Hi Nicola,
                that is exactly what I'm looking for, however, how do I execute 
the script/tool? I would like to import all published workflows. What is the 
name of the script to run and the arguments ? Can you give an example please?

Thanks again
Neil
________________________________________
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Today's Topics:

   1. Re: creating a hierarchy of students teachers and courses
      (Fernandez Edgar)
   2. Re: making tools with Galaxy (Greg Von Kuster)
   3. Re: making tools with Galaxy (Bj?rn Gr?ning)
   4. Import workflows via API (neil.burd...@csiro.au)
   5. Can't view file_name in histories via API unless admin?
      (neil.burd...@csiro.au)
   6. Re: moving galaxy instance to different location
      (Hans-Rudolf Hotz)
   7. Re: Can't view file_name in histories via API unless      admin?
      (neil.burd...@csiro.au)
   8. Re: Can't view file_name in histories via API unless      admin?
      (Charles Girardot)
   9. Re: Pick-you-own columns in BLAST+ tabular output (Bossers, Alex)
  10. Re: Pick-you-own columns in BLAST+ tabular output (Peter Cock)
  11. Re: Import workflows via API (Nicola Soranzo)
  12. Re: Can't view file_name in histories via API unless admin?
      (neil.burd...@csiro.au)
  13. DRMAA bug in galaxy-central (Bjoern Gruening)
  14. Re: moving galaxy instance to different location (John Chilton)
  15. Re: Can't view file_name in histories via API unless      admin?
      (Dannon Baker)
  16. html network (Lionel Chiron)
  17. Help (Pasquale Notarangelo)
  18. Re: A new tool_data_table_conf.xml created under tool-data
      directory (Nicola Soranzo)
  19. Re: DRMAA bug in galaxy-central (John Chilton)
  20. Galaxy Reports link - registed users per month - does     not
      work (Liisa Koski)


----------------------------------------------------------------------

Message: 1
Date: Thu, 16 Jan 2014 17:18:55 +0000
From: Fernandez Edgar <edgar.fernan...@umontreal.ca>
To: Dannon Baker <dannon.ba...@gmail.com>, John Chilton
        <chil...@msi.umn.edu>
Cc: "galaxy-...@bx.psu.edu" <galaxy-...@bx.psu.edu>
Subject: Re: [galaxy-dev] creating a hierarchy of students teachers
        and courses
Message-ID:
        
<0f2d4f593e660f4eb76fc7c8bfb6a7e343ae2...@ashfield-cour.sim.umontreal.ca>

Content-Type: text/plain; charset="iso-8859-1"

Hello Dannon,

You are right, I've just tried it and it is extremely lighter than my previous 
solution.
I've successfully made a teacher share a complete history with her students and 
vice-versa a student sharing its history with teacher.

Cordialement / Regards,
Edgar Fernandez

De : Dannon Baker [mailto:dannon.ba...@gmail.com]
Envoy? : January-16-14 8:24 AM
? : John Chilton
Cc : Fernandez Edgar; galaxy-...@bx.psu.edu
Objet : Re: [galaxy-dev] creating a hierarchy of students teachers and courses

Would direct-sharing histories work as a significantly lighter weight solution? 
 Each student could just create a history named "DannonBaker_SharedResults" or 
the like, share it directly with their instructor, and put via dataset copy 
and/or perform any work to be shared in that?

-Dannon

On Wed, Jan 15, 2014 at 11:21 PM, John Chilton 
<chil...@msi.umn.edu<mailto:chil...@msi.umn.edu>> wrote:
On Wed, Jan 15, 2014 at 12:03 PM, Fernandez Edgar
<edgar.fernan...@umontreal.ca<mailto:edgar.fernan...@umontreal.ca>> wrote:
> Hello John,
>
> Thank you very much for your answer!
> It's sounds logical and do-able.
>
> However, I've thought of the following and I would like your opinion about it:
> (this is to create a workspace for each student which is accessible only by 
> them and their teacher)
> 1. create a data library for each user (student, teacher and class)
> 2. the data library for each student will have the following permissions:
>         a. modify library item          = student private role (email address)
>         b. access library               = student private role (email 
> address) and teacher private role
Here is where this starts to break down. I think roles do not work the
way most people I talk to about them find intuitive (myself included).
When determining if action X can be performed on a library item - a
user must belong to an intersection of all of the roles not a union of
them. Put another way - each role is restricting the universe of
people that can perform action X on an item not expanding it.

So I am pretty sure Galaxy will not even let you specify this. The
workaround is to create a new role for each student and teacher
combination. This joint role would be the access role and all of the
rest would be the student private role.

>         c. add library item             = student private role (email address)
>         d. manage library permissions   = student private role (email address)
> 3. the data library for each teacher will have the following permissions:
>         a. modify library item          = teacher private role (email address)
>         b. access library               = teacher private role (email address)
>         c. add library item             = teacher private role (email address)
>         d. manage library permissions   = teacher private role (email address)
> 4. the data library for each class will have the following permissions:
>         a. modify library item          = teacher private role (email address)
>         b. access library               = teacher private role (email address)
>         c. add library item             = teacher private role (email 
> address) and all students privates roles
I think add library item has to be a subset of access library. So I
suspect this will not work (though feel free to try).

A work around here might again be to create a new data library for
each combination of student and teacher. This is obviously more
overhead for the teacher though :(.

-John

>         d. manage library permissions   = teacher private role (email address)
>
> Now, here's the one million dollar questions:
> Will the permission 4c permit to every student to drop some work into the 
> class workspace but not cheap by seeing the work of another student ?
>
> Cordialement / Regards,
> Edgar Fernandez
>
>
> -----Message d'origine-----
> De : jmchil...@gmail.com<mailto:jmchil...@gmail.com> 
> [mailto:jmchil...@gmail.com<mailto:jmchil...@gmail.com>] De la part de John 
> Chilton
> Envoy? : January-15-14 12:12 PM
> ? : Fernandez Edgar
> Cc : galaxy-...@bx.psu.edu<mailto:galaxy-...@bx.psu.edu>
> Objet : Re: [galaxy-dev] creating a hierarchy of students teachers and courses
>
> Galaxy can do some these and maybe not others. This is a really big topic, 
> and I hope you let us all know how progress on this goes - it is a really 
> interesting use case. I can comment a little on each part of this, but they 
> are all connected and there are different ways to approach each of these 
> things.
>
> On Tue, Jan 14, 2014 at 12:03 PM, Fernandez Edgar 
> <edgar.fernan...@umontreal.ca<mailto:edgar.fernan...@umontreal.ca>> wrote:
>> Hello galaxy team,
>>
>>
>>
>> First and foremost, I would like to thank you for your assistance with
>> my galaxy installation with apache proxy.
>>
>> It works very well.
>>
>>
>>
>> Secondly, I would like your help with creating users, groups, roles
>> and permissions that would allow me to:
>>
>> 1.       differentiate a student from a teacher
>
> Are you creating these accounts inside of Galaxy or using an external 
> authentication method?
>
> Because if your are creating these accounts yourself - I would suggest using 
> naming scheme to distinguish these:
>
> std_cls_lastname
> teach_cls_lastname
>
> Another idea to consider is to make all teachers admins. This provides a lot 
> of extra functionality that can cover some additional requirements below and 
> can serve as the basis for differentiating.
>
>>
>> 2.       differentiate a student in course A or in course B
>
> You could use a naming scheme, or your could create a group and role for each 
> course. It looks like there is an API for managing groups and roles. This can 
> help automate some of this - it would be very laborious to do this through 
> the UI I imagine.
>
>>
>> 3.       teachers having read access to students' work
>
> This one is why I would give the teachers admin access - I think they could 
> impersonate the students to access their work (set allow_user_impersonation = 
> True in universe_wsgi.ini). It would mean that every teacher would have full 
> access to every students work - if this is a problem you might want to 
> consider standing up a Galaxy instance per class - there is some up front 
> overhead with this - but it would make cleaning things up really easy.
>
> If these aren't realistic solutions, I think producing course documentation 
> describing for students how to manually share their work with teachers is 
> probably the best bet. Any user can share a history with any other user or 
> produce links and e-mail these to the teacher.
>
>>
>> 4.       teachers sharing with students
>
> I would look at having the teachers setup pages for individual courses or 
> lesson plans. These can be made public and students would be able to import 
> histories, datasets, and workflows right in from these. If more targeted 
> sharing is needed again I think the best bet right now might just use 
> Galaxy's history sharing capabilities.
>
>>
>> Right now, I just have created users. There is no group or roles or
>> permissions or datasets.
>>
>>
>>
>> On another note, how can I disable the account of one specific user or
>> a whole group ?
>
> To enable this functionality for individual users and groups in the UI you 
> need to set allow_user_deletion to True in universe_wsgi.ini. I don't think 
> deleting a group will delete all the users in it though.
> This can be automated either by extending the API to support deleting users 
> and then writing a script to iterate over a group and delete all the users or 
> by writing a script that talks to the database directly or using 
> scripts/db_shell.py (which provides an external script access to the Galaxy's 
> data connection and model classes).
>
> Hope this helps,
>
> -John
>
>>
>>
>>
>> Cordialement / Regards,
>>
>>
>>
>> Edgar Fernandez
>>
>> System Administrator (Linux)
>>
>> Direction G?n?rale des Technologies de l'Information et de la
>> Communication
>>
>> (  Bur. : 1-514-343-6111<tel:1-514-343-6111> poste 16568
>>
>>
>>
>> Universit? de Montr?al
>>
>> PAVILLON ROGER-GAUDRY, bureau X-218
>>
>>
>>
>>
>> ___________________________________________________________
>> 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:
>>   http://lists.bx.psu.edu/
>>
>> 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:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
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------------------------------

Message: 2
Date: Thu, 16 Jan 2014 17:03:48 -0500
From: Greg Von Kuster <g...@bx.psu.edu>
To: Lionel Chiron <lionel.chi...@nmrtec.com>
Cc: Galaxy Dev <galaxy-...@bx.psu.edu>
Subject: Re: [galaxy-dev] making tools with Galaxy
Message-ID: <4d7eeb27-f1b2-447e-b849-454c49ce3...@bx.psu.edu>
Content-Type: text/plain; charset=iso-8859-1

Hello Lionel,

Please send correspondence like this to the galaxy-dev@lists.bx.psu.edu mailing 
list rather than individual email accounts as doing so will ensure more timely 
and optimal repoonses.

I'm not quite sure what code you are reading, so could you please clarify?

In general, though, when you write a Galaxy wrapper to integrate a tool into 
Galaxy, you will be able to load the tool into the Galaxy tool panel, and the 
tool UI will display in the main Galaxy panel.  When you execute the tool, a 
Galaxy job will get created which will produce an output in the form of a 
dataset.  This dataset will be displayed in you Galaxy history as the result of 
excuting the tool.  So, in your case, the history item will include the png 
file and, when clicked , it should display in your main Galaxy panel.

There are a lot of details that are calrified in the Galaxy wiki - a good place 
to start is probably:

https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax

Greg Von Kuster


On Jan 16, 2014, at 5:56 AM, Lionel Chiron <lionel.chi...@nmrtec.com> wrote:

> Hi Greg,
>
> I'm trying to make a tool in Galaxy for implementing our algorithm for mass 
> spectrometry treatment but it is a little tricky for me..
> To make run the algorithm in Python is ok, I produce a png with matplotlib .. 
> but after that I 'm a little lost since I don't know where the picture is 
> produced.. reading your code I can't figure out how you indicate where to 
> produce the png file..
> How can I do??
> Thanks
>
> Lionel




------------------------------

Message: 3
Date: Fri, 17 Jan 2014 00:39:57 +0100
From: Bj?rn Gr?ning <bjoern.gruen...@gmail.com>
To: Greg Von Kuster <g...@bx.psu.edu>
Cc: Galaxy Dev <galaxy-...@bx.psu.edu>, Lionel Chiron
        <lionel.chi...@nmrtec.com>
Subject: Re: [galaxy-dev] making tools with Galaxy
Message-ID: <1389915597.6263.1.camel@bag>
Content-Type: text/plain; charset="UTF-8"

Hi Lionel,

here is a simple example of an graphicsmagic wrapper, that consumes an
image and produce one. Maybe its useful for you.

https://github.com/bgruening/galaxytools/tree/master/image_processing

Cheers,
Bjoern

> Hello Lionel,
>
> Please send correspondence like this to the galaxy-dev@lists.bx.psu.edu 
> mailing list rather than individual email accounts as doing so will ensure 
> more timely and optimal repoonses.
>
> I'm not quite sure what code you are reading, so could you please clarify?
>
> In general, though, when you write a Galaxy wrapper to integrate a tool into 
> Galaxy, you will be able to load the tool into the Galaxy tool panel, and the 
> tool UI will display in the main Galaxy panel.  When you execute the tool, a 
> Galaxy job will get created which will produce an output in the form of a 
> dataset.  This dataset will be displayed in you Galaxy history as the result 
> of excuting the tool.  So, in your case, the history item will include the 
> png file and, when clicked , it should display in your main Galaxy panel.
>
> There are a lot of details that are calrified in the Galaxy wiki - a good 
> place to start is probably:
>
> https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax
>
> Greg Von Kuster
>
>
> On Jan 16, 2014, at 5:56 AM, Lionel Chiron <lionel.chi...@nmrtec.com> wrote:
>
> > Hi Greg,
> >
> > I'm trying to make a tool in Galaxy for implementing our algorithm for mass 
> > spectrometry treatment but it is a little tricky for me..
> > To make run the algorithm in Python is ok, I produce a png with matplotlib 
> > .. but after that I 'm a little lost since I don't know where the picture 
> > is produced.. reading your code I can't figure out how you indicate where 
> > to produce the png file..
> > How can I do??
> > Thanks
> >
> > Lionel
>
>
> ___________________________________________________________
> 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:
>   http://lists.bx.psu.edu/
>
> To search Galaxy mailing lists use the unified search at:
>   http://galaxyproject.org/search/mailinglists/




------------------------------

Message: 4
Date: Fri, 17 Jan 2014 05:45:17 +0000
From: <neil.burd...@csiro.au>
To: <galaxy-dev@lists.bx.psu.edu>
Subject: [galaxy-dev] Import workflows via API
Message-ID:
        <25bf49c282c04548a60517ffb251c20d2f724...@exmbx03-cdc.nexus.csiro.au>
Content-Type: text/plain; charset="us-ascii"

Hi,
    I execute workflows via the API. However, if I want another user to use my 
workflows, I can publish my workflows, but the new user then has to go on to 
the web browser and import this workflow.

Is there a method/script which I can call via the API which can import all 
available (published) workflows so the user doesn't have to click a button on 
the web browser "import workflow" ?

Thanks for any help

Neil

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------------------------------

Message: 5
Date: Fri, 17 Jan 2014 06:35:45 +0000
From: <neil.burd...@csiro.au>
To: <galaxy-dev@lists.bx.psu.edu>
Subject: [galaxy-dev] Can't view file_name in histories via API unless
        admin?
Message-ID:
        <25bf49c282c04548a60517ffb251c20d2f724...@exmbx03-cdc.nexus.csiro.au>
Content-Type: text/plain; charset="iso-8859-1"

Hi,
    it seems that the entry "file_name:" does not appear when running the 
command

/home/galaxy/milxcloud/scripts/api/display.py <api_key> 
http://barium-rbh:9100/extras/api/histories/ebfb8f50c6abde6d/contents/4a56addbcc836c23

unless you are stated as as admin user in the "universe_wsgi.ini"
i.e.
admin_users = t...@test.com,te...@test.com

is this known?

Is there anyway to get around this as we don't want all users to be admin, 
however, they need access to this field.

Note that you can't use an admin's <api_key> as you'll get the error
"Error in history API at listing dataset: History is not owned by the current 
user"

Thanks
Neil
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------------------------------

Message: 6
Date: Fri, 17 Jan 2014 09:12:02 +0100
From: Hans-Rudolf Hotz <h...@fmi.ch>
To: Ido Tamir <ta...@imp.ac.at>, "<galaxy-dev@lists.bx.psu.edu>"
        <galaxy-dev@lists.bx.psu.edu>
Subject: Re: [galaxy-dev] moving galaxy instance to different location
Message-ID: <52d8e5d2.8000...@fmi.ch>
Content-Type: text/plain; charset="ISO-8859-1"; format=flowed

Hi Ido

Over the last few years, we have moved our production server to
different hardware twice. And we also made copies of our production
server in order to have the right development environment.

It always work without much hassle, once we have taken care of the
'obvious', which usually was a combination of changing the absolute
paths the configuration files and creating sym-links.


As always, make sure you have a back-up of your PostgreSQL (or MySQL)
database.


Regards, Hans-Rudolf


On 01/16/2014 02:43 PM, Ido Tamir wrote:
> Hi,
>
> I have to move my galaxy instance to a different file system location.
> Is there anything that I have to look out for besides the obvious like 
> absolute paths in some data configs?
>
> thank you very much,
> ido
>
>
>
> ___________________________________________________________
> 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:
>    http://lists.bx.psu.edu/
>
> To search Galaxy mailing lists use the unified search at:
>    http://galaxyproject.org/search/mailinglists/
>


------------------------------

Message: 7
Date: Fri, 17 Jan 2014 08:19:51 +0000
From: <neil.burd...@csiro.au>
To: <galaxy-dev@lists.bx.psu.edu>
Subject: Re: [galaxy-dev] Can't view file_name in histories via API
        unless  admin?
Message-ID:
        <25bf49c282c04548a60517ffb251c20d2f724...@exmbx03-cdc.nexus.csiro.au>
Content-Type: text/plain; charset="us-ascii"

I need to get the file_name so I can get the file_id, because to execute the 
"workflow_execute.py" I need:

<step_id>=hda=<file_id>

Unless there is another way to execute the "workflow_execute.py" or to get the 
<file_id>

Thanks
Neil

From: Burdett, Neil (CCI, Herston - RBWH)
Sent: Friday, 17 January 2014 4:36 PM
To: galaxy-dev@lists.bx.psu.edu
Subject: Can't view file_name in histories via API unless admin?

Hi,
    it seems that the entry "file_name:" does not appear when running the 
command

/home/galaxy/milxcloud/scripts/api/display.py <api_key> 
http://barium-rbh:9100/extras/api/histories/ebfb8f50c6abde6d/contents/4a56addbcc836c23

unless you are stated as as admin user in the "universe_wsgi.ini"
i.e.
admin_users = t...@test.com,te...@test.com<mailto:t...@test.com,te...@test.com>

is this known?

Is there anyway to get around this as we don't want all users to be admin, 
however, they need access to this field.

Note that you can't use an admin's <api_key> as you'll get the error
"Error in history API at listing dataset: History is not owned by the current 
user"

Thanks
Neil
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Message: 8
Date: Fri, 17 Jan 2014 09:31:24 +0100
From: Charles Girardot <charles.girar...@embl.de>
To: <neil.burd...@csiro.au>
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] Can't view file_name in histories via API
        unless  admin?
Message-ID: <44f104b0-1d4b-43e7-a546-fbc41f98f...@embl.de>
Content-Type: text/plain; charset=us-ascii

Hi Neil,

sorry, this is not an answer to your post, I hope you won t mind me stepping in 
your thread this way.
Your message kept my attention because of your note: I am surprised by the 
error message you report when trying to use an admin API key.

How does galaxy know the user who is making the call?

Sorry if I am missing the obvious

bw

Charles

On 17 Jan 2014, at 07:35, <neil.burd...@csiro.au> wrote:

> Hi,
>     it seems that the entry "file_name:" does not appear when running the 
> command
>
> /home/galaxy/milxcloud/scripts/api/display.py <api_key> 
> http://barium-rbh:9100/extras/api/histories/ebfb8f50c6abde6d/contents/4a56addbcc836c23
>
> unless you are stated as as admin user in the "universe_wsgi.ini"
> i.e.
> admin_users = t...@test.com,te...@test.com
>
> is this known?
>
> Is there anyway to get around this as we don't want all users to be admin, 
> however, they need access to this field.
>
> Note that you can't use an admin's <api_key> as you'll get the error
> "Error in history API at listing dataset: History is not owned by the current 
> user"
>
> Thanks
> Neil
> ___________________________________________________________
> 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:
>  http://lists.bx.psu.edu/
>
> To search Galaxy mailing lists use the unified search at:
>  http://galaxyproject.org/search/mailinglists/




------------------------------

Message: 9
Date: Fri, 17 Jan 2014 08:34:49 +0000
From: "Bossers, Alex" <alex.boss...@wur.nl>
To: Peter Cock <p.j.a.c...@googlemail.com>,
        "galaxy-dev@lists.bx.psu.edu"   <galaxy-dev@lists.bx.psu.edu>
Subject: Re: [galaxy-dev] Pick-you-own columns in BLAST+ tabular
        output
Message-ID:
        <fe8945be2de3f34795261679dc2f333d0bfbc...@scomp0935.wurnet.nl>
Content-Type: text/plain; charset="us-ascii"

Peter,
We will definitely give them a try. I never understood why the tabular outputs 
did have an option to include the defline/hit decription. Just for that we 
needed to use the cloggy XML output and parse that into a table again.
Conserved header names are more useful to us than having column numbers. But 
either is fine with us.
Alex

-----Oorspronkelijk bericht-----
Van: galaxy-dev-boun...@lists.bx.psu.edu 
[mailto:galaxy-dev-boun...@lists.bx.psu.edu] Namens Peter Cock
Verzonden: woensdag 15 januari 2014 11:54
Aan: galaxy-dev@lists.bx.psu.edu
Onderwerp: [galaxy-dev] Pick-you-own columns in BLAST+ tabular output

Hello all,

For those interested in more flexible tabular output from BLAST+, please try 
out the wrappers on the *Test* Tool Shed which I have also just updated to wrap 
BLAST+ 2.2.29 as well:

http://testtoolshed.g2.bx.psu.edu/view/peterjc/ncbi_blast_plus

One open question is should the interface for picking columns include the 
current column numbers or not? e.g.

http://dev.list.galaxyproject.org/attachment/4662771/0/blast-pyo-columns-split.png

(Screenshot from this thread last month, where opinion was split) 
http://dev.list.galaxyproject.org/Including-descriptions-etc-in-extended-BLAST-tabular-output-tc4662704.html

In future work we'll add some of the new columns added in the
BLAST+ 2.2.28 release like taxonomy fields - but this needs a
bit of thought about how to handle the taxonomy database (i.e.
should we support multiple versions for full reproducibility, or just use the 
current version on disk regardless). Most of the time updates to the NCBI 
taxonomy will simply be additions, which should be harmless to reproducibility 
- but sometimes taxa can be rearranged.
https://github.com/peterjc/galaxy_blast/issues/20
https://github.com/peterjc/galaxy_blast/issues/21

Regards,

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:
  http://lists.bx.psu.edu/

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  http://galaxyproject.org/search/mailinglists/





------------------------------

Message: 10
Date: Fri, 17 Jan 2014 09:23:40 +0000
From: Peter Cock <p.j.a.c...@googlemail.com>
To: "Bossers, Alex" <alex.boss...@wur.nl>
Cc: "galaxy-dev@lists.bx.psu.edu" <galaxy-dev@lists.bx.psu.edu>
Subject: Re: [galaxy-dev] Pick-you-own columns in BLAST+ tabular
        output
Message-ID:
        <cakvj-_5ihmu5q-8+fkq-qzltvjn4w0vctzkndwx2kywh8tc...@mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1

On Fri, Jan 17, 2014 at 8:34 AM, Bossers, Alex <alex.boss...@wur.nl> wrote:
> Peter,
> We will definitely give them a try.

Great.

>
> I never understood why the tabular outputs did have an option to include
>  the defline/hit decryption.

That was a long standing gripe of mine too, fixed in BLAST+ 2.2.28 and
available in the BLAST+ wrappers on the main Tool Shed since Dec 2013,
http://toolshed.g2.bx.psu.edu/view/devteam/ncbi_blast_plus/ - see also:
http://blastedbio.blogspot.co.uk/2012/05/blast-tabular-missing-descriptions.html

> Just for that we needed to use the cloggy XML output and parse that into
> a table again.

Yes, that was a pain. It was the main reason for writing this tool:
http://toolshed.g2.bx.psu.edu/view/peterjc/blastxml_to_top_descr

> Conserved header names are more useful to us than having column
> numbers. But either is fine with us.
> Alex

Yes, I'd also like the standard BLAST+ tabular output to include a #
(hash) commented header line listing the fields (tab separated). They
do something like this in the extremely verbose commend tabular
output, but that adds a lot of other largely redundant comment lines
as well :(

Regards,

Peter


------------------------------

Message: 11
Date: Fri, 17 Jan 2014 11:36:03 +0100
From: Nicola Soranzo <sora...@crs4.it>
To: <galaxy-dev@lists.bx.psu.edu>
Subject: Re: [galaxy-dev] Import workflows via API
Message-ID: <d834d247437269704a26e8bbf8f67...@crs4.it>
Content-Type: text/plain; charset=UTF-8; format=flowed

Il 2014-01-17 06:45 neil.burd...@csiro.au ha scritto:
> Hi,
>
>  I execute workflows via the API. However, if I want another user to
> use my workflows, I can publish my workflows, but the new user then
> has to go on to the web browser and import this workflow.
>
> Is there a method/script which I can call via the API which can
> import
> all available (published) workflows so the user doesn't have to click
> a button on the web browser "import workflow" ?
>
> Thanks for any help

Hi Neil,
you are very lucky, just yesterday my pull request implementing exactly
this has been merged in galaxy-central:

https://bitbucket.org/galaxy/galaxy-central/pull-request/298/api-display-and-import-workflows-shared-by/diff

and is also available in BioBlend thanks to my colleague Simone Leo:

https://github.com/afgane/bioblend/pull/51

Best,
Nicola

--
Nicola Soranzo, Ph.D.
Bioinformatics Program, CRS4
Loc. Piscina Manna, 09010 Pula (CA), Italy
http://www.bioinformatica.crs4.it/


------------------------------

Message: 12
Date: Fri, 17 Jan 2014 11:12:32 +0000
From: <neil.burd...@csiro.au>
To: <charles.girar...@embl.de>
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] Can't view file_name in histories via API
        unless admin?
Message-ID:
        <25bf49c282c04548a60517ffb251c20d2f724...@exmbx03-cdc.nexus.csiro.au>
Content-Type: text/plain; charset="us-ascii"

Hi Charles,
               not a problem. In my previous post I specified the command line:

/home/galaxy/milxcloud/scripts/api/display.py <api_key> 
http://barium-rbh:9100/extras/api/histories/ebfb8f50c6abde6d/contents/4a56addbcc836c23

The <api_key> in your question refers to the api_key of an "admin" user, 
however, the history_id (ebfb8f50c6abde6d) refers to a history not "owned" by 
the admin user using the unique api_key i.e. another user, hence the error 
message

I hope that answers your question?

Neil

________________________________________
From: Charles Girardot [charles.girar...@embl.de]
Sent: Friday, January 17, 2014 6:31 PM
To: Burdett, Neil (CCI, Herston - RBWH)
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] Can't view file_name in histories via API unless 
admin?

Hi Neil,

sorry, this is not an answer to your post, I hope you won t mind me stepping in 
your thread this way.
Your message kept my attention because of your note: I am surprised by the 
error message you report when trying to use an admin API key.

How does galaxy know the user who is making the call?

Sorry if I am missing the obvious

bw

Charles

On 17 Jan 2014, at 07:35, <neil.burd...@csiro.au> wrote:

> Hi,
>     it seems that the entry "file_name:" does not appear when running the 
> command
>
> /home/galaxy/milxcloud/scripts/api/display.py <api_key> 
> http://barium-rbh:9100/extras/api/histories/ebfb8f50c6abde6d/contents/4a56addbcc836c23
>
> unless you are stated as as admin user in the "universe_wsgi.ini"
> i.e.
> admin_users = t...@test.com,te...@test.com
>
> is this known?
>
> Is there anyway to get around this as we don't want all users to be admin, 
> however, they need access to this field.
>
> Note that you can't use an admin's <api_key> as you'll get the error
> "Error in history API at listing dataset: History is not owned by the current 
> user"
>
> Thanks
> Neil
> ___________________________________________________________
> 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:
>  http://lists.bx.psu.edu/
>
> To search Galaxy mailing lists use the unified search at:
>  http://galaxyproject.org/search/mailinglists/




------------------------------

Message: 13
Date: Fri, 17 Jan 2014 13:15:08 +0100
From: Bjoern Gruening <bjoern.gruen...@gmail.com>
To: Galaxy Dev <galaxy-...@bx.psu.edu>
Subject: [galaxy-dev] DRMAA bug in galaxy-central
Message-ID:
        <1389960908.22645.25.ca...@bipc33.informatik.uni-freiburg.de>
Content-Type: text/plain; charset="ISO-8859-2"

Hi,

since a few days there are frequent error messages popping up in my
Galaxy log files.

galaxy.jobs.runners ERROR 2014-01-17 13:11:17,094 Unhandled exception
checking active jobs
Traceback (most recent call last):
  File
"/usr/local/galaxy/galaxy-dist/lib/galaxy/jobs/runners/__init__.py",
line 358, in monitor
    self.check_watched_items()
  File "/usr/local/galaxy/galaxy-dist/lib/galaxy/jobs/runners/drmaa.py",
line 238, in check_watched_items
    if self.runner_params[ retry_param ] > 0:
TypeError: 'RunnerParams' object has no attribute '__getitem__'

Cheers,
Bjoern




------------------------------

Message: 14
Date: Fri, 17 Jan 2014 08:11:45 -0600
From: John Chilton <chil...@msi.umn.edu>
To: Hans-Rudolf Hotz <h...@fmi.ch>
Cc: "galaxy-dev@lists.bx.psu.edu" <galaxy-dev@lists.bx.psu.edu>
Subject: Re: [galaxy-dev] moving galaxy instance to different location
Message-ID:
        <CANwbokfWaqXbfMpDfn-1VV1wShA_Um=9SaCgj9=fon9osh_...@mail.gmail.com>
Content-Type: text/plain; charset="iso-8859-1"

Just to follow up on this - you will want to explicitly check
dataset.external_filename in your database for any hard coded paths that
may have changed.

Also - all tool shed installed tools including migrated tools are creating
tool dependency files (env.sh) in tool_dependency_dir that contain hard
coded paths. These will all need to be updated.

I imagine some tools will no longer work after migration - for instance
anything installed with virtualenv :(. These will likely need to be
reinstalled. I wish I could say I thought that was going to be an easy
process.

Good luck.

-John

On Jan 17, 2014 2:13 AM, "Hans-Rudolf Hotz" <h...@fmi.ch> wrote:

> Hi Ido
>
> Over the last few years, we have moved our production server to different
> hardware twice. And we also made copies of our production server in order
> to have the right development environment.
>
> It always work without much hassle, once we have taken care of the
> 'obvious', which usually was a combination of changing the absolute paths
> the configuration files and creating sym-links.
>
>
> As always, make sure you have a back-up of your PostgreSQL (or MySQL)
> database.
>
>
> Regards, Hans-Rudolf
>
>
> On 01/16/2014 02:43 PM, Ido Tamir wrote:
>
>> Hi,
>>
>> I have to move my galaxy instance to a different file system location.
>> Is there anything that I have to look out for besides the obvious like
>> absolute paths in some data configs?
>>
>> thank you very much,
>> ido
>>
>>
>>
>> ___________________________________________________________
>> 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:
>>    http://lists.bx.psu.edu/
>>
>> 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:
>  http://lists.bx.psu.edu/
>
> To search Galaxy mailing lists use the unified search at:
>  http://galaxyproject.org/search/mailinglists/
>
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------------------------------

Message: 15
Date: Fri, 17 Jan 2014 09:34:54 -0500
From: Dannon Baker <dannon.ba...@gmail.com>
To: neil.burd...@csiro.au
Cc: Galaxy Dev <galaxy-dev@lists.bx.psu.edu>
Subject: Re: [galaxy-dev] Can't view file_name in histories via API
        unless  admin?
Message-ID:
        <cagn_wzmtyuniwcwkvitqsaz9+xid1vya8jovicyzdp0dttl...@mail.gmail.com>
Content-Type: text/plain; charset="iso-8859-1"

Hi Niel,

Galaxy does not expose filepaths to non-admin users intentionally.  For
executing a workflow with that particular script, the 'file_id' in question
in that example should be an hda, which is what api/history/contents will
display for your users as the 'id' for each history item.

-Dannon


On Fri, Jan 17, 2014 at 6:12 AM, <neil.burd...@csiro.au> wrote:

> Hi Charles,
>                not a problem. In my previous post I specified the command
> line:
>
> /home/galaxy/milxcloud/scripts/api/display.py <api_key>
> http://barium-rbh:9100/extras/api/histories/ebfb8f50c6abde6d/contents/4a56addbcc836c23
>
> The <api_key> in your question refers to the api_key of an "admin" user,
> however, the history_id (ebfb8f50c6abde6d) refers to a history not "owned"
> by the admin user using the unique api_key i.e. another user, hence the
> error message
>
> I hope that answers your question?
>
> Neil
>
> ________________________________________
> From: Charles Girardot [charles.girar...@embl.de]
> Sent: Friday, January 17, 2014 6:31 PM
> To: Burdett, Neil (CCI, Herston - RBWH)
> Cc: galaxy-dev@lists.bx.psu.edu
> Subject: Re: [galaxy-dev] Can't view file_name in histories via API unless
> admin?
>
> Hi Neil,
>
> sorry, this is not an answer to your post, I hope you won t mind me
> stepping in your thread this way.
> Your message kept my attention because of your note: I am surprised by the
> error message you report when trying to use an admin API key.
>
> How does galaxy know the user who is making the call?
>
> Sorry if I am missing the obvious
>
> bw
>
> Charles
>
> On 17 Jan 2014, at 07:35, <neil.burd...@csiro.au> wrote:
>
> > Hi,
> >     it seems that the entry "file_name:" does not appear when running
> the command
> >
> > /home/galaxy/milxcloud/scripts/api/display.py <api_key>
> http://barium-rbh:9100/extras/api/histories/ebfb8f50c6abde6d/contents/4a56addbcc836c23
> >
> > unless you are stated as as admin user in the "universe_wsgi.ini"
> > i.e.
> > admin_users = t...@test.com,te...@test.com
> >
> > is this known?
> >
> > Is there anyway to get around this as we don't want all users to be
> admin, however, they need access to this field.
> >
> > Note that you can't use an admin's <api_key> as you'll get the error
> > "Error in history API at listing dataset: History is not owned by the
> current user"
> >
> > Thanks
> > Neil
> > ___________________________________________________________
> > 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:
> >  http://lists.bx.psu.edu/
> >
> > 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:
>   http://lists.bx.psu.edu/
>
> To search Galaxy mailing lists use the unified search at:
>   http://galaxyproject.org/search/mailinglists/
>
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------------------------------

Message: 16
Date: Fri, 17 Jan 2014 09:50:33 +0100
From: Lionel Chiron <lionel.chi...@nmrtec.com>
To: galaxy-dev@lists.bx.psu.edu
Subject: [galaxy-dev] html network
Message-ID: <52d8eed9.8070...@nmrtec.com>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed

Hi all ,

I am able to write a tool for producing an html file through the network
on the Galaxy server but I can't figure out how to watch this html in
Galaxy.. I would need to write the address of the pictures(which are on
the server) in the html so that it is available through the port 8080
via the network but this is not clear for me how to do that.

Lionel


------------------------------

Message: 17
Date: Fri, 17 Jan 2014 12:32:50 +0100
From: Pasquale Notarangelo <pasquale.notarang...@ba.infn.it>
To: galaxy-...@bx.psu.edu, Alfonso Monaco <alfonso.mon...@ba.infn.it>
Subject: [galaxy-dev] Help
Message-ID: <bf9a2e8d57086e52f94cf1d53f445...@ba.infn.it>
Content-Type: text/plain; charset=UTF-8; format=flowed

Hi all,
we have installed a Galaxy istance on our server and we developed a new
workflow.

Also we have published this workflow and now is shared with every user.

How can we publish the workflow in only runnable mode and then make this
not editable for the other users?

Best regards
Pasquale & Alfonso


~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Dott. Pasquale Notarangelo
INFN Istituto Nazionale di Fisica Nucleare - Sezione Bari

Via Orabona, 4 - 70126 Bari, Italy

Tel. ufficio: +39 080-5443194
Interno ufficio: 3194
Mail: pasquale.notarang...@ba.infn.it
Skype: pasquale.notarangelo_1985
Msn: pasqualenotarang...@hotmail.it
Gmail: notarangelo....@gmail.com

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~


------------------------------

Message: 18
Date: Fri, 17 Jan 2014 15:45:30 +0000 (UTC)
From: Nicola Soranzo <sora...@crs4.it>
To: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] A new tool_data_table_conf.xml created under
        tool-data directory
Message-ID: <loom.20140117t160214-...@post.gmane.org>
Content-Type: text/plain; charset=utf-8

Greg Von Kuster <greg@...> writes:
> On Nov 9, 2012, at 12:56 AM, Derrick Lin wrote:
> > Also how does this change affect the existing shed tools like BWA that
is using?tool_data_table_conf.xml?
>
> The existing shed tools will contiue to function as usual, but entries for
them will be in the tool_data_table_conf.xml file. ?ANy new tools installed
from the tool shed that use entries like this will be added to the new
shed_tool_data_table_conf.xml file. ?Entries from both of these files are
loaded into the ToolDataTableManager. ?The intent is for the Galaxy admin to
be able to manuall make changes to the tool_data_table_conf.xml file and not
have them munged by the tool shed's installation process. ?This is the same
approach used for the tool_conf.xml file, where the Galaxy tool shed
repository installation process uses the shed_tool_conf.xml file.

Reviving an old thread...

I noticed that when I install a repository from the Tool Shed which contains
a tool_data_table_conf.xml.sample , the sample files mentioned therein are
copied to:
- tool-data/ (with AND without .sample extension)
- tool-data/toolshed.g2.bx.psu.edu/repos/OWNER/REPO/REVISION/ (without
.sample extension)
The tool_data_table_conf.xml file in
tool-data/toolshed.g2.bx.psu.edu/repos/OWNER/REPO/REVISION/ references the
files in the same directory, so I find the duplication confusing.

Moreover, there is an increasing number of repositories which install the
same .loc files, e.g.:
- the 4 cufflinks tools plus sam_pileup, sam_to_bam and samtools_mpileup
install fasta_indexes.loc ;
- blat, lastz and lastz_paired_reads install lastz_seqs.loc .
I suppose it was made to prevent repositories from getting in each other's
way, but I see 2 problems:
- system administrators have to manually hard-link these files;
- duplications in shed_tool_data_table_conf.xml generate errors like:
  "galaxy.tools.data ERROR 2014-01-17 15:29:41,409 Attempted to add fields
(['hg19full', 'hg19', 'Human Feb. 2009 (GRCh37/hg19) (hg19) Full',
'/mnt/genome/hg19/sam_index/hg19full/hg19full.fa']) to data table
'fasta_indexes', but this entry already exists and allow_duplicates is False."

Suggestions?

Thanks,
Nicola



------------------------------

Message: 19
Date: Fri, 17 Jan 2014 10:37:46 -0600
From: John Chilton <chil...@msi.umn.edu>
To: Bjoern Gruening <bjoern.gruen...@gmail.com>
Cc: Galaxy Dev <galaxy-...@bx.psu.edu>
Subject: Re: [galaxy-dev] DRMAA bug in galaxy-central
Message-ID:
        <canwbokchsea8ok-t-ze+qmz+12rqorxehmx88onkxr_vhdb...@mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1

It is hard to test error states... but I assume you have the setup for
it :). Any chance you can apply these patches and let me know if they
fix the problem? I assume they will.

https://bitbucket.org/galaxy/galaxy-central/pull-request/300/potential-drmaa-fixes

-John

On Fri, Jan 17, 2014 at 6:15 AM, Bjoern Gruening
<bjoern.gruen...@gmail.com> wrote:
> Hi,
>
> since a few days there are frequent error messages popping up in my
> Galaxy log files.
>
> galaxy.jobs.runners ERROR 2014-01-17 13:11:17,094 Unhandled exception
> checking active jobs
> Traceback (most recent call last):
>   File
> "/usr/local/galaxy/galaxy-dist/lib/galaxy/jobs/runners/__init__.py",
> line 358, in monitor
>     self.check_watched_items()
>   File "/usr/local/galaxy/galaxy-dist/lib/galaxy/jobs/runners/drmaa.py",
> line 238, in check_watched_items
>     if self.runner_params[ retry_param ] > 0:
> TypeError: 'RunnerParams' object has no attribute '__getitem__'
>
> Cheers,
> Bjoern
>
>
> ___________________________________________________________
> 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:
>   http://lists.bx.psu.edu/
>
> To search Galaxy mailing lists use the unified search at:
>   http://galaxyproject.org/search/mailinglists/


------------------------------

Message: 20
Date: Fri, 17 Jan 2014 11:38:41 -0500
From: Liisa Koski <liisa.ko...@basf.com>
To: galaxy-dev@lists.bx.psu.edu
Subject: [galaxy-dev] Galaxy Reports link - registed users per month -
        does    not work
Message-ID:
        <ofe42e1a3e.4acc3807-on85257c63.005b1535-85257c63.005b6...@basf-c-s.be>

Content-Type: text/plain; charset="us-ascii"

Hello,
First..I love the Galaxy Reports tool...thanks so much for this.

I did however come across an error when trying to few the Registered Users
per month link. It would be really nice to have this working :)

Thanks in advance,
Liisa


URL: http://domain:9001/users/registered_users_per_month
Module paste.exceptions.errormiddleware:144 in __call__
>>  app_iter = self.application(environ, sr_checker)
Module paste.debug.prints:106 in __call__
>>  environ, self.app)
Module paste.wsgilib:543 in intercept_output
>>  app_iter = application(environ, replacement_start_response)
Module paste.lint:170 in lint_app
>>  iterator = application(environ, start_response_wrapper)
Module paste.recursive:84 in __call__
>>  return self.application(environ, start_response)
Module paste.httpexceptions:633 in __call__
>>  return self.application(environ, start_response)
Module galaxy.web.framework.base:132 in __call__
>>  return self.handle_request( environ, start_response )
Module galaxy.web.framework.base:190 in handle_request
>>  body = method( trans, **kwargs )
Module galaxy.webapps.reports.controllers.users:29 in
registered_users_per_month
>>  for row in q.execute():
Module sqlalchemy.sql.expression:2841 in execute
Module sqlalchemy.engine.base:2453 in _execute_clauseelement
Module sqlalchemy.engine.base:1584 in _execute_clauseelement
Module sqlalchemy.engine.base:1698 in _execute_context
Module sqlalchemy.engine.base:1691 in _execute_context
Module sqlalchemy.engine.default:331 in do_execute
Module MySQLdb.cursors:173 in execute
Module MySQLdb.connections:36 in defaulterrorhandler
OperationalError: (OperationalError) (1305, 'FUNCTION
galaxy_production.date_trunc does not exist') 'SELECT date_trunc(%s,
date(galaxy_user.create_time)) AS date, count(galaxy_user.id) AS num_users
\nFROM galaxy_user GROUP BY date_trunc(%s, date(galaxy_user.create_time))
ORDER BY date DESC' ('month', 'month')

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End of galaxy-dev Digest, Vol 91, Issue 20
******************************************

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