Re: [galaxy-dev] apache on ubuntu

[Raymond Wan]

Hi Jochen,

I presume you looked at this already:

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

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

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

Ray



On Fri, Sep 2, 2016 at 5:53 AM, Jochen Bick  wrote:
> Hi,
>
> I'm having trouble setting up the apache to redirect my local running galaxy
> which runs on localhost:8080
> I would like that people could have access inside the lab knowing my local
> ip address. I read plenty of tutorials, can anyone help setting it up on
> Ubuntu? The files I have to modify are located at:
> /etc/apache2/sites-available/
> 000-default.conf and default-ssl.config ?
>
> apache is up and running.
>
> Cheers Jochen
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[galaxy-dev] Problem with conda on galaxy 16.07

[Léo Biscassi]

Hi folks,
Today after perform some tests with conda on galaxy 16.07 the follow
message was returned in my terminal:

"*Conda dependency seemingly installed but failed to build job environment.*
"

The error occurs when *build_isolated_environment()* function is call.
Below some variable values:

*is_installed* = *True*
*job_directory* = */home/leobiscassi/programs/galaxy/job_work_dir/000/17*
*env_path* =
*/home/leobiscassi/programs/galaxy/job_work_dir/000/17/conda-env*
*exit_code* = *127*

Analyzing inside of the *build_isolated_environment()*, the
*exec_create() *function
is executed because *path* variable (
*/home/leobiscassi/programs/galaxy/job_work_dir/000/17/conda-env*) don't
exists, the command executed by *exec_create* is showed below:

*deps/_conda/bin/conda create -y --unknown --offline --prefix
/home/leobiscassi/programs/galaxy/job_work_dir/000/17/conda-env --file
./database/tmp/jobdepsIGslWfe2bd2345d2ec1bb4aeb81211183570bae7db28a3bea4f7ff9e8e75074719a7ee/__mgltools@1.5.6
> /dev/null*

Some important values:

*env* = *{'HOME': 'deps/_conda', 'CONDARC':
'/home/leobiscassi/programs/galaxy/deps/_condarc'}*

The command return is '*/bin/sh: 1: deps/_conda/bin/conda: not found*', but
the binary exist. Anyone can help me with this?

Thanks in advance.
-- 
Best regards,
*Léo Biscassi*
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[galaxy-dev] apache on ubuntu

[Jochen Bick]

Hi,

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

/etc/apache2/sites-available/
000-default.conf and default-ssl.config ?

apache is up and running.

Cheers Jochen
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Re: [galaxy-dev] Introducing Conda as a new standard for Galaxy tool dependencies

[Léo Biscassi]

Hi Bjorn,
I read the documentation about conda shared early in this email and I have
one more question:

If I already a conda installation on computer and don't wish share this
installation to control galaxy dependencies, galaxy works fine with your
own conda auto installation or I have pay attention in more some detail?

On Mon, Aug 29, 2016 at 5:37 AM Peter Cock 
wrote:

> That's great Bjoern,
>
> I was thinking we should mention this on the wiki (with a link
> to the documentation rather than duplicating it). There are
> some existing pages about the tool_dependencies.xml
> system - but no obvious top level introduction that I saw?
>
> https://wiki.galaxyproject.org/ToolDependencyRecipes
> https://wiki.galaxyproject.org/ToolShed/PackageRecipes
> https://wiki.galaxyproject.org/ToolDependenciesTagSets
> https://wiki.galaxyproject.org/ToolsWithDependenciesInSeparateRepositories
>
> Where on the wiki do people think would be best?
>
> Peter
>
> On Sun, Aug 28, 2016 at 9:41 PM, Léo Biscassi 
> wrote:
> > Nice job! I was really anxious for some documentation about this theme!
> > Thanks all involved!
> >
> > On Fri, Aug 26, 2016 at 3:38 PM Björn Grüning  >
> > wrote:
> >>
> >> Hi all,
> >>
> >> Galaxy 16.07 was just released:
> >> https://docs.galaxyproject.org/en/master/releases/16.07_announce.html
> >> and the IUC has some news to share with you.
> >>
> >> For a more readable version please see:
> >> https://docs.galaxyproject.org/en/master/admin/conda_faq.html
> >>
> >> 
> >>
> >> Galaxy tools (also called wrappers) traditionally use Tool Shed package
> >> recipes to install their dependencies. At the tool’s installation time
> >> the recipe is downloaded and executed in order to provide the underlying
> >> software executables. Introduction of these Galaxy-specific recipes was
> >> a necessary step at the time, however nowadays there are other more
> >> mature and stable options to install software in a similar manner. The
> >> Galaxy community has taken steps to improve the tool dependency system
> >> in order to enable new features and expand its reach. This document aims
> >> to describe these and answer the FAQ.
> >>
> >> It is a pleasure to announce the adoption of a new standard for tool
> >> dependencies in Galaxy which has been integrated over the last six
> >> months: Conda packages!
> >> Not only do Conda packages make tool dependencies more reliable and
> >> stable, they are also easier to test and faster to develop than the
> >> traditional Tool Shed package recipes .
> >>
> >> Conda is a package manager like apt-get, yum, pip, brew or guix. We
> >> don’t want to argue about the relative merits of various package
> >> managers here, in fact Galaxy supports multiple package managers and we
> >> welcome community contributions (such as implementing a Guix package
> >> manager or enhancing the existing brew support to bring it on par with
> >> Conda).
> >>
> >> As a community, we have decided that Conda is the one that best fulfills
> >> our needs. The following are some of the crucial Conda features that led
> >> to this decision:
> >>
> >> * Installation of packages does not require root privileges
> >> (Installation at any location  the Galaxy user has write access to)
> >> * Multiple versions of software can be installed in parallel
> >> * HPC-ready
> >> * Faster and more robust package installations through pre-compiled
> >> packages (no build environment complications)
> >> * Independent of programming language (R, Perl, Python, Julia, Java,
> >> pre-compiled binaries, and more)
> >> * Easy to write recipes (1 YAML description file + 1 Bash install
> script)
> >> * An active, large and growing community (with more and more software
> >> authors managing their own recipes)
> >> * Extensive documentation: Conda documentation
> >> (http://conda.pydata.org/docs/building/build.html) and Conda
> quick-start
> >> (http://conda.pydata.org/docs/get-started.html)
> >>
> >> Below we answer some common questions (collected by Lance Parsons):
> >>
> >> 1. How do I enable Conda dependency resolution for existing Galaxy
> >> installations?
> >> ---
> >>
> >> Most Galaxy administrators have not set up a dependency resolvers
> >> configuration file (dependency_resolvers_conf.xml) which means they are
> >> using Galaxy’s default (dependency_resolvers_conf.xml.sample). Galaxy
> >> has enabled Conda dependency resolution by default since release 16.04
> >> (if Conda was installed already), so many existing installations can use
> >> Conda dependencies. Having Conda enabled in
> >> dependency_resolvers_conf.xml means that Galaxy will look for
> >> dependencies using the Conda system when it attempts to run tools. If
> >> conda_auto_install is True, and a dependency is not found, Galaxy will
> >> attempt to install it using the configured Conda channels. A graphical

[galaxy-dev] bug in fastqmcf

[Jochen Bick]

Hi

they migrated the code of e-utils to github. Download path is corrupted:

https://expressionanalysis.github.io/ea-utils/

Cheers Jochen
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Re: [galaxy-dev] error on startup

[Martin Čech]

Cris: maybe check what ports are configured for your Galaxy and/or Tool
Shed to make sure they are not in conflict. I don't know enough about AWS
to help you more, maybe someone else will jump in.

M.

On Thu, Sep 1, 2016 at 1:48 PM Cristel Thomas 
wrote:

> No previous instance of reports running, and I'm not sure what to check as
> far as ports.
> our AWS guy said it might be an issue with AWS but I don't know enough
> about all this to confirm (or to know how to confirm).
>
> thanks for your help.
>
> On Thu, Sep 1, 2016 at 1:39 PM, Martin Čech  wrote:
>
>> Cris: please check whether some previous instance of Reports isn't still
>> running and/or check your ports using e.g. `netstat`
>> M.
>>
>> On Thu, Sep 1, 2016 at 1:19 PM Cristel Thomas 
>> wrote:
>>
>>> Hi Martin,
>>> the config is:
>>> port = 8081
>>> host = 0.0.0.0
>>>
>>> this is the first time we have that issue though, and the instance has
>>> been running just fine until now. I don't think we've changed anything.
>>>
>>> On Thu, Sep 1, 2016 at 12:40 PM, Martin Čech  wrote:
>>>
 Hi Cris,

 what `host` and `port` is in your reports.ini config file? This
 stacktrace would point at something already running at the same port.

 Martin

 On Thu, Sep 1, 2016 at 12:36 PM Cristel Thomas <
 cristel.tho...@gmail.com> wrote:

> Galaxy admins,
> One of you has probably seen the below error before, can someone
> explain? for background, we're running our instance on a AWS server (if
> that makes a difference)
>
>
> galaxy.web.framework.base DEBUG 2016-05-19 12:43:40,545 Enabling
> 'sample_tracking' controller, class: SampleTracking
> galaxy.web.framework.base DEBUG 2016-05-19 12:43:40,545 Enabling
> 'system' controller, class: System
> galaxy.web.framework.base DEBUG 2016-05-19 12:43:40,546 Enabling
> 'workflows' controller, class: Workflows
> galaxy.web.framework.base DEBUG 2016-05-19 12:43:40,546 Enabling
> 'users' controller, class: Users
> galaxy.web.framework.base DEBUG 2016-05-19 12:43:40,547 Enabling
> 'jobs' controller, class: Jobs
> galaxy.web.framework.base DEBUG 2016-05-19 12:43:40,547 Enabling
> 'root' controller, class: Report
> galaxy.web.framework.base DEBUG 2016-05-19 12:43:40,547 Enabling
> 'home' controller, class: HomePage
> galaxy.webapps.reports.buildapp DEBUG 2016-05-19 12:43:40,548 Enabling
> 'httpexceptions' middleware
> galaxy.webapps.reports.buildapp DEBUG 2016-05-19 12:43:40,549 Enabling
> 'recursive' middleware
> galaxy.webapps.reports.buildapp DEBUG 2016-05-19 12:43:40,551 Enabling
> 'error' middleware
> galaxy.webapps.reports.buildapp DEBUG 2016-05-19 12:43:40,551 Enabling
> 'trans logger' middleware
> galaxy.webapps.reports.buildapp DEBUG 2016-05-19 12:43:40,552 Enabling
> 'x-forwarded-host' middleware
> Starting server in PID 14676.
> Traceback (most recent call last):
>   File "./scripts/paster.py", line 26, in 
> serve.run()
>   File
> "/home/galaxy/immport-galaxy/lib/galaxy/util/pastescript/serve.py", line
> 1061, in run
> invoke(command, command_name, options, args[1:])
>   File
> "/home/galaxy/immport-galaxy/lib/galaxy/util/pastescript/serve.py", line
> 1067, in invoke
> exit_code = runner.run(args)
>   File
> "/home/galaxy/immport-galaxy/lib/galaxy/util/pastescript/serve.py", line
> 223, in run
> result = self.command()
>   File
> "/home/galaxy/immport-galaxy/lib/galaxy/util/pastescript/serve.py", line
> 673, in command
> serve()
>   File
> "/home/galaxy/immport-galaxy/lib/galaxy/util/pastescript/serve.py", line
> 650, in serve
> server(app)
>   File
> "/home/galaxy/immport-galaxy/lib/galaxy/util/pastescript/loadwsgi.py", 
> line
> 234, in server_wrapper
> **context.local_conf)
>   File
> "/home/galaxy/immport-galaxy/lib/galaxy/util/pastescript/loadwsgi.py", 
> line
> 94, in fix_call
> val = callable(*args, **kw)
>   File
> "/home/galaxy/immport-galaxy/.venv/local/lib/python2.7/site-packages/paste/httpserver.py",
> line 1361, in server_runner
> serve(wsgi_app, **kwargs)
>   File
> "/home/galaxy/immport-galaxy/.venv/local/lib/python2.7/site-packages/paste/httpserver.py",
> line 1310, in serve
> request_queue_size=request_queue_size)
>   File
> "/home/galaxy/immport-galaxy/.venv/local/lib/python2.7/site-packages/paste/httpserver.py",
> line 1153, in __init__
> request_queue_size=request_queue_size)
>   File
> "/home/galaxy/immport-galaxy/.venv/local/lib/python2.7/site-packages/paste/httpserver.py",
> line 1132, in __init__
> request_queue_size=request_queue_size)
>   File
> 

Re: [galaxy-dev] error on startup

[Cristel Thomas]

No previous instance of reports running, and I'm not sure what to check as
far as ports.
our AWS guy said it might be an issue with AWS but I don't know enough
about all this to confirm (or to know how to confirm).

thanks for your help.

On Thu, Sep 1, 2016 at 1:39 PM, Martin Čech  wrote:

> Cris: please check whether some previous instance of Reports isn't still
> running and/or check your ports using e.g. `netstat`
> M.
>
> On Thu, Sep 1, 2016 at 1:19 PM Cristel Thomas 
> wrote:
>
>> Hi Martin,
>> the config is:
>> port = 8081
>> host = 0.0.0.0
>>
>> this is the first time we have that issue though, and the instance has
>> been running just fine until now. I don't think we've changed anything.
>>
>> On Thu, Sep 1, 2016 at 12:40 PM, Martin Čech  wrote:
>>
>>> Hi Cris,
>>>
>>> what `host` and `port` is in your reports.ini config file? This
>>> stacktrace would point at something already running at the same port.
>>>
>>> Martin
>>>
>>> On Thu, Sep 1, 2016 at 12:36 PM Cristel Thomas 
>>> wrote:
>>>
 Galaxy admins,
 One of you has probably seen the below error before, can someone
 explain? for background, we're running our instance on a AWS server (if
 that makes a difference)


 galaxy.web.framework.base DEBUG 2016-05-19 12:43:40,545 Enabling
 'sample_tracking' controller, class: SampleTracking
 galaxy.web.framework.base DEBUG 2016-05-19 12:43:40,545 Enabling
 'system' controller, class: System
 galaxy.web.framework.base DEBUG 2016-05-19 12:43:40,546 Enabling
 'workflows' controller, class: Workflows
 galaxy.web.framework.base DEBUG 2016-05-19 12:43:40,546 Enabling
 'users' controller, class: Users
 galaxy.web.framework.base DEBUG 2016-05-19 12:43:40,547 Enabling 'jobs'
 controller, class: Jobs
 galaxy.web.framework.base DEBUG 2016-05-19 12:43:40,547 Enabling 'root'
 controller, class: Report
 galaxy.web.framework.base DEBUG 2016-05-19 12:43:40,547 Enabling 'home'
 controller, class: HomePage
 galaxy.webapps.reports.buildapp DEBUG 2016-05-19 12:43:40,548 Enabling
 'httpexceptions' middleware
 galaxy.webapps.reports.buildapp DEBUG 2016-05-19 12:43:40,549 Enabling
 'recursive' middleware
 galaxy.webapps.reports.buildapp DEBUG 2016-05-19 12:43:40,551 Enabling
 'error' middleware
 galaxy.webapps.reports.buildapp DEBUG 2016-05-19 12:43:40,551 Enabling
 'trans logger' middleware
 galaxy.webapps.reports.buildapp DEBUG 2016-05-19 12:43:40,552 Enabling
 'x-forwarded-host' middleware
 Starting server in PID 14676.
 Traceback (most recent call last):
   File "./scripts/paster.py", line 26, in 
 serve.run()
   File "/home/galaxy/immport-galaxy/lib/galaxy/util/pastescript/serve.py",
 line 1061, in run
 invoke(command, command_name, options, args[1:])
   File "/home/galaxy/immport-galaxy/lib/galaxy/util/pastescript/serve.py",
 line 1067, in invoke
 exit_code = runner.run(args)
   File "/home/galaxy/immport-galaxy/lib/galaxy/util/pastescript/serve.py",
 line 223, in run
 result = self.command()
   File "/home/galaxy/immport-galaxy/lib/galaxy/util/pastescript/serve.py",
 line 673, in command
 serve()
   File "/home/galaxy/immport-galaxy/lib/galaxy/util/pastescript/serve.py",
 line 650, in serve
 server(app)
   File 
 "/home/galaxy/immport-galaxy/lib/galaxy/util/pastescript/loadwsgi.py",
 line 234, in server_wrapper
 **context.local_conf)
   File 
 "/home/galaxy/immport-galaxy/lib/galaxy/util/pastescript/loadwsgi.py",
 line 94, in fix_call
 val = callable(*args, **kw)
   File 
 "/home/galaxy/immport-galaxy/.venv/local/lib/python2.7/site-packages/paste/httpserver.py",
 line 1361, in server_runner
 serve(wsgi_app, **kwargs)
   File 
 "/home/galaxy/immport-galaxy/.venv/local/lib/python2.7/site-packages/paste/httpserver.py",
 line 1310, in serve
 request_queue_size=request_queue_size)
   File 
 "/home/galaxy/immport-galaxy/.venv/local/lib/python2.7/site-packages/paste/httpserver.py",
 line 1153, in __init__
 request_queue_size=request_queue_size)
   File 
 "/home/galaxy/immport-galaxy/.venv/local/lib/python2.7/site-packages/paste/httpserver.py",
 line 1132, in __init__
 request_queue_size=request_queue_size)
   File 
 "/home/galaxy/immport-galaxy/.venv/local/lib/python2.7/site-packages/paste/httpserver.py",
 line 345, in __init__
 HTTPServer.__init__(self, server_address, RequestHandlerClass)
   File "/usr/lib/python2.7/SocketServer.py", line 419, in __init__
 self.server_bind()
   File "/usr/lib/python2.7/BaseHTTPServer.py", line 108, in server_bind
 SocketServer.TCPServer.server_bind(self)
   File "/usr/lib/python2.7/SocketServer.py", line 430, in 

Re: [galaxy-dev] error on startup

[Martin Čech]

Cris: please check whether some previous instance of Reports isn't still
running and/or check your ports using e.g. `netstat`
M.

On Thu, Sep 1, 2016 at 1:19 PM Cristel Thomas 
wrote:

> Hi Martin,
> the config is:
> port = 8081
> host = 0.0.0.0
>
> this is the first time we have that issue though, and the instance has
> been running just fine until now. I don't think we've changed anything.
>
> On Thu, Sep 1, 2016 at 12:40 PM, Martin Čech  wrote:
>
>> Hi Cris,
>>
>> what `host` and `port` is in your reports.ini config file? This
>> stacktrace would point at something already running at the same port.
>>
>> Martin
>>
>> On Thu, Sep 1, 2016 at 12:36 PM Cristel Thomas 
>> wrote:
>>
>>> Galaxy admins,
>>> One of you has probably seen the below error before, can someone
>>> explain? for background, we're running our instance on a AWS server (if
>>> that makes a difference)
>>>
>>>
>>> galaxy.web.framework.base DEBUG 2016-05-19 12:43:40,545 Enabling
>>> 'sample_tracking' controller, class: SampleTracking
>>> galaxy.web.framework.base DEBUG 2016-05-19 12:43:40,545 Enabling
>>> 'system' controller, class: System
>>> galaxy.web.framework.base DEBUG 2016-05-19 12:43:40,546 Enabling
>>> 'workflows' controller, class: Workflows
>>> galaxy.web.framework.base DEBUG 2016-05-19 12:43:40,546 Enabling 'users'
>>> controller, class: Users
>>> galaxy.web.framework.base DEBUG 2016-05-19 12:43:40,547 Enabling 'jobs'
>>> controller, class: Jobs
>>> galaxy.web.framework.base DEBUG 2016-05-19 12:43:40,547 Enabling 'root'
>>> controller, class: Report
>>> galaxy.web.framework.base DEBUG 2016-05-19 12:43:40,547 Enabling 'home'
>>> controller, class: HomePage
>>> galaxy.webapps.reports.buildapp DEBUG 2016-05-19 12:43:40,548 Enabling
>>> 'httpexceptions' middleware
>>> galaxy.webapps.reports.buildapp DEBUG 2016-05-19 12:43:40,549 Enabling
>>> 'recursive' middleware
>>> galaxy.webapps.reports.buildapp DEBUG 2016-05-19 12:43:40,551 Enabling
>>> 'error' middleware
>>> galaxy.webapps.reports.buildapp DEBUG 2016-05-19 12:43:40,551 Enabling
>>> 'trans logger' middleware
>>> galaxy.webapps.reports.buildapp DEBUG 2016-05-19 12:43:40,552 Enabling
>>> 'x-forwarded-host' middleware
>>> Starting server in PID 14676.
>>> Traceback (most recent call last):
>>>   File "./scripts/paster.py", line 26, in 
>>> serve.run()
>>>   File
>>> "/home/galaxy/immport-galaxy/lib/galaxy/util/pastescript/serve.py", line
>>> 1061, in run
>>> invoke(command, command_name, options, args[1:])
>>>   File
>>> "/home/galaxy/immport-galaxy/lib/galaxy/util/pastescript/serve.py", line
>>> 1067, in invoke
>>> exit_code = runner.run(args)
>>>   File
>>> "/home/galaxy/immport-galaxy/lib/galaxy/util/pastescript/serve.py", line
>>> 223, in run
>>> result = self.command()
>>>   File
>>> "/home/galaxy/immport-galaxy/lib/galaxy/util/pastescript/serve.py", line
>>> 673, in command
>>> serve()
>>>   File
>>> "/home/galaxy/immport-galaxy/lib/galaxy/util/pastescript/serve.py", line
>>> 650, in serve
>>> server(app)
>>>   File
>>> "/home/galaxy/immport-galaxy/lib/galaxy/util/pastescript/loadwsgi.py", line
>>> 234, in server_wrapper
>>> **context.local_conf)
>>>   File
>>> "/home/galaxy/immport-galaxy/lib/galaxy/util/pastescript/loadwsgi.py", line
>>> 94, in fix_call
>>> val = callable(*args, **kw)
>>>   File
>>> "/home/galaxy/immport-galaxy/.venv/local/lib/python2.7/site-packages/paste/httpserver.py",
>>> line 1361, in server_runner
>>> serve(wsgi_app, **kwargs)
>>>   File
>>> "/home/galaxy/immport-galaxy/.venv/local/lib/python2.7/site-packages/paste/httpserver.py",
>>> line 1310, in serve
>>> request_queue_size=request_queue_size)
>>>   File
>>> "/home/galaxy/immport-galaxy/.venv/local/lib/python2.7/site-packages/paste/httpserver.py",
>>> line 1153, in __init__
>>> request_queue_size=request_queue_size)
>>>   File
>>> "/home/galaxy/immport-galaxy/.venv/local/lib/python2.7/site-packages/paste/httpserver.py",
>>> line 1132, in __init__
>>> request_queue_size=request_queue_size)
>>>   File
>>> "/home/galaxy/immport-galaxy/.venv/local/lib/python2.7/site-packages/paste/httpserver.py",
>>> line 345, in __init__
>>> HTTPServer.__init__(self, server_address, RequestHandlerClass)
>>>   File "/usr/lib/python2.7/SocketServer.py", line 419, in __init__
>>> self.server_bind()
>>>   File "/usr/lib/python2.7/BaseHTTPServer.py", line 108, in server_bind
>>> SocketServer.TCPServer.server_bind(self)
>>>   File "/usr/lib/python2.7/SocketServer.py", line 430, in server_bind
>>> self.socket.bind(self.server_address)
>>>   File "/usr/lib/python2.7/socket.py", line 224, in meth
>>> return getattr(self._sock,name)(*args)
>>> socket.error: [Errno 99] Cannot assign requested address
>>> Removing PID file reports_webapp.pid
>>>
>>>
>>> Thanks,
>>> Cris
>>> ___
>>> Please keep all replies on the list by using "reply 

Re: [galaxy-dev] error on startup

[Cristel Thomas]

Hi Martin,
the config is:
port = 8081
host = 0.0.0.0

this is the first time we have that issue though, and the instance has been
running just fine until now. I don't think we've changed anything.

On Thu, Sep 1, 2016 at 12:40 PM, Martin Čech  wrote:

> Hi Cris,
>
> what `host` and `port` is in your reports.ini config file? This stacktrace
> would point at something already running at the same port.
>
> Martin
>
> On Thu, Sep 1, 2016 at 12:36 PM Cristel Thomas 
> wrote:
>
>> Galaxy admins,
>> One of you has probably seen the below error before, can someone explain?
>> for background, we're running our instance on a AWS server (if that makes a
>> difference)
>>
>>
>> galaxy.web.framework.base DEBUG 2016-05-19 12:43:40,545 Enabling
>> 'sample_tracking' controller, class: SampleTracking
>> galaxy.web.framework.base DEBUG 2016-05-19 12:43:40,545 Enabling 'system'
>> controller, class: System
>> galaxy.web.framework.base DEBUG 2016-05-19 12:43:40,546 Enabling
>> 'workflows' controller, class: Workflows
>> galaxy.web.framework.base DEBUG 2016-05-19 12:43:40,546 Enabling 'users'
>> controller, class: Users
>> galaxy.web.framework.base DEBUG 2016-05-19 12:43:40,547 Enabling 'jobs'
>> controller, class: Jobs
>> galaxy.web.framework.base DEBUG 2016-05-19 12:43:40,547 Enabling 'root'
>> controller, class: Report
>> galaxy.web.framework.base DEBUG 2016-05-19 12:43:40,547 Enabling 'home'
>> controller, class: HomePage
>> galaxy.webapps.reports.buildapp DEBUG 2016-05-19 12:43:40,548 Enabling
>> 'httpexceptions' middleware
>> galaxy.webapps.reports.buildapp DEBUG 2016-05-19 12:43:40,549 Enabling
>> 'recursive' middleware
>> galaxy.webapps.reports.buildapp DEBUG 2016-05-19 12:43:40,551 Enabling
>> 'error' middleware
>> galaxy.webapps.reports.buildapp DEBUG 2016-05-19 12:43:40,551 Enabling
>> 'trans logger' middleware
>> galaxy.webapps.reports.buildapp DEBUG 2016-05-19 12:43:40,552 Enabling
>> 'x-forwarded-host' middleware
>> Starting server in PID 14676.
>> Traceback (most recent call last):
>>   File "./scripts/paster.py", line 26, in 
>> serve.run()
>>   File "/home/galaxy/immport-galaxy/lib/galaxy/util/pastescript/serve.py",
>> line 1061, in run
>> invoke(command, command_name, options, args[1:])
>>   File "/home/galaxy/immport-galaxy/lib/galaxy/util/pastescript/serve.py",
>> line 1067, in invoke
>> exit_code = runner.run(args)
>>   File "/home/galaxy/immport-galaxy/lib/galaxy/util/pastescript/serve.py",
>> line 223, in run
>> result = self.command()
>>   File "/home/galaxy/immport-galaxy/lib/galaxy/util/pastescript/serve.py",
>> line 673, in command
>> serve()
>>   File "/home/galaxy/immport-galaxy/lib/galaxy/util/pastescript/serve.py",
>> line 650, in serve
>> server(app)
>>   File "/home/galaxy/immport-galaxy/lib/galaxy/util/pastescript/loadwsgi.py",
>> line 234, in server_wrapper
>> **context.local_conf)
>>   File "/home/galaxy/immport-galaxy/lib/galaxy/util/pastescript/loadwsgi.py",
>> line 94, in fix_call
>> val = callable(*args, **kw)
>>   File 
>> "/home/galaxy/immport-galaxy/.venv/local/lib/python2.7/site-packages/paste/httpserver.py",
>> line 1361, in server_runner
>> serve(wsgi_app, **kwargs)
>>   File 
>> "/home/galaxy/immport-galaxy/.venv/local/lib/python2.7/site-packages/paste/httpserver.py",
>> line 1310, in serve
>> request_queue_size=request_queue_size)
>>   File 
>> "/home/galaxy/immport-galaxy/.venv/local/lib/python2.7/site-packages/paste/httpserver.py",
>> line 1153, in __init__
>> request_queue_size=request_queue_size)
>>   File 
>> "/home/galaxy/immport-galaxy/.venv/local/lib/python2.7/site-packages/paste/httpserver.py",
>> line 1132, in __init__
>> request_queue_size=request_queue_size)
>>   File 
>> "/home/galaxy/immport-galaxy/.venv/local/lib/python2.7/site-packages/paste/httpserver.py",
>> line 345, in __init__
>> HTTPServer.__init__(self, server_address, RequestHandlerClass)
>>   File "/usr/lib/python2.7/SocketServer.py", line 419, in __init__
>> self.server_bind()
>>   File "/usr/lib/python2.7/BaseHTTPServer.py", line 108, in server_bind
>> SocketServer.TCPServer.server_bind(self)
>>   File "/usr/lib/python2.7/SocketServer.py", line 430, in server_bind
>> self.socket.bind(self.server_address)
>>   File "/usr/lib/python2.7/socket.py", line 224, in meth
>> return getattr(self._sock,name)(*args)
>> socket.error: [Errno 99] Cannot assign requested address
>> Removing PID file reports_webapp.pid
>>
>>
>> Thanks,
>> Cris
>> ___
>> 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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>>   http://galaxyproject.org/search/mailinglists/
>
>
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Please keep all 

Re: [galaxy-dev] error on startup

[Martin Čech]

Hi Cris,

what `host` and `port` is in your reports.ini config file? This stacktrace
would point at something already running at the same port.

Martin

On Thu, Sep 1, 2016 at 12:36 PM Cristel Thomas 
wrote:

> Galaxy admins,
> One of you has probably seen the below error before, can someone explain?
> for background, we're running our instance on a AWS server (if that makes a
> difference)
>
>
> galaxy.web.framework.base DEBUG 2016-05-19 12:43:40,545 Enabling
> 'sample_tracking' controller, class: SampleTracking
> galaxy.web.framework.base DEBUG 2016-05-19 12:43:40,545 Enabling 'system'
> controller, class: System
> galaxy.web.framework.base DEBUG 2016-05-19 12:43:40,546 Enabling
> 'workflows' controller, class: Workflows
> galaxy.web.framework.base DEBUG 2016-05-19 12:43:40,546 Enabling 'users'
> controller, class: Users
> galaxy.web.framework.base DEBUG 2016-05-19 12:43:40,547 Enabling 'jobs'
> controller, class: Jobs
> galaxy.web.framework.base DEBUG 2016-05-19 12:43:40,547 Enabling 'root'
> controller, class: Report
> galaxy.web.framework.base DEBUG 2016-05-19 12:43:40,547 Enabling 'home'
> controller, class: HomePage
> galaxy.webapps.reports.buildapp DEBUG 2016-05-19 12:43:40,548 Enabling
> 'httpexceptions' middleware
> galaxy.webapps.reports.buildapp DEBUG 2016-05-19 12:43:40,549 Enabling
> 'recursive' middleware
> galaxy.webapps.reports.buildapp DEBUG 2016-05-19 12:43:40,551 Enabling
> 'error' middleware
> galaxy.webapps.reports.buildapp DEBUG 2016-05-19 12:43:40,551 Enabling
> 'trans logger' middleware
> galaxy.webapps.reports.buildapp DEBUG 2016-05-19 12:43:40,552 Enabling
> 'x-forwarded-host' middleware
> Starting server in PID 14676.
> Traceback (most recent call last):
>   File "./scripts/paster.py", line 26, in 
> serve.run()
>   File "/home/galaxy/immport-galaxy/lib/galaxy/util/pastescript/serve.py",
> line 1061, in run
> invoke(command, command_name, options, args[1:])
>   File "/home/galaxy/immport-galaxy/lib/galaxy/util/pastescript/serve.py",
> line 1067, in invoke
> exit_code = runner.run(args)
>   File "/home/galaxy/immport-galaxy/lib/galaxy/util/pastescript/serve.py",
> line 223, in run
> result = self.command()
>   File "/home/galaxy/immport-galaxy/lib/galaxy/util/pastescript/serve.py",
> line 673, in command
> serve()
>   File "/home/galaxy/immport-galaxy/lib/galaxy/util/pastescript/serve.py",
> line 650, in serve
> server(app)
>   File
> "/home/galaxy/immport-galaxy/lib/galaxy/util/pastescript/loadwsgi.py", line
> 234, in server_wrapper
> **context.local_conf)
>   File
> "/home/galaxy/immport-galaxy/lib/galaxy/util/pastescript/loadwsgi.py", line
> 94, in fix_call
> val = callable(*args, **kw)
>   File
> "/home/galaxy/immport-galaxy/.venv/local/lib/python2.7/site-packages/paste/httpserver.py",
> line 1361, in server_runner
> serve(wsgi_app, **kwargs)
>   File
> "/home/galaxy/immport-galaxy/.venv/local/lib/python2.7/site-packages/paste/httpserver.py",
> line 1310, in serve
> request_queue_size=request_queue_size)
>   File
> "/home/galaxy/immport-galaxy/.venv/local/lib/python2.7/site-packages/paste/httpserver.py",
> line 1153, in __init__
> request_queue_size=request_queue_size)
>   File
> "/home/galaxy/immport-galaxy/.venv/local/lib/python2.7/site-packages/paste/httpserver.py",
> line 1132, in __init__
> request_queue_size=request_queue_size)
>   File
> "/home/galaxy/immport-galaxy/.venv/local/lib/python2.7/site-packages/paste/httpserver.py",
> line 345, in __init__
> HTTPServer.__init__(self, server_address, RequestHandlerClass)
>   File "/usr/lib/python2.7/SocketServer.py", line 419, in __init__
> self.server_bind()
>   File "/usr/lib/python2.7/BaseHTTPServer.py", line 108, in server_bind
> SocketServer.TCPServer.server_bind(self)
>   File "/usr/lib/python2.7/SocketServer.py", line 430, in server_bind
> self.socket.bind(self.server_address)
>   File "/usr/lib/python2.7/socket.py", line 224, in meth
> return getattr(self._sock,name)(*args)
> socket.error: [Errno 99] Cannot assign requested address
> Removing PID file reports_webapp.pid
>
>
> Thanks,
> Cris
> ___
> 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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[galaxy-dev] error on startup

[Cristel Thomas]

Galaxy admins,
One of you has probably seen the below error before, can someone explain?
for background, we're running our instance on a AWS server (if that makes a
difference)


galaxy.web.framework.base DEBUG 2016-05-19 12:43:40,545 Enabling
'sample_tracking' controller, class: SampleTracking
galaxy.web.framework.base DEBUG 2016-05-19 12:43:40,545 Enabling 'system'
controller, class: System
galaxy.web.framework.base DEBUG 2016-05-19 12:43:40,546 Enabling
'workflows' controller, class: Workflows
galaxy.web.framework.base DEBUG 2016-05-19 12:43:40,546 Enabling 'users'
controller, class: Users
galaxy.web.framework.base DEBUG 2016-05-19 12:43:40,547 Enabling 'jobs'
controller, class: Jobs
galaxy.web.framework.base DEBUG 2016-05-19 12:43:40,547 Enabling 'root'
controller, class: Report
galaxy.web.framework.base DEBUG 2016-05-19 12:43:40,547 Enabling 'home'
controller, class: HomePage
galaxy.webapps.reports.buildapp DEBUG 2016-05-19 12:43:40,548 Enabling
'httpexceptions' middleware
galaxy.webapps.reports.buildapp DEBUG 2016-05-19 12:43:40,549 Enabling
'recursive' middleware
galaxy.webapps.reports.buildapp DEBUG 2016-05-19 12:43:40,551 Enabling
'error' middleware
galaxy.webapps.reports.buildapp DEBUG 2016-05-19 12:43:40,551 Enabling
'trans logger' middleware
galaxy.webapps.reports.buildapp DEBUG 2016-05-19 12:43:40,552 Enabling
'x-forwarded-host' middleware
Starting server in PID 14676.
Traceback (most recent call last):
  File "./scripts/paster.py", line 26, in 
serve.run()
  File "/home/galaxy/immport-galaxy/lib/galaxy/util/pastescript/serve.py",
line 1061, in run
invoke(command, command_name, options, args[1:])
  File "/home/galaxy/immport-galaxy/lib/galaxy/util/pastescript/serve.py",
line 1067, in invoke
exit_code = runner.run(args)
  File "/home/galaxy/immport-galaxy/lib/galaxy/util/pastescript/serve.py",
line 223, in run
result = self.command()
  File "/home/galaxy/immport-galaxy/lib/galaxy/util/pastescript/serve.py",
line 673, in command
serve()
  File "/home/galaxy/immport-galaxy/lib/galaxy/util/pastescript/serve.py",
line 650, in serve
server(app)
  File
"/home/galaxy/immport-galaxy/lib/galaxy/util/pastescript/loadwsgi.py", line
234, in server_wrapper
**context.local_conf)
  File
"/home/galaxy/immport-galaxy/lib/galaxy/util/pastescript/loadwsgi.py", line
94, in fix_call
val = callable(*args, **kw)
  File
"/home/galaxy/immport-galaxy/.venv/local/lib/python2.7/site-packages/paste/httpserver.py",
line 1361, in server_runner
serve(wsgi_app, **kwargs)
  File
"/home/galaxy/immport-galaxy/.venv/local/lib/python2.7/site-packages/paste/httpserver.py",
line 1310, in serve
request_queue_size=request_queue_size)
  File
"/home/galaxy/immport-galaxy/.venv/local/lib/python2.7/site-packages/paste/httpserver.py",
line 1153, in __init__
request_queue_size=request_queue_size)
  File
"/home/galaxy/immport-galaxy/.venv/local/lib/python2.7/site-packages/paste/httpserver.py",
line 1132, in __init__
request_queue_size=request_queue_size)
  File
"/home/galaxy/immport-galaxy/.venv/local/lib/python2.7/site-packages/paste/httpserver.py",
line 345, in __init__
HTTPServer.__init__(self, server_address, RequestHandlerClass)
  File "/usr/lib/python2.7/SocketServer.py", line 419, in __init__
self.server_bind()
  File "/usr/lib/python2.7/BaseHTTPServer.py", line 108, in server_bind
SocketServer.TCPServer.server_bind(self)
  File "/usr/lib/python2.7/SocketServer.py", line 430, in server_bind
self.socket.bind(self.server_address)
  File "/usr/lib/python2.7/socket.py", line 224, in meth
return getattr(self._sock,name)(*args)
socket.error: [Errno 99] Cannot assign requested address
Removing PID file reports_webapp.pid


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

[Peter Cock]

Ah - I understand what you mean now. Using the code tag is
discouraged, but you may find some of these examples useful
for what you are trying to do:

https://github.com/galaxyproject/galaxy/issues/2714

I hope that helps,

Peter



On Thu, Sep 1, 2016 at 2:37 PM, Katherine Beaulieu
 wrote:
>
>
> On Thu, Sep 1, 2016 at 9:36 AM, Katherine Beaulieu
>  wrote:
>>
>> Hi Peter,
>> The code file tag is generally used in populating select lists. So
>> basically you have a function from a code file that is loaded before runtime
>> of the tool and you can dynamically load content based on that function and
>> you can pass it parameters from your tool but I'm wondering how you would
>> pass it the contents of a repeat parameter.
>> This is how the code file tag works:
>> https://wiki.galaxyproject.org/Admin/Tools/Custom%20Code
>> Thanks,
>> Katherine
>>
>> On Thu, Sep 1, 2016 at 8:23 AM, Peter Cock 
>> wrote:
>>>
>>> I'm not quite sure what you mean by a "code file", but if you
>>> mean using the  tag, here's an example:
>>>
>>>
>>> https://github.com/peterjc/galaxy_mira/blob/master/tools/mira4_0/mira4_de_novo.xml
>>>
>>> I am using a Cheetah syntax for loop to access each entry
>>> in a repeat parameter.
>>>
>>> Peter
>>>
>>> On Thu, Sep 1, 2016 at 12:58 PM, Katherine Beaulieu
>>>  wrote:
>>> > Hello Galaxy Community,
>>> > I was wondering if anyone had ever come across a situation where they
>>> > have
>>> > had to pass the contents of a repeat parameter to a code file in a
>>> > Galaxy
>>> > tool config? Is there any way to do this?
>>> > Katherine
>>> >
>>> > ___
>>> > 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
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Re: [galaxy-dev] Send repeat parameter to code file for multiple select list

[Katherine Beaulieu]

On Thu, Sep 1, 2016 at 9:36 AM, Katherine Beaulieu <
katherine.beaulieu...@gmail.com> wrote:

> Hi Peter,
> The code file tag is generally used in populating select lists. So
> basically you have a function from a code file that is loaded before
> runtime of the tool and you can dynamically load content based on that
> function and you can pass it parameters from your tool but I'm wondering
> how you would pass it the contents of a repeat parameter.
> This is how the code file tag works:
> https://wiki.galaxyproject.org/Admin/Tools/Custom%20Code
> Thanks,
> Katherine
>
> On Thu, Sep 1, 2016 at 8:23 AM, Peter Cock 
> wrote:
>
>> I'm not quite sure what you mean by a "code file", but if you
>> mean using the  tag, here's an example:
>>
>> https://github.com/peterjc/galaxy_mira/blob/master/tools/mir
>> a4_0/mira4_de_novo.xml
>>
>> I am using a Cheetah syntax for loop to access each entry
>> in a repeat parameter.
>>
>> Peter
>>
>> On Thu, Sep 1, 2016 at 12:58 PM, Katherine Beaulieu
>>  wrote:
>> > Hello Galaxy Community,
>> > I was wondering if anyone had ever come across a situation where they
>> have
>> > had to pass the contents of a repeat parameter to a code file in a
>> Galaxy
>> > tool config? Is there any way to do this?
>> > Katherine
>> >
>> > ___
>> > 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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Re: [galaxy-dev] Send repeat parameter to code file for multiple select list

[Peter Cock]

I'm not quite sure what you mean by a "code file", but if you
mean using the  tag, here's an example:

https://github.com/peterjc/galaxy_mira/blob/master/tools/mira4_0/mira4_de_novo.xml

I am using a Cheetah syntax for loop to access each entry
in a repeat parameter.

Peter

On Thu, Sep 1, 2016 at 12:58 PM, Katherine Beaulieu
 wrote:
> Hello Galaxy Community,
> I was wondering if anyone had ever come across a situation where they have
> had to pass the contents of a repeat parameter to a code file in a Galaxy
> tool config? Is there any way to do this?
> Katherine
>
> ___
> 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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>
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[galaxy-dev] Send repeat parameter to code file for multiple select list

[Katherine Beaulieu]

Hello Galaxy Community,
I was wondering if anyone had ever come across a situation where they have
had to pass the contents of a repeat parameter to a code file in a Galaxy
tool config? Is there any way to do this?
Katherine
___
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Re: [galaxy-dev] Conda: confused dependencies with multiple R versions and rpy

[Marius van den Beek]

Hi Steve,

The scatterplot tool is relatively old and has not had its dependencies
updated to be conda compatible.
https://github.com/galaxyproject/tools-devteam/blob/master/tools/scatterplot/scatterplot.xml

The relevant lines are these:

  
numpy
rpy
   wrote:

> Hi,
>   trying to get my tools going, part 29.  I have a Docker image with the
> latest Galaxy release, patched to fix the Conda install bug I found
> earlier, my tools are installed ok and I’ve added a few from the toolshed
> for good measure.
>
> One of my tools requires R 3.0.2 which is installed ok.   I also installed
> scatterplot from the toolshed which requires R 2.11; that is also installed
> ok by conda. However, I get this message when trying to run scatterplot:
>
> Traceback (most recent call last):
>   File 
> "/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/scatterplot/d243056b22ed/scatterplot/scatterplot.py",
>  line 5, in 
> from rpy import *
>   File 
> "/tool_deps/rpy/1.0.3/devteam/package_rpy_1_0_3/82170c94ca7c/lib/python/rpy.py",
>  line 134, in 
> """ % RVERSION)
> RuntimeError: No module named _rpy3002
>
>   RPy module can not be imported. Please check if your rpy
>   installation supports R 3.0.2. If you have multiple R versions
>   installed, you may need to set RHOME before importing rpy. For
>   example:
>
>   >>> from rpy_options import set_options
>   >>> set_options(RHOME='c:/progra~1/r/rw2011/')
>   >>> from rpy import *
>
>
> So it seems that rpy is installed and is aware of one version of R but not
> the other, and the other is being found (perhaps because it’s the default
> install in the Docker image?)
>
> FYI my docker image recipe is here:
>
> https://github.com/Alveo/docker-galaxy-alveo
>
> and the image itself is here:
>
> https://hub.docker.com/r/stevecassidy/alveo-galaxy/
>
> Any pointers to the way forward appreciated.
>
> Thanks,
> Steve
> —
> Department of Computing, Macquarie University
> http://web.science.mq.edu.au/~cassidy
>
>
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Re: [galaxy-dev] Conda: confused dependencies with multiple R versions and rpy

[Marius van den Beek]

Forgot to paste the link:
https://github.com/galaxyproject/tools-devteam/issues/385

On 1 September 2016 at 11:08, Marius van den Beek 
wrote:

> Hi Steve,
>
> The scatterplot tool is relatively old and has not had its dependencies
> updated to be conda compatible.
> https://github.com/galaxyproject/tools-devteam/
> blob/master/tools/scatterplot/scatterplot.xml
>
> The relevant lines are these:
>
>   
> numpy
> rpy
>   
>
>
> So it would attempt to get the R version via the rpy package. So my guess
> is that there is no rpy(1)
> package in conda. We can try to update the tool to use rpy2 and hope that
> that'll just work,
> and if that doesn't work we can explicitly add a requirement on R (which
> we can get through conda).
> I've opened an issue here:
>
> Best,
> Marius
>
> On 1 September 2016 at 09:50, Steve Cassidy 
> wrote:
>
>> Hi,
>>   trying to get my tools going, part 29.  I have a Docker image with the
>> latest Galaxy release, patched to fix the Conda install bug I found
>> earlier, my tools are installed ok and I’ve added a few from the toolshed
>> for good measure.
>>
>> One of my tools requires R 3.0.2 which is installed ok.   I also
>> installed scatterplot from the toolshed which requires R 2.11; that is also
>> installed ok by conda. However, I get this message when trying to run
>> scatterplot:
>>
>> Traceback (most recent call last):
>>   File 
>> "/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/scatterplot/d243056b22ed/scatterplot/scatterplot.py",
>>  line 5, in 
>> from rpy import *
>>   File 
>> "/tool_deps/rpy/1.0.3/devteam/package_rpy_1_0_3/82170c94ca7c/lib/python/rpy.py",
>>  line 134, in 
>> """ % RVERSION)
>> RuntimeError: No module named _rpy3002
>>
>>   RPy module can not be imported. Please check if your rpy
>>   installation supports R 3.0.2. If you have multiple R versions
>>   installed, you may need to set RHOME before importing rpy. For
>>   example:
>>
>>   >>> from rpy_options import set_options
>>   >>> set_options(RHOME='c:/progra~1/r/rw2011/')
>>   >>> from rpy import *
>>
>>
>> So it seems that rpy is installed and is aware of one version of R but
>> not the other, and the other is being found (perhaps because it’s the
>> default install in the Docker image?)
>>
>> FYI my docker image recipe is here:
>>
>> https://github.com/Alveo/docker-galaxy-alveo
>>
>> and the image itself is here:
>>
>> https://hub.docker.com/r/stevecassidy/alveo-galaxy/
>>
>> Any pointers to the way forward appreciated.
>>
>> Thanks,
>> Steve
>> —
>> Department of Computing, Macquarie University
>> http://web.science.mq.edu.au/~cassidy
>>
>>
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>>
>
>
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[galaxy-dev] Conda: confused dependencies with multiple R versions and rpy

[Steve Cassidy]

Hi,
  trying to get my tools going, part 29.  I have a Docker image with the latest 
Galaxy release, patched to fix the Conda install bug I found earlier, my tools 
are installed ok and I’ve added a few from the toolshed for good measure.

One of my tools requires R 3.0.2 which is installed ok.   I also installed 
scatterplot from the toolshed which requires R 2.11; that is also installed ok 
by conda. However, I get this message when trying to run scatterplot:


Traceback (most recent call last):
  File 
"/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/scatterplot/d243056b22ed/scatterplot/scatterplot.py",
 line 5, in 
from rpy import *
  File 
"/tool_deps/rpy/1.0.3/devteam/package_rpy_1_0_3/82170c94ca7c/lib/python/rpy.py",
 line 134, in 
""" % RVERSION)
RuntimeError: No module named _rpy3002

  RPy module can not be imported. Please check if your rpy
  installation supports R 3.0.2. If you have multiple R versions
  installed, you may need to set RHOME before importing rpy. For
  example:

  >>> from rpy_options import set_options
  >>> set_options(RHOME='c:/progra~1/r/rw2011/')
  >>> from rpy import *


So it seems that rpy is installed and is aware of one version of R but not the 
other, and the other is being found (perhaps because it’s the default install 
in the Docker image?)

FYI my docker image recipe is here:

https://github.com/Alveo/docker-galaxy-alveo

and the image itself is here:

https://hub.docker.com/r/stevecassidy/alveo-galaxy/

Any pointers to the way forward appreciated.

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

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