the resource (CPU time and memory) requirements for RNA
> STAR at the moment. Specifically, we'd like to build up a database of input
> size to resource usage so that we can use this to feed a dynamic
> destination mapper (currently our STAR configuration uses a thumbsuck for
> RAM and CPU requirements that is not optimal but works in many cases).
>
> Has anyone collected these metrics before? And more generally, is anyone
> collecting metrics for a range of bioinformatics tools? A database like
> this could be very useful!
>
> 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:
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>
> To search Galaxy mailing lists use the unified search at:
>   http://galaxyproject.org/search/mailinglists/
>
>
> --
> --
> Eric Rasche
> Programmer II
>
> Center for Phage Technology
> Rm 312A, BioBio
> Texas A University
> College Station, TX 77843
> 404-692-2048
> e...@tamu.edu
> Not responding quickly enough?
> 
>
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