Re: [galaxy-dev] ERROR: PIP is not a legl parament of an Ansible Play

[William Ge]

From: Marius van den Beek 
Sent: Friday, March 4, 2016 12:26 PM
To: William Ge
Cc: Dannon Baker; galaxy-dev@lists.galaxyproject.org
Subject: Re: [galaxy-dev] ERROR: PIP is not a legl parament of an Ansible Play
Thanks, Marius!  That got me through!

The Galaxy Team has done a wonderful job putting together such a complex 
system. It is very well packaged and documented good enough for developers. But 
for new people like me, a more fool-proof step-by-step guide will be very 
helpful. I have worked with ACEDB, GCG, LionBioscience SRS and other early 
bioinformatics packages in the past, but have been out of touch for a while. 
The most challenging portion for me is to sort out the configuration files, 
retrieve/download data and install tools. The web admin application is a good 
tool. It would be very helpful for new people if there is a check box in front 
of the categories of tools, and in front of each individual tools, so that we 
can check to select and click install to perform batch install there.

Best regards,
Bill


On 4 March 2016 at 20:47, William Ge 
> wrote:

Thanks a lot, Marius!

Sure, you're welcome!


I am a newbie to this complex system and want a quick clone/install locally. I 
have spent over two weeks on the process. There are many configuration files 
and environment variables or dependencies to sort out. I wish the sample 
configuration files would include most of the options so that new installation 
just needs to comment out or delete unwanted ones.


The galaxy team definitely aims for this, and usually you should (tm) be able 
to clone galaxy and use run.sh to get going.
If you can tell us the steps where you were struggling we can try to update or 
clarify the documentation (A lot of it is on the wiki).

Anyway, here is the error I got:

[galaxy@Pegasus ansible-galaxy-tools]$ python files/install_tool_shed_tools.py 
-h
Traceback (most recent call last):
  File "files/install_tool_shed_tools.py", line 49, in 
logging.captureWarnings(True)  # Capture HTTPS warngings from urllib3
AttributeError: 'module' object has no attribute 'captureWarnings'


If I run this after activating the galaxy_env and install ensible, bioblend, 
argparse and importlib, the same error came up. I guess this is Python 2.6 
issue. Any solutions known?


This is indeed a python2.6 issue. Note that python2.6 has reached it's EOL in 
October 2013 (https://www.python.org/download/releases/2.6.9/), and python2.6 
support for galaxy will be phased out with the next release 
(https://github.com/galaxyproject/galaxy/issues/1596), so it's probably a good 
idea to look into migrating to python2.7. That said, you can try this patch 
https://github.com/galaxyproject/ansible-galaxy-tools/compare/master...galaxyproject:python26_workaround.diff
In addition, there may be a bioblend problem in combination with recent galaxy 
releases. I'll let you know once this is sorted out.


Thanks,

Bill




From: Marius van den Beek 
>
Sent: Friday, March 4, 2016 11:03 AM
To: William Ge
Cc: Dannon Baker; 
galaxy-dev@lists.galaxyproject.org
Subject: Re: [galaxy-dev] ERROR: PIP is not a legl parament of an Ansible Play

The list of tools installed on usegalaxy.org is 
conviniently desposited here:
Galaxy
usegalaxy.org
The Galaxy analysis interface requires a browser with Javascript enabled. 
Please enable Javascript and refresh this page. Galaxy. Javascript Required for 
Galaxy

https://github.com/galaxyproject/usegalaxy-playbook/blob/master/files/galaxy/usegalaxy.org/tool_list.yaml

Normally you should be able to use this command outlined above to get all the 
tools that usegalaxy.org has,
including the dependencies.

PS. please keep all traffic on the mailing list

On 4 March 2016 at 19:59, Marius van den Beek 
> wrote:

There is no real step by step guide, but the script itself has a help text:

$ python install_tool_shed_tools.py -h


Also make sure you have bioblend installed (pip install bioblend)
It does more things than just installing tools. To just install tools you would 
use a command line like this:


python install_tool_shed_tools.py -a "your new admin api key" -g "your new 
galaxy instance url" -t tool_list.yml


tool_list.yml follows the format outlined here:
https://github.com/galaxyproject/ansible-galaxy-tools/blob/master/files/tool_list.yaml.sample

Cheers,
Marius

On 4 March 2016 at 19:11, William Ge 
> wrote:

Thank you both, Marius and Dannon!

Since I am not familiar with ansible, I will just run the python script. I am 
reading about the usage of the script, trying 

[galaxy-dev] Planemo test with SGE

[D K]

Hi,

I posted this question to biostars but didn't get an answer

Is it possible to use "planemo test" functionality on an SGE cluster? I can
correctly run a custom tool on an SGE cluster when I manually run a job
through the galaxy interface. If I change the job_conf.xml so that the job
is run locally, I can use "planemo test" successfully, but if I change the
job_conf.xml so that Galaxy uses the SGE cluster, planemo fails:

Traceback (most recent call last):
  File "/remote/home/galaxyd/galaxy-test-SGE/test/functional/test_toolbox.py",
line 289, in test_tool
self.do_it( td )
  File "/remote/home/galaxyd/galaxy-test-SGE/test/functional/test_toolbox.py",
line 38, in do_it
stage_data_in_history( galaxy_interactor, testdef.test_data(),
test_history, shed_tool_id )
  File "/remote/home/galaxyd/galaxy-test-SGE/test/base/interactor.py",
line 43, in stage_data_in_history
upload_wait()
  File "/remote/home/galaxyd/galaxy-test-SGE/test/base/interactor.py",
line 280, in wait
while not self.__history_ready( history_id ):
  File "/remote/home/galaxyd/galaxy-test-SGE/test/base/interactor.py",
line 298, in __history_ready
return self._state_ready( state, error_msg="History in error state." )
  File "/remote/home/galaxyd/galaxy-test-SGE/test/base/interactor.py",
line 361, in _state_ready
raise Exception( error_msg )
Exception: History in error state.
 >> begin captured stdout << -
History with id 2891970512fa2d5a in error - summary of datasets in error below.
--
| 1 - MTB_Genes.fasta (HID - NAME)
| Dataset Blurb:
|  tool error
| Dataset Info:
|  The cluster DRM system terminated this job
| Dataset Job Standard Output:
|  *Standard output was empty.*
| Dataset Job Standard Error:
|  *Standard error was empty.*
|
--

- >> end captured stdout << --

Is this a problem with my configuration or a limitation of planemo?


Thanks!
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Re: [galaxy-dev] ERROR: PIP is not a legl parament of an Ansible Play

[Marius van den Beek]

The list of tools installed on usegalaxy.org is conviniently desposited
here:
https://github.com/galaxyproject/usegalaxy-playbook/blob/master/files/galaxy/usegalaxy.org/tool_list.yaml

Normally you should be able to use this command outlined above to get all
the tools that usegalaxy.org has,
including the dependencies.

PS. please keep all traffic on the mailing list

On 4 March 2016 at 19:59, Marius van den Beek 
wrote:

> There is no real step by step guide, but the script itself has a help text:
>
> $ python install_tool_shed_tools.py -h
>
> Also make sure you have bioblend installed (pip install bioblend)
> It does more things than just installing tools. To just install tools you
> would use a command line like this:
>
>
> python install_tool_shed_tools.py -a "your new admin api key" -g "your new 
> galaxy instance url" -t tool_list.yml
>
> tool_list.yml follows the format outlined here:
>
> https://github.com/galaxyproject/ansible-galaxy-tools/blob/master/files/tool_list.yaml.sample
>
> Cheers,
> Marius
> ​
>
> On 4 March 2016 at 19:11, William Ge  wrote:
>
>> Thank you both, Marius and Dannon!
>>
>> Since I am not familiar with ansible, I will just run the python script.
>> I am reading about the usage of the script, trying to figure out what
>> configuration needs  to be in place and what options to use. Is there  a
>> step-by-step guide for using this script somewhere?
>>
>>
>> Best regards,
>> Bill
>>
>> --
>> *From:* Marius van den Beek 
>> *Sent:* Friday, March 4, 2016 7:25 AM
>> *To:* Dannon Baker
>> *Cc:* William Ge; galaxy-dev@lists.galaxyproject.org
>> *Subject:* Re: [galaxy-dev] ERROR: PIP is not a legl parament of an
>> Ansible Play
>>
>> Hi Bill,
>>
>> I think you're trying to use the ansible-galaxy-tools role as a playbook:
>> This won't work, you can only include the role in your playbook,
>> or use this playbook https://github.com/afgane/galaxy-tools-playbook
>> 
>> afgane/galaxy-tools-playbook · GitHub
>> 
>> github.com
>> README.md A ready-to-use Ansible playbook for the Galaxy Tools role.
>> Before you can use this playbook, you need to install Ansible: $ pip
>> install ansible
>> You can also directly use the python script in
>> https://github.com/galaxyproject/ansible-galaxy-tools/blob/master/files/install_tool_shed_tools.py
>> if you're more comfortable not using ansible.
>>
>> Cheers,
>> Marius
>>
>> On 4 March 2016 at 13:43, Dannon Baker  wrote:
>>
>>> I haven't seen this before but did a little googling.  What version is
>>> your ansible installation?   If it's a little bit older, (
>>> https://github.com/ansible/ansible/issues/5412) might be what you're
>>> seeing.
>>>
>>> It's a bit of a long read, but it looks like reinstalling or updating
>>> your ansible (or installing a new one in a fresh virtualenv for isolation)
>>> should resolve it.
>>>
>>> Let me know if that doesn't fix it up for you.
>>>
>>> On Thu, Mar 3, 2016 at 10:08 PM, William Ge 
>>> wrote:
>>>
 Hi, all,



 Sorry to bother you again. I am trying to install tools using the
 script. I have downloaded the playbook, but stuck here:



 [galaxy@Pegasus ansible-galaxy-tools]$ ansible-playbook
 tasks/tools.yml -i "localhost," --extra-vars galaxy_tools_api_key=xcd2Glx

 ERROR: pip is not a legal parameter of an Ansible Play



 I did not find anything related on the Galaxy search either. Any help
 will be appreciated.



 The web Admin interface only allows tool installation one by one. I
 wish it allows batch installation there.



 Thanks,

 Bill





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>>>
>>>
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>>>
>>
>>
>
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Re: [galaxy-dev] ERROR: PIP is not a legl parament of an Ansible Play

[Marius van den Beek]

There is no real step by step guide, but the script itself has a help text:

$ python install_tool_shed_tools.py -h

Also make sure you have bioblend installed (pip install bioblend)
It does more things than just installing tools. To just install tools you
would use a command line like this:


python install_tool_shed_tools.py -a "your new admin api key" -g "your
new galaxy instance url" -t tool_list.yml

tool_list.yml follows the format outlined here:
https://github.com/galaxyproject/ansible-galaxy-tools/blob/master/files/tool_list.yaml.sample

Cheers,
Marius
​

On 4 March 2016 at 19:11, William Ge  wrote:

> Thank you both, Marius and Dannon!
>
> Since I am not familiar with ansible, I will just run the python script. I
> am reading about the usage of the script, trying to figure out what
> configuration needs  to be in place and what options to use. Is there  a
> step-by-step guide for using this script somewhere?
>
>
> Best regards,
> Bill
>
> --
> *From:* Marius van den Beek 
> *Sent:* Friday, March 4, 2016 7:25 AM
> *To:* Dannon Baker
> *Cc:* William Ge; galaxy-dev@lists.galaxyproject.org
> *Subject:* Re: [galaxy-dev] ERROR: PIP is not a legl parament of an
> Ansible Play
>
> Hi Bill,
>
> I think you're trying to use the ansible-galaxy-tools role as a playbook:
> This won't work, you can only include the role in your playbook,
> or use this playbook https://github.com/afgane/galaxy-tools-playbook
> 
> afgane/galaxy-tools-playbook · GitHub
> 
> github.com
> README.md A ready-to-use Ansible playbook for the Galaxy Tools role.
> Before you can use this playbook, you need to install Ansible: $ pip
> install ansible
> You can also directly use the python script in
> https://github.com/galaxyproject/ansible-galaxy-tools/blob/master/files/install_tool_shed_tools.py
> if you're more comfortable not using ansible.
>
> Cheers,
> Marius
>
> On 4 March 2016 at 13:43, Dannon Baker  wrote:
>
>> I haven't seen this before but did a little googling.  What version is
>> your ansible installation?   If it's a little bit older, (
>> https://github.com/ansible/ansible/issues/5412) might be what you're
>> seeing.
>>
>> It's a bit of a long read, but it looks like reinstalling or updating
>> your ansible (or installing a new one in a fresh virtualenv for isolation)
>> should resolve it.
>>
>> Let me know if that doesn't fix it up for you.
>>
>> On Thu, Mar 3, 2016 at 10:08 PM, William Ge 
>> wrote:
>>
>>> Hi, all,
>>>
>>>
>>>
>>> Sorry to bother you again. I am trying to install tools using the
>>> script. I have downloaded the playbook, but stuck here:
>>>
>>>
>>>
>>> [galaxy@Pegasus ansible-galaxy-tools]$ ansible-playbook tasks/tools.yml
>>> -i "localhost," --extra-vars galaxy_tools_api_key=xcd2Glx
>>>
>>> ERROR: pip is not a legal parameter of an Ansible Play
>>>
>>>
>>>
>>> I did not find anything related on the Galaxy search either. Any help
>>> will be appreciated.
>>>
>>>
>>>
>>> The web Admin interface only allows tool installation one by one. I wish
>>> it allows batch installation there.
>>>
>>>
>>>
>>> Thanks,
>>>
>>> Bill
>>>
>>>
>>>
>>>
>>>
>>> ___
>>> 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/
>>>
>>
>>
>> ___
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>> 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/
>>
>
>
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Re: [galaxy-dev] switch to git

[Nate Coraor]

On Thu, Mar 3, 2016 at 10:20 AM, Briand, Sheldon (NRC/CNRC) <
sheldon.bri...@canada.ca> wrote:

> Hi,
>
>
>
> I’ve done the recently announced security update for my running release
> which is 15.01.  I figured I had better switch to git now while I was at
> it.  However I’m having trouble matching revisions in git.
>
>
>
> I have looked at the instructions in the Develop/SourceCode page of the
> Wiki.  I’ve used git log show-notes=hg2git after fetching them.  It seems
> those notes stop at changeset 16698 while I am now showing changeset 17151
> with the hg log –b $(hg branch) command and 17161 with hg tip.
>
>
>
> What should my next step be?
>

Hi Sheldon,

The notes cover the period up to when we switched to git, nothing after
that point. Since you are on a "point" release of Galaxy post-git-migration
(17151:7ca8f0ecb2ae == 15.01.4), you can use the `v15.01.4` tag in Git to
get updated to the same version.

--nate


>
>
> Thanks,
>
> -Sheldon
>
>
>
>
>
>
>
> Sheldon Briand
>
> Computer Systems and Applications Analyst
>
> National Research Council/Government of Canada
>
> sheldon.bri...@canada.ca/ Tel: (902) 426-1677
>
>
>
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>
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Re: [galaxy-dev] trouble with python packages after galaxy update

[Nate Coraor]

On Thu, Mar 3, 2016 at 3:24 AM, Linda Bakker  wrote:

> Hi Guys,
> So i updated my galaxy instance to release_16.01
> I usually started galaxy in a venv and used pip to install any packages my
> tool needed. (in this case, numpy and scipy)
>
> source my_galaxy_dir/.venv/bin/activate
> pip install scipy (dependency numpy also installed)
> ./run.sh
>
> But since the last update, i am having problems with this.
> Did something change? because it looks like it searches for an existing
> venv and then activates a new venv in my already active one??
>
> Depending on what i try, when i execute my tool in galaxy, my messages
> range from
>
> ImportError: No module named scipy
> or ValueError: numpy.dtype has the wrong size, try recompiling
> 
>
> I tried running galaxy without a venv, re-creating my venv. renaming my
> venv
> installing numpy, then scipy, not using pip at all.
> removing numpy and reinstalling without cache.
> I also played around with pip, doing nothing after creating my venv, or
> first upgrading my pip, but then after i start galaxy i get this message:
>

Hi Linda,

There are two options here:

1. You can install your dependencies inside Galaxy's virtualenv, (by
default, .venv)
2. You can set up a separate virtualenv to be used only by jobs. Depending
on how you run jobs, this one may also need to include Galaxy's
dependencies (to run the metadata detection step).

Details can be found here:

  https://docs.galaxyproject.org/en/master/admin/framework_dependencies.html

And specifically, the instructions for setting up a separate virtualenv for
job handlers:


https://docs.galaxyproject.org/en/master/admin/framework_dependencies.html#galaxy-job-handlers

--nate


> (.venv)@server:/galaxy-dist$ ./run.sh
> Activating virtualenv at .venv
> Ignoring indexes: https://pypi.python.org/simple
> Collecting pip==8.0.2+gx2
>   Downloading
> https://wheels.galaxyproject.org/packages/pip-8.0.2+gx2-py2.py3-none-any.whl
> (1.2MB)
> 100% || 1.2MB 339kB/s
> Installing collected packages: pip
>   Found existing installation: pip 8.0.3
> Uninstalling pip-8.0.3:
>   Successfully uninstalled pip-8.0.3
> Successfully installed pip-8.0.2+gx2
>
> And later on i get the message that i should upgrade my pip...
> I am confused...can someone tell me the correct way to start galalxy
> within or without my venv and how to correctly install my packages?
> Thanks!
>
>
> with regards,
> Linda Bakker
>
> --
> Linda Bakker
> Bioinformatics Research Assistant
> Plant Research International, Wageningen UR
> Building 107 (Radix), room W1.Fa.054
> Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
> tel: +31-317-480756
> email: linda.bak...@wur.nl
>
>
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>
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[galaxy-dev] Fwd: Galaxy Conference

[Scott Szakonyi]

Hi Martin,

Thank you for the quick response! However, I'm unclear... is "Training Day
One" different from the mix of individual session listed there, or does
training day one consist of those other sessions that I sign up for? I have
created a sched account, I'm just a bit confused about the relationship of
things.

Thanks!

Scott

On Fri, Mar 4, 2016 at 11:35 AM, Martin Čech  wrote:

> Hello Scott,
>
> have you seen the schedule at https://gcc16.sched.org/ ?
>
> The trainings are all listed, described, and categorized there, it should
> help you decide what to attend.
> From my experience in addition to scientists there are many admins and
> developers attending the conference so you should be able to find your
> flock easily.
>
> Plus we are all nice. :)
>
> Best,
> Martin
>
> On Fri, Mar 4, 2016 at 11:32 AM Scott Szakonyi 
> wrote:
>
>> Hi all,
>>
>> I know this is not a technical question per se, but this seems my best
>> option for getting better information.
>>
>> I am planning on attending the Galaxy Conference this year. I
>> administrate the Galaxy server for VectorBase (vectorbase.org), but I'm
>> a computer scientist, not a bioinformatics specialist. I'm uncertain what
>> would be the most informative things for me to attend... for instance, I
>> see there is a training day 1 and 2, but there's no real description on the
>> site of what those are. If someone could offer some guidance, I would be
>> most appreciative.
>>
>> Also, would the conference days be useful for someone in my position?
>>
>> Thanks!
>>
>> --
>> Scott B. Szakonyi
>> Research Programmer
>>
>> *Center for Research Computing*
>> 107 Information Technology Center
>> Notre Dame, IN 46556
>> http://crc.nd.edu
>> ___
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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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>>
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>>   http://galaxyproject.org/search/mailinglists/
>
>


-- 
Scott B. Szakonyi
Research Programmer

*Center for Research Computing*
107 Information Technology Center
Notre Dame, IN 46556
http://crc.nd.edu



-- 
Scott B. Szakonyi
Research Programmer

*Center for Research Computing*
107 Information Technology Center
Notre Dame, IN 46556
http://crc.nd.edu
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Re: [galaxy-dev] Galaxy Conference

[Martin Čech]

Hello Scott,

have you seen the schedule at https://gcc16.sched.org/ ?

The trainings are all listed, described, and categorized there, it should
help you decide what to attend.
>From my experience in addition to scientists there are many admins and
developers attending the conference so you should be able to find your
flock easily.

Plus we are all nice. :)

Best,
Martin

On Fri, Mar 4, 2016 at 11:32 AM Scott Szakonyi 
wrote:

> Hi all,
>
> I know this is not a technical question per se, but this seems my best
> option for getting better information.
>
> I am planning on attending the Galaxy Conference this year. I administrate
> the Galaxy server for VectorBase (vectorbase.org), but I'm a computer
> scientist, not a bioinformatics specialist. I'm uncertain what would be the
> most informative things for me to attend... for instance, I see there is a
> training day 1 and 2, but there's no real description on the site of what
> those are. If someone could offer some guidance, I would be most
> appreciative.
>
> Also, would the conference days be useful for someone in my position?
>
> Thanks!
>
> --
> Scott B. Szakonyi
> Research Programmer
>
> *Center for Research Computing*
> 107 Information Technology Center
> Notre Dame, IN 46556
> http://crc.nd.edu
> ___
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>
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[galaxy-dev] Galaxy Conference

[Scott Szakonyi]

Hi all,

I know this is not a technical question per se, but this seems my best
option for getting better information.

I am planning on attending the Galaxy Conference this year. I administrate
the Galaxy server for VectorBase (vectorbase.org), but I'm a computer
scientist, not a bioinformatics specialist. I'm uncertain what would be the
most informative things for me to attend... for instance, I see there is a
training day 1 and 2, but there's no real description on the site of what
those are. If someone could offer some guidance, I would be most
appreciative.

Also, would the conference days be useful for someone in my position?

Thanks!

-- 
Scott B. Szakonyi
Research Programmer

*Center for Research Computing*
107 Information Technology Center
Notre Dame, IN 46556
http://crc.nd.edu
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Re: [galaxy-dev] Python 2.7 six egg fetching issue

[Peter Cock]

On Fri, Mar 4, 2016 at 3:13 PM, Yves Gagnon  wrote:
> Hi everyone,
>
> When I try to run galaxy using python 2.7 I get this error message while
> fetching eggs.  Under python 2.6 I do not have that issue:
>
> DistributionNotFound: six==1.9.0
>
> The galaxy release I use is still 15.07.
>
> Is there any fix for that other than building the egg myself, or maybe newer
> release do not have that issue?
>
> Thanks in advance!
>
> Yves Gagnon

Good news & bad news regarding the latest Galaxy releases.

Galaxy v16.01 will not have any egg problems because all the
Python dependencies are now done using the wheel format,
plus a Galaxy modified version of pip to handle tracking Linux
binary compatibility.

Also Galaxy v16.01 will likely be the final release to support
Python 2.6, so its good you're already looking at Python 2.7 :)

https://github.com/galaxyproject/galaxy/issues/1596

Peter
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Re: [galaxy-dev] Python 2.7 six egg fetching issue

[Yves Gagnon]

Thanks Peter,

I heard support for 2.6 will be dropped, that is why I was investigating using 
2.7 right now.
I will try to stage an update to 16.01 then and see how that works!

>From eggs to wheel, that's one big step in evolution :)  haha

Yves Gagnon

-Original Message-
From: Peter Cock [mailto:p.j.a.c...@googlemail.com]
Sent: Friday, March 04, 2016 10:22 AM
To: Yves Gagnon 
Cc: galaxy-dev@lists.galaxyproject.org
Subject: Re: [galaxy-dev] Python 2.7 six egg fetching issue

On Fri, Mar 4, 2016 at 3:13 PM, Yves Gagnon  wrote:
> Hi everyone,
>
> When I try to run galaxy using python 2.7 I get this error message
> while fetching eggs.  Under python 2.6 I do not have that issue:
>
> DistributionNotFound: six==1.9.0
>
> The galaxy release I use is still 15.07.
>
> Is there any fix for that other than building the egg myself, or maybe
> newer release do not have that issue?
>
> Thanks in advance!
>
> Yves Gagnon

Good news & bad news regarding the latest Galaxy releases.

Galaxy v16.01 will not have any egg problems because all the Python 
dependencies are now done using the wheel format, plus a Galaxy modified 
version of pip to handle tracking Linux binary compatibility.

Also Galaxy v16.01 will likely be the final release to support Python 2.6, so 
its good you're already looking at Python 2.7 :)

https://github.com/galaxyproject/galaxy/issues/1596

Peter


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Re: [galaxy-dev] ERROR: PIP is not a legl parament of an Ansible Play

[Marius van den Beek]

Hi Bill,

I think you're trying to use the ansible-galaxy-tools role as a playbook:
This won't work, you can only include the role in your playbook,
or use this playbook https://github.com/afgane/galaxy-tools-playbook
You can also directly use the python script in
https://github.com/galaxyproject/ansible-galaxy-tools/blob/master/files/install_tool_shed_tools.py
if you're more comfortable not using ansible.

Cheers,
Marius

On 4 March 2016 at 13:43, Dannon Baker  wrote:

> I haven't seen this before but did a little googling.  What version is
> your ansible installation?   If it's a little bit older, (
> https://github.com/ansible/ansible/issues/5412) might be what you're
> seeing.
>
> It's a bit of a long read, but it looks like reinstalling or updating your
> ansible (or installing a new one in a fresh virtualenv for isolation)
> should resolve it.
>
> Let me know if that doesn't fix it up for you.
>
> On Thu, Mar 3, 2016 at 10:08 PM, William Ge 
> wrote:
>
>> Hi, all,
>>
>>
>>
>> Sorry to bother you again. I am trying to install tools using the script.
>> I have downloaded the playbook, but stuck here:
>>
>>
>>
>> [galaxy@Pegasus ansible-galaxy-tools]$ ansible-playbook tasks/tools.yml
>> -i "localhost," --extra-vars galaxy_tools_api_key=xcd2Glx
>>
>> ERROR: pip is not a legal parameter of an Ansible Play
>>
>>
>>
>> I did not find anything related on the Galaxy search either. Any help
>> will be appreciated.
>>
>>
>>
>> The web Admin interface only allows tool installation one by one. I wish
>> it allows batch installation there.
>>
>>
>>
>> Thanks,
>>
>> Bill
>>
>>
>>
>>
>>
>> ___
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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/
>>
>
>
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[galaxy-dev] Python 2.7 six egg fetching issue

[Yves Gagnon]

Hi everyone,

 

When I try to run galaxy using python 2.7 I get this error message while
fetching eggs.  Under python 2.6 I do not have that issue:

 

DistributionNotFound: six==1.9.0

 

 

The galaxy release I use is still 15.07.

Is there any fix for that other than building the egg myself, or maybe newer
release do not have that issue?

 

Thanks in advance!


Yves Gagnon



 



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Re: [galaxy-dev] Problems with planemo functional tests

[Léo Biscassi]

Hi Gildas, thanks for the reply.
I had renamed galaxy.ini.sample file to galaxy.ini and performed my
configurations to the server.
In fact, I created the file galaxy.ini.sample and command works fine!

Thanks a lot!

Best regards,

On Thu, Mar 3, 2016 at 5:46 AM Gildas Le Corguillé <
lecorgui...@sb-roscoff.fr> wrote:

> Hi,
>
> Do you still have the config/galaxy.ini.sample file unchanged ?
>
> We observed this message when some .sample are missing or were modified.
>
> 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 3 mars 2016 à 07:31, Léo Biscassi  a écrit :
>
> Hi, the command that you suggested not working, the same output is
> presented. I tested with the following commands:
>
> *sudo planemo test
> /home/leobiscassi/programs/galaxy/tools/planemo-tutorial/seqtk_seq.xml
> --galaxy_root=/home/leobiscassi/programs/galaxy*
>
> *sudo planemo test
> /home/leobiscassi/programs/galaxy/tools/planemo-tutorial/seqtk_seq.xml*
>
> What is the influence of xUnit file in the process? I did the question
> because the warning message showing "*Cannot locate xUnit report option
> for tests - update Galaxy for more detailed breakdown*".
>
> P.S.: My Galaxy instance is the latest stable version.
>
> Best regards,
>
> On Thu, Mar 3, 2016 at 2:53 AM Björn Grüning 
> wrote:
>
>> Hi,
>>
>> maybe I'm mistaken something, its way to early here ... but you need to
>> specify a path to the tool you want to test.
>>
>> For example:
>>
>> planemo test /foo/bar/foo.xml
>>
>> or to a directory full of tools.
>>
>> planemo test /foo/bar
>>
>> Hope this helps,
>> Bjoern
>>
>> Am 03.03.2016 um 04:48 schrieb Léo Biscassi:
>> > Hi Folks,
>> > I tried follow this tutorial [1], but I have problems in execute the
>> > command "planemo t --galaxy_root=/home/leobiscassi/programs/galaxy" for
>> > perform functional tests, any suggestion?
>> > Bellow some images about this problem:
>> >
>> > imagem1.jpg
>> > *Figure 1: *Command
>> >
>> > imagem2.jpg
>> > *Figure 2:* Error
>> >
>> > imagem3.jpg
>> > *Figure 3: *Galaxy Path
>> >
>> > Planemo's version is 0.23.0.
>> >
>> > [1] https://planemo.readthedocs.org/en/latest/writing_standalone.html
>> >
>> > P.S: The command is utilized for same tool presented in tutorial.
>> >
>> > Att.
>> > --
>> > *Léo Biscassi*
>> > Facebook - https://pt-br.facebook.com/lbiscassi
>> > Linkedin - https://br.linkedin.com/in/leobiscassi
>> > Skype - biscassi.leo
>> > Twitter - https://twitter.com/leobiscassi
>> >
>> >
>> > ___
>> > 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/
>> >
>>
> --
> *Léo Biscassi*
> Facebook - https://pt-br.facebook.com/lbiscassi
> Linkedin - https://br.linkedin.com/in/leobiscassi
> Skype - biscassi.leo
> Twitter - https://twitter.com/leobiscassi
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>
>
> --
*Léo Biscassi*
Facebook - https://pt-br.facebook.com/lbiscassi
Linkedin - https://br.linkedin.com/in/leobiscassi
Skype - biscassi.leo
Twitter - https://twitter.com/leobiscassi
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Re: [galaxy-dev] ERROR: PIP is not a legl parament of an Ansible Play

[Dannon Baker]

I haven't seen this before but did a little googling.  What version is your
ansible installation?   If it's a little bit older, (
https://github.com/ansible/ansible/issues/5412) might be what you're seeing.

It's a bit of a long read, but it looks like reinstalling or updating your
ansible (or installing a new one in a fresh virtualenv for isolation)
should resolve it.

Let me know if that doesn't fix it up for you.

On Thu, Mar 3, 2016 at 10:08 PM, William Ge  wrote:

> Hi, all,
>
>
>
> Sorry to bother you again. I am trying to install tools using the script.
> I have downloaded the playbook, but stuck here:
>
>
>
> [galaxy@Pegasus ansible-galaxy-tools]$ ansible-playbook tasks/tools.yml
> -i "localhost," --extra-vars galaxy_tools_api_key=xcd2Glx
>
> ERROR: pip is not a legal parameter of an Ansible Play
>
>
>
> I did not find anything related on the Galaxy search either. Any help will
> be appreciated.
>
>
>
> The web Admin interface only allows tool installation one by one. I wish
> it allows batch installation there.
>
>
>
> Thanks,
>
> Bill
>
>
>
>
>
> ___
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> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
>   https://lists.galaxyproject.org/
>
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>   http://galaxyproject.org/search/mailinglists/
>
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Re: [galaxy-dev] error loading files into galaxy

[Peter Cock]

Hello Hakeem,

Did you ever solve this import problem?

We suddenly started seeing this on our main (old) Galaxy server,
which we have not intentionally changed recently:


$ hg log | head
changeset:   17125:e837a68e8d14
tag: tip
parent:  17121:7a4e3a661a76
parent:  17124:46a4ef8850b5
user:Nate Coraor 
date:Fri May 15 15:21:34 2015 -0400
summary: Merge stable to default


I suspect either a system update, or an accidental change
where I meant to edit the test instance on the same machine,
or a new Galaxy instance we're working on using a new VM.

Turning on debug level logging, I could deduce the ImportError
happens when the local job runner tries to run the upload1
tool's Python script:


galaxy.jobs.runners DEBUG 2016-03-04 11:14:17,449 (13809) command is:
python /mnt/galaxy/galaxy-dist/tools/data_source/upload.py
/mnt/galaxy/galaxy-dist /mnt/galaxy/galaxy-dist/database/tmp/tmp2qzTWC
/mnt/galaxy/galaxy-dist/database/tmp/tmpC6Tq0J
16915:/mnt/galaxy/galaxy-dist/database/job_working_directory/013/13809/dataset_16915_files:/mnt/galaxy/galaxy-dist/database/files/016/dataset_16915.dat;
return_code=$?; python
/mnt/galaxy/galaxy-dist/database/job_working_directory/013/13809/set_metadata_SP3B7H.py
/mnt/galaxy/galaxy-dist/database/tmp/tmp2qzTWC
/mnt/galaxy/galaxy-dist/database/job_working_directory/013/13809/galaxy.json
/mnt/galaxy/galaxy-dist/database/job_working_directory/013/13809/metadata_in_HistoryDatasetAssociation_16276_0wz2tR,/mnt/galaxy/galaxy-dist/database/job_working_directory/013/13809/metadata_kwds_HistoryDatasetAssociation_16276_1IeKfn,/mnt/galaxy/galaxy-dist/database/job_working_directory/013/13809/metadata_out_HistoryDatasetAssociation_16276_cKjsLG,/mnt/galaxy/galaxy-dist/database/job_working_directory/013/13809/metadata_results_HistoryDatasetAssociation_16276_iyGIDI,/mnt/galaxy/galaxy-dist/database/files/016/dataset_16915.dat,/mnt/galaxy/galaxy-dist/database/job_working_directory/013/13809/metadata_override_HistoryDatasetAssociation_16276_K9ebdM;
sh -c "exit $return_code"


I can reproduce the error at the command line with just:


$ python /mnt/galaxy/galaxy-dist/tools/data_source/upload.py
Traceback (most recent call last):
  File "/mnt/galaxy/galaxy-dist/tools/data_source/upload.py", line 8,
in 
from galaxy import eggs
ImportError: cannot import name eggs


I could hack this script based on how Galaxy adds its libraries to
the Python import path, and now uploads work again:


$ hg diff tools/data_source/upload.py
diff -r c3cef260df88 tools/data_source/upload.py
--- a/tools/data_source/upload.pyFri May 15 15:20:17 2015 -0400
+++ b/tools/data_source/upload.pyFri Mar 04 11:12:51 2016 +
@@ -5,6 +5,10 @@
 # to be reflected in galaxy.web.controllers.tool_runner and galaxy.tools

 import urllib, sys, os, gzip, tempfile, shutil, re, gzip, zipfile,
codecs, binascii
+
+# Peter hack 2016/03/04 due to unexplained import failure...
+sys.path.insert(1, "/mnt/galaxy/galaxy-dist/lib")
+
 from galaxy import eggs
 # need to import model before sniff to resolve a circular import dependency
 import galaxy.model


However, this is only treating the symptoms rather than the as yet
unexplained root cause of the problem.

Peter

On Thu, Sep 5, 2013 at 8:22 PM, Hakeem Almabrazi  wrote:
> Hi,
>
>
>
> I started getting the following error whenever I try to load a file into
> Galaxy local.
>
> Traceback (most recent call last):
>
>   File "/usr/local/galaxy/galaxy-dist/tools/data_source/upload.py", line 8,
> in 
>
> from galaxy import eggs
>
> ImportError: cannot import name eggs
>
>
>
>
>
> I will appreciate if someone can tell me what could happen to cause such
> issue and how to resolve it.
>
>
>
> Regards,
>
>
>
>
>
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