date:20130930

The previous code doesn't work in the command line, but this yes:

file=file("output.txt","w")source("/home/ramao/Galaxy-ES/tools/my_tools/modeloCancroEuropeu.R")close(file)
Sweave("/home/ramao/Galaxy-ES/tools/my_tools/relatorio.Rnw")
pdf=file("relatorio.pdf","w")  ## I changed here
texi2dvi("/home/ramao/Galaxy-ES/tools/my_tools/relatorio.tex", pdf = TRUE, 
clean = TRUE) 
This code works in the command line, but I didn't use this because of 
"pdf=file("relatorio.pdf","w")", the problem is that if I use this code on 
Galaxy, it don't recognizes my pdf output. In fact, my code creates an pdf 
file, and my intention is override it with the last command, but to do this I 
need that the name declared in Galaxy be the same of the generated by the 
function, that is "relatorio.pdf". Do you understand me?
Thank you
> Subject: Re: [galaxy-dev] How can I get a txt output file from R
> From: bjoern.gruen...@pharmazie.uni-freiburg.de
> To: ramao_tiago_tibur...@hotmail.com
> CC: bjoern.gruen...@gmail.com; galaxy-...@bx.psu.edu
> Date: Mon, 30 Sep 2013 23:03:34 +0200
> 
> Hi,
> 
> > 
> > 
> > 
> > file=file("output.txt","w")
> > source("/home/ramao/Galaxy-ES/tools/my_tools/modeloCancroEuropeu.R")
> > close(file)
> > 
> > Sweave("/home/ramao/Galaxy-ES/tools/my_tools/relatorio.Rnw")
> >  ##generate the relatorio.tex file based on the output.txt file
> > 
> > pdf=file("${relatorio}","w")  ##I used this to declare an file to
> > output
> > 
> > texi2dvi("/home/ramao/Galaxy-ES/tools/my_tools/relatorio.tex", pdf =
> > TRUE, clean = TRUE)   ##generate the relatorio.pdf file
> > 
> > close(pdf)
> 
> 
> I can't see any obvious error. Is the R code correct if you test it on
> commandline? Also please use a $tmp file path and clean up afterwards. I
> can imagine, that output.txt is not found by Sweave.
> 
> > 
> > ...
> > 
> > 
> > 
> > 
> > 
> > Now I want to write the txt file (output.txt) to a pdf file using
> > Latex (Sweave), so the function "Sweave" generate the file
> > "relatorio.tex" e this is used by the function "texi2dvi" to generate
> > the pdf file, but it is generate with the name "relatorio.pdf" and I
> > don't know what to do, because with the code above I get an empty pdf
> > file. What can I do?
> > 
> > 
> > Thank you
> > 
> > > Subject: Re: [galaxy-dev] How can I get a txt output file from R
> > > From: bjoern.gruen...@gmail.com
> > > To: ramao_tiago_tibur...@hotmail.com
> > > CC: galaxy-...@bx.psu.edu
> > > Date: Mon, 30 Sep 2013 20:01:41 +0200
> > > 
> > > Am Montag, den 30.09.2013, 20:32 +0300 schrieb Ramon Tiburski:
> > > > Thank you, you solved my problem. Maybe you can help with one more
> > > > thing, Can I interact in the middle of an workflow execution ? For
> > > > example: I have a workflow with ten steps and after I started
> > this, I
> > > > want to select options always before each step (like a software
> > > > instalation). Is it possible? Thank you one more time.
> > > 
> > > I don't think that is possible. Is that still a workflow?
> > > 
> > > Ciao,
> > > Bjoern
> > > 
> > > > > Subject: Re: [galaxy-dev] How can I get a txt output file from R
> > > > > From: bjoern.gruen...@gmail.com
> > > > > To: ramao_tiago_tibur...@hotmail.com
> > > > > CC: galaxy-...@bx.psu.edu
> > > > > Date: Mon, 30 Sep 2013 19:18:55 +0200
> > > > > 
> > > > > Hi Ramon,
> > > > > 
> > > > > 
> > > > > > Code:
> > > > > >
> > 
> > > > > > 
> > > > > > ...
> > > > > > r_wrapper.sh
> > $script_file
> > > > > > 
> > > > > > ...
> > > > > > 
> > > > > > 
> > > > > > 
> > > > > > 
> > > > > > ...
> > > > > > 
> > > > > > file=file("output.txt","w")
> > > > > 
> > > > > Do not hardcode a filepath here, you need to reference the
> > template
> > > > > variable from your output section (name="output").
> > > > > 
> > > > > For example:
> > > > > file=file("${output}","w")
> > > > > 
> > > > > >
> > > >
> > source("/home/ramao/Galaxy-ES/tools/my_tools/modeloCancroEuropeu.R")
> > > > > > close(file)
> > > > > > 
> > > > > > 
> > > > > > ...
> > > > > > 
> > > > > > 
> > > > > > 
> > > > > > 
> > > > > > 
> > > > > 
> > > > > and here change that to:
> > > > > 
> > > > > 
> > > > > 
> > > > > Cheers,
> > > > > Bjoern
> > > > > > 
> > > > > > ...
> > > > > > 
> > > > > >
> > 
> > > > > > 
> > > > > > 
> > > > > > I'm having the output "empty" and I need that the result be
> > > > generated
> > > > > > in a text file. What can I do?
> > > > > > 
> > > > > > 
> > > > > > Thank you
> > > > > > ___
> > > > > > 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/se

Re: [galaxy-dev] Test Toolshed Biopython package dependency Atlas fails to install (Was: Re: UnboundLocalError: local variable 'prior_installation_required' referenced before assignment)

2013-09-30 Thread John Chilton

On Sun, Sep 29, 2013 at 10:43 PM, Guest, Simon
 wrote:
> At Fri, 27 Sep 2013 00:23:37 -0500,
> John Chilton wrote:
>>
>> Simon,
>>
>> What is the advantage of putting that XML definition in the tool shed?
>> It is not 100% true because of prior_install_required dependencies,
>> but for the most part sourcing/load the environment for tools is a
>> Galaxy problem, not so much a tool shed one. What if we did this
>> instead?
>>
>> Add an option to Galaxy's universe_wsgi.ini with the following default:
>>
>> tool_dependency_resolution_order = gx_package_manual, gx_package_toolshed
>>
>> Which essentially implements my idea above, with James' additional
>> configuration. But which can be overridden as:
>>
>> tool_dependency_resolution_order = plugin_module, gx_package_manual,
>> gx_package_toolshed
>>
>> If set this way then placing > package="0.5.9">bwa in a tool will result in the module
>> bwa/0.5.9 being loaded if it is 'avail'able, else it will check for a
>> manually installed env.sh (which is where MSI is currently putting its
>> module loads), and else it will fallback to source the tool shed
>> installed dependency.
>>
>> I feel like this will give you everything you want without any extra
>> XML or configuration. Let me know if I am wrong.
>
> Hi John,
>
> I think you're right.  Your scheme is neater than what I was
> proposing.  The extra flexibility I was aiming at via some toolshed
> XML stuff appears not to be necessary upon further reflection.  (I
> wanted to ensure a Galaxy admin could just install some RPMs, install
> a toolshed tool, and have everything resolve nicely.  You seem to have
> achieved that with your scheme.)
>
> I haven't had a chance to try your code yet, but as soon as I can I
> will do so, and get back to you.
>
> If I leave out gx_package_toolshed altogether from
> tool_dependency_resolution_order, will the tool installation in Galaxy
> simply fail with a nice error message if the environment module and/or
> env.sh files are not found?  (This is what I would like, as it would
> serve as a prompt to the Galaxy admin to install some extra RPMs or
> whatever.)


First tool_dependency_resolution_order is not how I landed up
implementing it. Each "resolver" may need parameters so I decided to
do an XML configuration kind of like Nate's job_conf.xml stuff. So to
leave the tool shed stuff off you can just add
dependency_resolvers_conf.xml to your Galaxy root.


  
  
  


You can also just leave galaxy_packages off if you are not using any
manually installed env.sh files.

The first modules resolver will try to match each tag like this:

  R

with a module load like:

  R/3.0.1

if that exact module is available. The second versionless form of the
tag will result in Galaxy just falling back to auto-load whatever the
default R module is if the exact version specified (3.0.1) is not
available.

This code doesn't touch the tool shed at all, so if you check to
install dependencies, they will still be installed and if you don't
they will not be installed. This configuration just tells the Galaxy
how to use the dependencies that happen to be installed. You will need
to review installed tools and make sure you have matching modules.
Additionally, some tools may use this set_environment requirement
type, I am not sure how to implement this or how prevalent its use is.

-John

>
> Will this also work for those toolshed packages which bundle their
> package definitions (to download, make and install the tool
> dependency) along with their wrappers?

Can you opt not to install packages for such repositories? Either way,
the answer is I guess the same as above, the tool shed is unchanged,
its just how Galaxy utilizes the installed dependencies that is being
modified here.

>
> Thanks for working on this.
>
> cheers,
> Simon
>
> ===
> Attention: The information contained in this message and/or attachments
> from AgResearch Limited is intended only for the persons or entities
> to which it is addressed and may contain confidential and/or privileged
> material. Any review, retransmission, dissemination or other use of, or
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Re: [galaxy-dev] How can I get a txt output file from R

2013-09-30 Thread Björn Grüning

Hi,

> 
> 
> 
> file=file("output.txt","w")
> source("/home/ramao/Galaxy-ES/tools/my_tools/modeloCancroEuropeu.R")
> close(file)
> 
> Sweave("/home/ramao/Galaxy-ES/tools/my_tools/relatorio.Rnw")
>  ##generate the relatorio.tex file based on the output.txt file
> 
> pdf=file("${relatorio}","w")  ##I used this to declare an file to
> output
> 
> texi2dvi("/home/ramao/Galaxy-ES/tools/my_tools/relatorio.tex", pdf =
> TRUE, clean = TRUE)   ##generate the relatorio.pdf file
> 
> close(pdf)


I can't see any obvious error. Is the R code correct if you test it on
commandline? Also please use a $tmp file path and clean up afterwards. I
can imagine, that output.txt is not found by Sweave.

> 
> ...
> 
> 
> 
> 
> 
> Now I want to write the txt file (output.txt) to a pdf file using
> Latex (Sweave), so the function "Sweave" generate the file
> "relatorio.tex" e this is used by the function "texi2dvi" to generate
> the pdf file, but it is generate with the name "relatorio.pdf" and I
> don't know what to do, because with the code above I get an empty pdf
> file. What can I do?
> 
> 
> Thank you
> 
> > Subject: Re: [galaxy-dev] How can I get a txt output file from R
> > From: bjoern.gruen...@gmail.com
> > To: ramao_tiago_tibur...@hotmail.com
> > CC: galaxy-...@bx.psu.edu
> > Date: Mon, 30 Sep 2013 20:01:41 +0200
> > 
> > Am Montag, den 30.09.2013, 20:32 +0300 schrieb Ramon Tiburski:
> > > Thank you, you solved my problem. Maybe you can help with one more
> > > thing, Can I interact in the middle of an workflow execution ? For
> > > example: I have a workflow with ten steps and after I started
> this, I
> > > want to select options always before each step (like a software
> > > instalation). Is it possible? Thank you one more time.
> > 
> > I don't think that is possible. Is that still a workflow?
> > 
> > Ciao,
> > Bjoern
> > 
> > > > Subject: Re: [galaxy-dev] How can I get a txt output file from R
> > > > From: bjoern.gruen...@gmail.com
> > > > To: ramao_tiago_tibur...@hotmail.com
> > > > CC: galaxy-...@bx.psu.edu
> > > > Date: Mon, 30 Sep 2013 19:18:55 +0200
> > > > 
> > > > Hi Ramon,
> > > > 
> > > > 
> > > > > Code:
> > > > >
> 
> > > > > 
> > > > > ...
> > > > > r_wrapper.sh
> $script_file
> > > > > 
> > > > > ...
> > > > > 
> > > > > 
> > > > > 
> > > > > 
> > > > > ...
> > > > > 
> > > > > file=file("output.txt","w")
> > > > 
> > > > Do not hardcode a filepath here, you need to reference the
> template
> > > > variable from your output section (name="output").
> > > > 
> > > > For example:
> > > > file=file("${output}","w")
> > > > 
> > > > >
> > >
> source("/home/ramao/Galaxy-ES/tools/my_tools/modeloCancroEuropeu.R")
> > > > > close(file)
> > > > > 
> > > > > 
> > > > > ...
> > > > > 
> > > > > 
> > > > > 
> > > > > 
> > > > > 
> > > > 
> > > > and here change that to:
> > > > 
> > > > 
> > > > 
> > > > Cheers,
> > > > Bjoern
> > > > > 
> > > > > ...
> > > > > 
> > > > >
> 
> > > > > 
> > > > > 
> > > > > I'm having the output "empty" and I need that the result be
> > > generated
> > > > > in a text file. What can I do?
> > > > > 
> > > > > 
> > > > > Thank you
> > > > > ___
> > > > > 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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Re: [galaxy-dev] How can I get a txt output file from R

Hi, I need one more help. The code that I cite before now is this:
...
file=file("output.txt","w")source("/home/ramao/Galaxy-ES/tools/my_tools/modeloCancroEuropeu.R")close(file)Sweave("/home/ramao/Galaxy-ES/tools/my_tools/relatorio.Rnw")
  ##generate the relatorio.tex file based on the output.txt 
filepdf=file("${relatorio}","w")  ##I used this to declare an file to 
outputtexi2dvi("/home/ramao/Galaxy-ES/tools/my_tools/relatorio.tex", pdf = 
TRUE, clean = TRUE)   ##generate the relatorio.pdf fileclose(pdf)
...





Now I want to write the txt file (output.txt) to a pdf file using Latex 
(Sweave), so the function "Sweave" generate the file "relatorio.tex" e this is 
used by the function "texi2dvi" to generate the pdf file, but it is generate 
with the name "relatorio.pdf" and I don't know what to do, because with the 
code above I get an empty pdf file. What can I do?
Thank you

> Subject: Re: [galaxy-dev] How can I get a txt output file from R
> From: bjoern.gruen...@gmail.com
> To: ramao_tiago_tibur...@hotmail.com
> CC: galaxy-...@bx.psu.edu
> Date: Mon, 30 Sep 2013 20:01:41 +0200
> 
> Am Montag, den 30.09.2013, 20:32 +0300 schrieb Ramon Tiburski:
> > Thank you, you solved my problem. Maybe you can help with one more
> > thing, Can I interact in the middle of an workflow execution ? For
> > example: I have a workflow with ten steps and after I started this, I
> > want to select options always before each step (like a software
> > instalation). Is it possible? Thank you one more time.
> 
> I don't think that is possible. Is that still a workflow?
> 
> Ciao,
> Bjoern
> 
> > > Subject: Re: [galaxy-dev] How can I get a txt output file from R
> > > From: bjoern.gruen...@gmail.com
> > > To: ramao_tiago_tibur...@hotmail.com
> > > CC: galaxy-...@bx.psu.edu
> > > Date: Mon, 30 Sep 2013 19:18:55 +0200
> > > 
> > > Hi Ramon,
> > > 
> > > 
> > > > Code:
> > > > 
> > > > 
> > > > ...
> > > > r_wrapper.sh $script_file
> > > > 
> > > > ...
> > > > 
> > > > 
> > > > 
> > > > 
> > > > ...
> > > > 
> > > > file=file("output.txt","w")
> > > 
> > > Do not hardcode a filepath here, you need to reference the template
> > > variable from your output section (name="output").
> > > 
> > > For example:
> > > file=file("${output}","w")
> > > 
> > > >
> > source("/home/ramao/Galaxy-ES/tools/my_tools/modeloCancroEuropeu.R")
> > > > close(file)
> > > > 
> > > > 
> > > > ...
> > > > 
> > > > 
> > > > 
> > > > 
> > > > 
> > > 
> > > and here change that to:
> > > 
> > > 
> > > 
> > > Cheers,
> > > Bjoern
> > > > 
> > > > ...
> > > > 
> > > > 
> > > > 
> > > > 
> > > > I'm having the output "empty" and I need that the result be
> > generated
> > > > in a text file. What can I do?
> > > > 
> > > > 
> > > > Thank you
> > > > ___
> > > > 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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Re: [galaxy-dev] Dynamic data library

2013-09-30 Thread Martin Čech

Hi Nathan,

Dannon answered similar question few days ago:

There's an import mechanism in libraries that'll allow you to simply link
> to the file on disk without copy/upload.  I believe the
> "example_watch_folder.py" sample script (in the distribution) does just
> this via the API, if you want an example.


This might be what you are looking for.

Martin


On Mon, Sep 30, 2013 at 2:43 PM, Cole, Nathan (NIH/NCI) [C] <
nathan.c...@nih.gov> wrote:

>  Hello, we’ve set up a local Galaxy instance in our genotyping and
> next-gen sequencing lab with local Apache LDAP (AD) integration, NFS mounts
> to a large NAS, and cluster integration coming.  Do to the high volume of
> samples and staff that will be using the system, I want to set up data
> libraries (without copying to Galaxy).  This is obviously no problem the
> first time, however I was wondering if there was a way to make a library,
> added from a system path, be dynamic so that it would stay synchronized
> with the underlying file structure?
>
> ** **
>
> If a try dynamic library is not possible, is there a method for adding
> files to an existing library via that same system path that would not
> duplicate all of the original files in the data library?
>
> ** **
>
> I did some scouring of the list and found some old unanswered questions
> and some things tangentially related topics, but I was unable to find a
> true answer or solution to my problem.  Any information on how to do the
> tasks above or other solutions to provide the same functionality would be
> greatly appreciated.
>
> ** **
>
> Thanks,
>
> Nathan
>
> ** **
>
> ___
> 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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[galaxy-dev] Dynamic data library

2013-09-30 Thread Cole, Nathan (NIH/NCI) [C]

Hello, we've set up a local Galaxy instance in our genotyping and next-gen 
sequencing lab with local Apache LDAP (AD) integration, NFS mounts to a large 
NAS, and cluster integration coming.  Do to the high volume of samples and 
staff that will be using the system, I want to set up data libraries (without 
copying to Galaxy).  This is obviously no problem the first time, however I was 
wondering if there was a way to make a library, added from a system path, be 
dynamic so that it would stay synchronized with the underlying file structure?

If a try dynamic library is not possible, is there a method for adding files to 
an existing library via that same system path that would not duplicate all of 
the original files in the data library?

I did some scouring of the list and found some old unanswered questions and 
some things tangentially related topics, but I was unable to find a true answer 
or solution to my problem.  Any information on how to do the tasks above or 
other solutions to provide the same functionality would be greatly appreciated.

Thanks,
Nathan

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Re: [galaxy-dev] How can I get a txt output file from R

Surely not, but I had some doubts about this. No more. Thank you

> Subject: Re: [galaxy-dev] How can I get a txt output file from R
> From: bjoern.gruen...@gmail.com
> To: ramao_tiago_tibur...@hotmail.com
> CC: galaxy-...@bx.psu.edu
> Date: Mon, 30 Sep 2013 20:01:41 +0200
> 
> Am Montag, den 30.09.2013, 20:32 +0300 schrieb Ramon Tiburski:
> > Thank you, you solved my problem. Maybe you can help with one more
> > thing, Can I interact in the middle of an workflow execution ? For
> > example: I have a workflow with ten steps and after I started this, I
> > want to select options always before each step (like a software
> > instalation). Is it possible? Thank you one more time.
> 
> I don't think that is possible. Is that still a workflow?
> 
> Ciao,
> Bjoern
> 
> > > Subject: Re: [galaxy-dev] How can I get a txt output file from R
> > > From: bjoern.gruen...@gmail.com
> > > To: ramao_tiago_tibur...@hotmail.com
> > > CC: galaxy-...@bx.psu.edu
> > > Date: Mon, 30 Sep 2013 19:18:55 +0200
> > > 
> > > Hi Ramon,
> > > 
> > > 
> > > > Code:
> > > > 
> > > > 
> > > > ...
> > > > r_wrapper.sh $script_file
> > > > 
> > > > ...
> > > > 
> > > > 
> > > > 
> > > > 
> > > > ...
> > > > 
> > > > file=file("output.txt","w")
> > > 
> > > Do not hardcode a filepath here, you need to reference the template
> > > variable from your output section (name="output").
> > > 
> > > For example:
> > > file=file("${output}","w")
> > > 
> > > >
> > source("/home/ramao/Galaxy-ES/tools/my_tools/modeloCancroEuropeu.R")
> > > > close(file)
> > > > 
> > > > 
> > > > ...
> > > > 
> > > > 
> > > > 
> > > > 
> > > > 
> > > 
> > > and here change that to:
> > > 
> > > 
> > > 
> > > Cheers,
> > > Bjoern
> > > > 
> > > > ...
> > > > 
> > > > 
> > > > 
> > > > 
> > > > I'm having the output "empty" and I need that the result be
> > generated
> > > > in a text file. What can I do?
> > > > 
> > > > 
> > > > Thank you
> > > > ___
> > > > 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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Re: [galaxy-dev] How can I get a txt output file from R

Am Montag, den 30.09.2013, 20:32 +0300 schrieb Ramon Tiburski:
> Thank you, you solved my problem. Maybe you can help with one more
> thing, Can I interact in the middle of an workflow execution ? For
> example: I have a workflow with ten steps and after I started this, I
> want to select options always before each step (like a software
> instalation). Is it possible? Thank you one more time.

I don't think that is possible. Is that still a workflow?

Ciao,
Bjoern

> > Subject: Re: [galaxy-dev] How can I get a txt output file from R
> > From: bjoern.gruen...@gmail.com
> > To: ramao_tiago_tibur...@hotmail.com
> > CC: galaxy-...@bx.psu.edu
> > Date: Mon, 30 Sep 2013 19:18:55 +0200
> > 
> > Hi Ramon,
> > 
> > 
> > > Code:
> > > 
> > > 
> > > ...
> > > r_wrapper.sh $script_file
> > > 
> > > ...
> > > 
> > > 
> > > 
> > > 
> > > ...
> > > 
> > > file=file("output.txt","w")
> > 
> > Do not hardcode a filepath here, you need to reference the template
> > variable from your output section (name="output").
> > 
> > For example:
> > file=file("${output}","w")
> > 
> > >
> source("/home/ramao/Galaxy-ES/tools/my_tools/modeloCancroEuropeu.R")
> > > close(file)
> > > 
> > > 
> > > ...
> > > 
> > > 
> > > 
> > > 
> > > 
> > 
> > and here change that to:
> > 
> > 
> > 
> > Cheers,
> > Bjoern
> > > 
> > > ...
> > > 
> > > 
> > > 
> > > 
> > > I'm having the output "empty" and I need that the result be
> generated
> > > in a text file. What can I do?
> > > 
> > > 
> > > Thank you
> > > ___
> > > 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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[galaxy-dev] October Galaxy Update Newsletter is out

2013-09-30 Thread Dave Clements

Hello all,

The October 2013 Galaxy Update is
out
:

*Highlights:*

   -

   A record *six new public
servers
   *
   -

   44 new papers
   -

   Open 
Positions
at
   nine different organizations
   -

   Upcoming Events,
   lots of them in
Australia
plus 3 other
continents.

   -

   Online materials from past
events,
   including all GCC2013 videos on Vimeo 
and course
   materials for the 2013 UC Davis Bioinformatics Short
Course.
   The UC Davis course featured 5 great days of lecture and hands-on exercises.
   -

   More Tool Shed
contributions
than
   you can shake a stick at.

If you have anything you would like to see in the next *Galaxy
Update
*, please let us know.

Dave Clements and the Galaxy Team 
-- 
http://galaxyproject.org/
http://getgalaxy.org/
http://usegalaxy.org/
http://wiki.galaxyproject.org/
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[galaxy-dev] Problem with get data/uploading file.

2013-09-30 Thread Luobin Yang

Hi, guys,

Recently I found the Upload File tool under the Get Data category runs
forever on my locally installed Galaxy system. It worked fine for a long
time, but now it's not working anymore. Have you guys experienced similar
things?

Thanks,
Luobin
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Re: [galaxy-dev] How can I get a txt output file from R

Thank you, you solved my problem. Maybe you can help with one more thing, Can I 
interact in the middle of an workflow execution ? For example: I have a 
workflow with ten steps and after I started this, I want to select options 
always before each step (like a software instalation). Is it possible? Thank 
you one more time.

> Subject: Re: [galaxy-dev] How can I get a txt output file from R
> From: bjoern.gruen...@gmail.com
> To: ramao_tiago_tibur...@hotmail.com
> CC: galaxy-...@bx.psu.edu
> Date: Mon, 30 Sep 2013 19:18:55 +0200
> 
> Hi Ramon,
> 
> 
> > Code:
> > 
> > 
> > ...
> > r_wrapper.sh $script_file
> > 
> > ...
> > 
> > 
> > 
> > 
> > ...
> > 
> > file=file("output.txt","w")
> 
> Do not hardcode a filepath here, you need to reference the template
> variable from your output section (name="output").
> 
> For example:
> file=file("${output}","w")
> 
> > source("/home/ramao/Galaxy-ES/tools/my_tools/modeloCancroEuropeu.R")
> > close(file)
> > 
> > 
> > ...
> > 
> > 
> > 
> > 
> > 
> 
> and here change that to:
> 
> 
> 
> Cheers,
> Bjoern
> > 
> > ...
> > 
> > 
> > 
> > 
> > I'm having the output "empty" and I need that the result be generated
> > in a text file. What can I do?
> > 
> > 
> > Thank you
> > ___
> > 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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Re: [galaxy-dev] How can I get a txt output file from R

Hi Ramon,


> Code:
> 
> 
> ...
> r_wrapper.sh $script_file
> 
> ...
> 
> 
> 
> 
> ...
> 
> file=file("output.txt","w")

Do not hardcode a filepath here, you need to reference the template
variable from your output section (name="output").

For example:
file=file("${output}","w")

> source("/home/ramao/Galaxy-ES/tools/my_tools/modeloCancroEuropeu.R")
> close(file)
> 
> 
> ...
> 
> 
> 
> 
> 

and here change that to:



Cheers,
Bjoern
> 
> ...
> 
> 
> 
> 
> I'm having the output "empty" and I need that the result be generated
> in a text file. What can I do?
> 
> 
> Thank you
> ___
> 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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[galaxy-dev] How can I get a txt output file from R

Code:...r_wrapper.sh $script_file...




...

file=file("output.txt","w")
source("/home/ramao/Galaxy-ES/tools/my_tools/modeloCancroEuropeu.R")
close(file)

...





...

I'm having the output "empty" and I need that the result be generated in a text 
file. What can I do?
Thank you ___
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Re: [galaxy-dev] pbkdf2 encryption - disabling does not work

2013-09-30 Thread Martin Čech

Jan,

I just ran it on pure galaxy-dist (https://bitbucket.org/galaxy/galaxy-dist)
and it runs OK. I recommend you updating your Galaxy instance towards tip
of the galaxy-dist.

Martin


On Thu, Sep 26, 2013 at 3:54 PM, Jan Hapala  wrote:

> I could not find a "Galaxy version" in the application but speaking about
> hg, it is Aug 19 (10411:c42567f43aa7).
> Jan
>
>
> 2013/9/26 Martin Čech 
>
>> Jan,
>>
>> It works for me with the newest galaxy-central version. I registered new
>> user without a problem having the pbkdf2 turned off.
>>
>> What version are you using now?
>>
>> Martin
>>
>>
>> On Thu, Sep 26, 2013 at 4:02 AM, Jan Hapala  wrote:
>>
>>> Ahoj Martine,
>>>
>>> thanks for your response. That was a pretty stupid mistake, hard to
>>> notice even though I program in Python.
>>> However, this has not solved my problem, I get the same error. (I have
>>> also made sure that it is in the right section.)
>>>
>>> Jan
>>>
>>>
>>> 2013/9/25 Martin Čech 
>>>
 Ahoj Honzo,

 Python is case-sensitive. Use 'use_pbkdf2 = False' and make sure you
 put it under the '[app:main]' section in the config file.

 Enjoy Galaxy!

 best

 Martin Cech





 On Wed, Sep 25, 2013 at 9:15 AM, Jan Hapala  wrote:

> Hi,
>
> I need to run Galaxy with ProFTPd, therefore I need to disable the
> PBKDF2 encryption of the passwords (as stated here
> http://dev.list.galaxyproject.org/disable-PBKDF2-revert-to-SHA1-td4661274.html
> ).
>
> However, when I do add this line:
> use_pbkdf2 = false
> to the universe_wsgi.ini, restart Galaxy, submit the form for the
> password change (or register as a new user) I get an error "_hashlib.HASH
> object has no attribute __getitem__".
>
> I got the same result with a version as of Jul 2 and the most recent
> tag (10411:c42567f43aa7, Aug 19).
>
> I would be much grateful for your suggestions!
>
> Regards,
> Jan
>
>
> URL:
> http://127.0.0.1:8080/user/edit_info?cntrller=user&user_id=f2db41e1fa331b3e
> File
> '.../eggs/WebError-0.8a-py2.7.egg/weberror/evalexception/middleware.py',
> line 364 in respond
>   app_iter = self.application(environ, detect_start_response)
> File '.../eggs/Paste-1.7.5.1-py2.7.egg/paste/recursive.py', line 84 in
> __call__
>   return self.application(environ, start_response)
> File '.../eggs/Paste-1.7.5.1-py2.7.egg/paste/httpexceptions.py', line
> 633 in __call__
>   return self.application(environ, start_response)
> File '.../lib/galaxy/web/framework/base.py', line 132 in __call__
>   return self.handle_request( environ, start_response )
> File '.../lib/galaxy/web/framework/base.py', line 190 in handle_request
>   body = method( trans, **kwargs )
> File '.../lib/galaxy/webapps/galaxy/controllers/user.py', line 842 in
> edit_info
>   trans.sa_session.flush()
> File
> '.../eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/scoping.py',
> line 114 in do
> File
> '.../eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/session.py',
> line 1718 in flush
> File
> '.../eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/session.py',
> line 1789 in _flush
> File
> '.../eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/unitofwork.py',
> line 331 in execute
> File
> '.../eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/unitofwork.py',
> line 475 in execute
> File
> '.../eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/persistence.py',
> line 59 in save_obj
> File
> '.../eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/persistence.py',
> line 485 in _emit_update_statements
> File
> '.../eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py',
> line 1449 in execute
> File
> '.../eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py',
> line 1584 in _execute_clauseelement
> File
> '.../eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py',
> line 1651 in _execute_context
> File
> '.../eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py',
> line 1647 in _execute_context
> File
> '.../eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/default.py',
> line 475 in _init_compiled
> File
> '.../eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/types.py',
> line 626 in process
> File '.../lib/galaxy/model/custom_types.py', line 125 in
> process_bind_param
>   value = value[0:self.impl.length]
> StatementError: '_hashlib.HASH' object has no attribute '__getitem__'
> (original cause: TypeError: '_hashlib.HASH' object has no attribute
> '__getitem__') 'UPDATE galaxy_user SET update

Re: [galaxy-dev] Download URL not accepted in tool_dependencies.xml


Hi Joachim,

I had such problems if my XML file is invalid. Than I get immediately
the 'installed:' text and can click install again, without any change.
Also I would really recommend to reset your toolshed. These "white
ghosts" can have unpredictable effects.

If you can upload your tools to the test tool shed I can try to install it 
debug it.

Please make sure that you run the latest Galaxy central version. Greg and 
Dave invested a lot of time to get rid of "white ghosts". But these changes are
only in central.

Cheers,
Bjoern



> Still having a hard time and some strange situations. It is almost too 
> much to report via email.
> 
> Basically, the tool_dependencies.xml get recognised sometimes. Please, 
> watch this video to see what I mean (1'30''), and pause as you like:
> https://dl.dropboxusercontent.com/u/18352887/toolshedissues.ogv
> 
> I am afraid I cannot invest this amount of time to make my repo's 
> public-proof. There are weird things happening which make no sense to 
> me. And debugging of tool_dependencies.xml is very hard, since I find 
> almost no logs of this process.
> 
> 
> Joachim.
> 
> Joachim Jacob
> Contact details: http://www.bits.vib.be/index.php/about/80-team
> 
> 
> On 09/30/2013 02:53 PM, Dave Bouvier wrote:
> > Joachim,
> >
> > For sourceforge URLs, you can safely omit the question mark and 
> > everything after it, since that's part of the browser download load 
> > balancing process. When downloading with wget, curl, or python's 
> > urllib, downloads.sourceforge.net does its own behind-the-scenes load 
> > balancing. As for hyphens, I don't believe they need to be escaped, 
> > since they're not XML entities like the ampersand is. The following 
> > download_by_url action should work:
> >
> >  > type="download_by_url">http://downloads.sourceforge.net/project/transpose/transpose/transpose-2.0/2.0/transpose-2.0.zip
> >  
> >
> >
> >--Dave B.
> >
> > On 09/30/2013 08:45 AM, Joachim Jacob | VIB | wrote:
> >> Hi all,
> >>
> >>
> >> Not fixed yet. Somehow the download does not work: I have escaped the
> >> ampersands and the hyphens. The download seems to have to proceed, since
> >> I receive no error from the download step. The next step in the
> >> dependencies file gives an error: mv: cannot stat transpose.zip': No
> >> such file or directory
> >>
> >>
> >>
> >> Cheers,
> >> J
> >>
> >>
> >> Joachim Jacob
> >> Contact details: http://www.bits.vib.be/index.php/about/80-team
> >>
> >>
> >> On 09/30/2013 02:06 PM, Peter Cock wrote:
> >>> You must escape any ampersand in the XML as & and then it should
> >>> work.
> >>>
> >>> Peter
> >>>
> >>> On Mon, Sep 30, 2013 at 12:51 PM, Joachim Jacob | VIB |
> >>>  wrote:
>  Hi all,
> 
> 
>  The download URL seems not to be accepted in tool_dependencies.xml.
>  It is an
>  URL from sourceforge, the direct link to a package.
> 
>  The error upon uploading the tool to my toolshed:
>  **
>  Metadata may have been defined for some items in revision
>  '5665a799775d'.
>  Correct the following problems if necessary and reset metadata.
>  tool_dependencies.xml - Exception attempting to parse
>  /mnt/toolsheddb/database/000/repo_26/tool_dependencies.xml: not
>  well-formed
>  (invalid token): line 6, column 149
>  **
> 
>  The tool_dependencies.xml file:
>  **
>  1 
>  2 
>  3 
>  4
>  5 
>  6   type="download_by_url">http://downloads.sourceforge.net/project/transpose/transpose/transpose-2.0/2.0/transpose-2.0.zip?r=&ts=1380535239&use_mirror=surfnet
>   
> 
> 
>  7mkdir bin
>  8  unzip
>  transpose-2.0.zip
>   cd
>  transpose-2.0/src
>   gcc transpose.c -o
>  transpose
>   
>  $INSTALL_DIR/transpose-2.0/src/transpose
>  $INSTALL_DIR/bin
>   
>   chmod +x
>  $INSTALL_DIR/bin/transpose
>   
>     action="prepend_to">$INSTALL_DIR/bin
>   
>   
>   
>   
>   Compiling transpose and putting in the path.
>   
>  
>  
>  **
> 
> 
>  Cheers,
>  Joachim
> 
>  -- 
>  Joachim Jacob
>  Contact details: http://www.bits.vib.be/index.php/about/80-team
> 
> 
>  ___
>  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/
> >>>
> >>
> >> __

Re: [galaxy-dev] problems with toolshed package update process

2013-09-30 Thread Lukasse, Pieter

Hi Greg,

Yes, we have an older Mercurial installation (2.0.2 !) . We will try a newer 
version.

Thanks!

Pieter.

From: Greg Von Kuster [mailto:g...@bx.psu.edu]
Sent: vrijdag 13 september 2013 13:56
To: Lukasse, Pieter
Cc: Kuijt, Eric; 'galaxy-...@bx.psu.edu'
Subject: Re: problems with toolshed package update process

Hello Pieter,

The version of mercurial you are using is likely older than version 2.2.3.  See:

http://wiki.galaxyproject.org/ToolShedRepositoryFeatures#Pushing_changes_to_a_repository_using_hg_from_the_command_line

Can you check this?

Greg Von Kuster

On Sep 13, 2013, at 5:54 AM, "Lukasse, Pieter" 
mailto:pieter.luka...@wur.nl>> wrote:


Hi Greg,

We have been trying out the update process as follows:

1-Make changes to one of the files in the repository
2-Commit and push changes to hg

After these two steps we expected to be able to update the tool in Galaxy. 
However this was not possible. We noticed that every time we pushed a new 
revision to the toolshed hg we had to use the option "Reset all repository 
metadata", i.e. the new revision would be seen as an update only after doing 
this reset. Is this the normal behaviour? I can imagine that in some cases the 
admin would like to review a new committed changeset before enabling it as an 
update...could it be this is a configuration we forgot to change somewhere?

Best regards,

Pieter.



Pieter Lukasse
Wageningen UR, Plant Research International
Departments of Bioscience and Bioinformatics
Wageningen Campus, Building 107, Droevendaalsesteeg 1, 6708 PB,
Wageningen, the Netherlands
+31-317480891; skype: pieter.lukasse.wur
http://www.pri.wur.nl


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Re: [galaxy-dev] Download URL not accepted in tool_dependencies.xml

Still having a hard time and some strange situations. It is almost too
much to report via email.

Basically, the tool_dependencies.xml get recognised sometimes. Please,
watch this video to see what I mean (1'30''), and pause as you like:

https://dl.dropboxusercontent.com/u/18352887/toolshedissues.ogv

I am afraid I cannot invest this amount of time to make my repo's
public-proof. There are weird things happening which make no sense to
me. And debugging of tool_dependencies.xml is very hard, since I find
almost no logs of this process.

Joachim.

Joachim Jacob
Contact details: http://www.bits.vib.be/index.php/about/80-team

On 09/30/2013 02:53 PM, Dave Bouvier wrote:

Joachim,

For sourceforge URLs, you can safely omit the question mark and
everything after it, since that's part of the browser download load
balancing process. When downloading with wget, curl, or python's
urllib, downloads.sourceforge.net does its own behind-the-scenes load
balancing. As for hyphens, I don't believe they need to be escaped,
since they're not XML entities like the ampersand is. The following
download_by_url action should work:

type="download_by_url">http://downloads.sourceforge.net/project/transpose/transpose/transpose-2.0/2.0/transpose-2.0.zip

--Dave B.

On 09/30/2013 08:45 AM, Joachim Jacob | VIB | wrote:

Hi all,

Not fixed yet. Somehow the download does not work: I have escaped the
ampersands and the hyphens. The download seems to have to proceed, since
I receive no error from the download step. The next step in the
dependencies file gives an error: mv: cannot stat transpose.zip': No
such file or directory

Cheers,
J

Joachim Jacob
Contact details: http://www.bits.vib.be/index.php/about/80-team

On 09/30/2013 02:06 PM, Peter Cock wrote:

You must escape any ampersand in the XML as & and then it should
work.

Peter

On Mon, Sep 30, 2013 at 12:51 PM, Joachim Jacob | VIB |
wrote:

Hi all,

The download URL seems not to be accepted in tool_dependencies.xml.
It is an
URL from sourceforge, the direct link to a package.

The error upon uploading the tool to my toolshed:
**
Metadata may have been defined for some items in revision
'5665a799775d'.
Correct the following problems if necessary and reset metadata.
tool_dependencies.xml - Exception attempting to parse
/mnt/toolsheddb/database/000/repo_26/tool_dependencies.xml: not
well-formed
(invalid token): line 6, column 149
**

The tool_dependencies.xml file:
**
1
2
3
4
5
6 type="download_by_url">http://downloads.sourceforge.net/project/transpose/transpose/transpose-2.0/2.0/transpose-2.0.zip?r=&ts=1380535239&use_mirror=surfnet

7mkdir bin
8 unzip
transpose-2.0.zip
cd
transpose-2.0/src
gcc transpose.c -o
transpose

$INSTALL_DIR/transpose-2.0/src/transpose
$INSTALL_DIR/bin

chmod +x
$INSTALL_DIR/bin/transpose

$INSTALL_DIR/bin

Compiling transpose and putting in the path.

Cheers,
Joachim

--
Joachim Jacob
Contact details: http://www.bits.vib.be/index.php/about/80-team

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Re: [galaxy-dev] Test Toolshed Biopython package dependency & NumPy

Am Montag, den 30.09.2013, 14:02 +0100 schrieb Peter Cock:
> On Mon, Sep 30, 2013 at 1:58 PM, Dave Bouvier  wrote:
> > Peter,
> >
> > It looks like there may be a version conflict between package_numpy and
> > either a system numpy or the Galaxy numpy egg. I'll investigate and keep you
> > updated on my progress.
> >
> >--Dave B.
> 
> Thanks Dave,
> 
> If Tool authors can assume NumPy is already present via the Galaxy
> numpy egg and/or the system Python's numpy, that might be simpler...

The question is how to import the eggs into the tools? Is that possible
at all? For example pysam is shipped with Galaxy right? But is there a
way to use it inside of a tool?
But I think even if that is possible we need separate pysam/numpy
repositories for reproducibility.

Cheers,
Bjoern

> Peter
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Re: [galaxy-dev] Test Toolshed Biopython package dependency & NumPy

On Mon, Sep 30, 2013 at 1:58 PM, Dave Bouvier  wrote:
> Peter,
>
> It looks like there may be a version conflict between package_numpy and
> either a system numpy or the Galaxy numpy egg. I'll investigate and keep you
> updated on my progress.
>
>--Dave B.

Thanks Dave,

If Tool authors can assume NumPy is already present via the Galaxy
numpy egg and/or the system Python's numpy, that might be simpler...

Peter
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Re: [galaxy-dev] Messed up a tool installation from a local toolshed




Joachim Jacob
Contact details: http://www.bits.vib.be/index.php/about/80-team


On 09/30/2013 02:15 PM, Greg Von Kuster wrote:

Hello Joachim,

What version of Galaxy / Tool Shed code are you using?

[galaxy@galaxy galaxy-dist]$ hg tip
changeset:   10411:c42567f43aa7



On Sep 30, 2013, at 8:05 AM, Joachim Jacob | VIB |  wrote:


Hi Greg,


Sorry to dig up this unsolved thread from a few months back.

Recap of the bug: I have developed a small tool. I have put it in my local 
Toolshed, and installed it. After applying some changes to the tool, I 'hg 
push'ed the changes to my repository on my toolshed. I uninstalled the tool, 
and reinstalled it. Since I work with job handlers, I have to restart Galaxy. 
Since I had about ~4 committed changes, I have repeated these steps about 4 
times.


What process do you use for "applying some changes to the tool"?  Do you make 
these changes in a separate development repository and push them to your repository in 
your tool shed?  Or are you making changes to the installed repository in your Galaxy 
instance and attempting to push them back to the repository in your Tool Shed?

First I develop an XML, README, and tool_dependencies.xml in a 
development directory. When finished, I put them in a tool shed repo, by 
uploading a tar ball of these files. I clone the tool shed repo, and 
delete my development directory.  I adjust files in that cloned tool 
shed repo (e.g. fixing typos, adding help,...) and push them back to the 
tool shed repo.


Now, I did some changes to the tool_dependencies.xml and pushed them 
back to the tool shed. Next I update or remove/reinstall the tool via 
the Admin menu. I try to install the dependencies.


That's how I work. I have a feeling that I know what's coming next. :-)


The bug: the tool appears multiple times in the tool management window. 2 times 
as new, and 1 time as uninstalled (since I uninstalled it). The tool is still 
available in the toolbox, although it should not. The 2 installed tools have an 
option 'install', but when I click this I get an internal server error 500.

Galaxy version:
*
[galaxy@galaxy galaxy-dist]$ hg tip
changeset:   10411:c42567f43aa7
tag: tip
user:greg
date:Mon Aug 19 13:19:56 2013 -0400
summary: Filter invalid objects when generating the list of 
repository_dependencies objects that are associated with a tool shed repository 
installed into Galaxy.
*

As per your request: the web log of this internal server error.


193.191.128.2 - - [30/Sep/2013:13:15:19 +0200] "GET 
/admin_toolshed/prepare_for_install?tool_shed_url=http://toolshed.bits.vib.be/&repository_ids=968205d9ed31733d&changeset_revisions=e08a6d9e97a3
 HTTP/1.1" 500 - "http://galaxy.bits.vib.be/admin_toolshed/browse_repositories"; "Mozilla/5.0 
(X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Ubuntu Chromium/28.0.1500.71 Chrome/28.0.1500.71 
Safari/537.36"
Debug at: http://galaxy.bits.vib.be/_debug/view/1380535486


When you point your browser to the above "Debug URL", what is the stack trace 
that is displayed?
URL: 
http://galaxy.bits.vib.be/admin_toolshed/prepare_for_install?tool_shed_url=http://toolshed.bits.vib.be/&repository_ids=968205d9ed31733d&changeset_revisions=e08a6d9e97a3
File 
'/home/galaxy/galaxy-dist/eggs/WebError-0.8a-py2.6.egg/weberror/evalexception/middleware.py', 
line 364 in respond

  app_iter = self.application(environ, detect_start_response)
File 
'/home/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.6.egg/paste/recursive.py', 
line 84 in __call__

  return self.application(environ, start_response)
File 
'/home/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpexceptions.py', 
line 633 in __call__

  return self.application(environ, start_response)
File '/home/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 
132 in __call__

  return self.handle_request( environ, start_response )
File '/home/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 
190 in handle_request

  body = method( trans, **kwargs )
File '/home/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py', 
line 221 in decorator

  return func( self, trans, *args, **kwargs )
File 
'/home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py', 
line 840 in prepare_for_install

  raw_text = common_util.tool_shed_get( trans.app, tool_shed_url, url )
File '/home/galaxy/galaxy-dist/lib/tool_shed/util/common_util.py', line 
110 in tool_shed_get

  response = urlopener.open( uri )
File '/usr/lib64/python2.6/urllib2.py', line 397 in open
  response = meth(req, response)
File '/usr/lib64/python2.6/urllib2.py', line 510 in http_response
  'http', request, response, code, msg, hdrs)
File '/usr/lib64/python2.6/urllib2.py', line 435 in error
  return self._call_chain(*args)
File '/usr/lib64/python2.6/urllib2.py', line 369 in _call_chain
  result = func(*args)
File '/usr/lib64/python2.6/urllib2.py', line 518 in http_error_default
  raise HTTPError(req

Re: [galaxy-dev] Test Toolshed Biopython package dependency & NumPy

2013-09-30 Thread Dave Bouvier


Peter,

It looks like there may be a version conflict between package_numpy and 
either a system numpy or the Galaxy numpy egg. I'll investigate and keep 
you updated on my progress.


   --Dave B.

On 09/30/2013 05:08 AM, Peter Cock wrote:

On Sun, Sep 29, 2013 at 1:17 PM, Björn Grüning wrote:

I updated R, numpy, scipy, scikit and removed the atlas dependency. It
seems to work fine for the ChemicalToolBox. I do not remove the lapack
dependency, because I did not get any complains until now.


I'm seeing problems on the Test Tool Shed with NumPy :(

The updated no-ATLAS numpy is revision f0490401cfff
http://testtoolshed.g2.bx.psu.edu/view/iuc/package_numpy_1_7

My tools using NumPy via Biopython 1.62 do seem to be
picking up this new NumPy package, which is good.

However, the install of NumPy seems to be failing in strange
and *different* ways - which I suspect points to a Tool Shed
test framework bug, perhaps in sharing the dependencies
between tools?

--

http://testtoolshed.g2.bx.psu.edu/view/peterjc/seq_select_by_id /9e9e3b860aa0
Looks like partial NumPy install?

Installation errors - no functional tests were run for any tools in
this changeset revision
Tool dependencies
TypeNameVersion
biopython package 1.62
Error
Traceback (most recent call last): File "setup.py", line 463, in
 setup(**setup_args) File
"/usr/lib/python2.7/distutils/core.py", line 152, in setup
dist.run_commands() File "/usr/lib/python2.7/distutils/dist.py", line
953, in run_commands self.run_command(cmd) File
"/usr/lib/python2.7/distutils/dist.py", line 972, in run_command
cmd_obj.run() File "setup.py", line 216, in run if
check_dependencies_once(): File "setup.py", line 123, in
check_dependencies_once _CHECKED = check_dependencies() File
"setup.py", line 163, in check_dependencies if is_Numpy_installed():
File "setup.py", line 282, in is_Numpy_installed return
bool(can_import("numpy")) File "setup.py", line 274, in can_import
return __import__(module_name) File
"/ToolDependencies/numpy/1.7.1/iuc/package_numpy_1_7/f0490401cfff/lib/python/numpy/__init__.py",
line 137, in  import add_newdocs File
"/ToolDependencies/numpy/1.7.1/iuc/package_numpy_1_7/f0490401cfff/lib/python/numpy/add_newdocs.py",
line 9, in  from numpy.lib import add_newdoc File
"/ToolDependencies/numpy/1.7.1/iuc/package_numpy_1_7/f0490401cfff/lib/python/numpy/lib/__init__.py",
line 13, in  from polynomial import * File
"/ToolDependencies/numpy/1.7.1/iuc/package_numpy_1_7/f0490401cfff/lib/python/numpy/lib/polynomial.py",
line 11, in  import numpy.core.numeric as NX AttributeError:
'module' object has no attribute 'core'

--

http://testtoolshed.g2.bx.psu.edu/view/peterjc/seq_select_by_id/9e9e3b860aa0
Apparently the same error:

Installation errors - no functional tests were run for any tools in
this changeset revision
Tool dependencies
TypeNameVersion
biopython package 1.62
Error
Traceback (most recent call last): File "setup.py", line 463, in
 setup(**setup_args) File
"/usr/lib/python2.7/distutils/core.py", line 152, in setup
dist.run_commands() File "/usr/lib/python2.7/distutils/dist.py", line
953, in run_commands self.run_command(cmd) File
"/usr/lib/python2.7/distutils/dist.py", line 972, in run_command
cmd_obj.run() File "setup.py", line 216, in run if
check_dependencies_once(): File "setup.py", line 123, in
check_dependencies_once _CHECKED = check_dependencies() File
"setup.py", line 163, in check_dependencies if is_Numpy_installed():
File "setup.py", line 282, in is_Numpy_installed return
bool(can_import("numpy")) File "setup.py", line 274, in can_import
return __import__(module_name) File
"/ToolDependencies/numpy/1.7.1/iuc/package_numpy_1_7/f0490401cfff/lib/python/numpy/__init__.py",
line 137, in  import add_newdocs File
"/ToolDependencies/numpy/1.7.1/iuc/package_numpy_1_7/f0490401cfff/lib/python/numpy/add_newdocs.py",
line 9, in  from numpy.lib import add_newdoc File
"/ToolDependencies/numpy/1.7.1/iuc/package_numpy_1_7/f0490401cfff/lib/python/numpy/lib/__init__.py",
line 13, in  from polynomial import * File
"/ToolDependencies/numpy/1.7.1/iuc/package_numpy_1_7/f0490401cfff/lib/python/numpy/lib/polynomial.py",
line 11, in  import numpy.core.numeric as NX AttributeError:
'module' object has no attribute 'core'

--

http://testtoolshed.g2.bx.psu.edu/view/peterjc/seq_rename/d08767ae73ce
Looks like a different partial NumPy install?

Installation errors - no functional tests were run for any tools in
this changeset revision
Tool dependencies
TypeNameVersion
biopython package 1.62
Error
Traceback (most recent call last): File "setup.py", line 393, in
 if is_Numpy_installed(): File "setup.py", line 282, in
is_Numpy_installed return bool(can_import("numpy")) File "setup.py",
line 274, in can_import return __import__(module_name) File
"/ToolDependencies/numpy/1.7.1/iuc/package_numpy_1_7/f0490401cfff/lib/python/numpy/__init__.py",
line 137, in  import add_newdocs File
"/ToolDependencies/numpy/1.7.1/iuc/package

Re: [galaxy-dev] Download URL not accepted in tool_dependencies.xml

2013-09-30 Thread Dave Bouvier


Joachim,

For sourceforge URLs, you can safely omit the question mark and 
everything after it, since that's part of the browser download load 
balancing process. When downloading with wget, curl, or python's urllib, 
downloads.sourceforge.net does its own behind-the-scenes load balancing. 
As for hyphens, I don't believe they need to be escaped, since they're 
not XML entities like the ampersand is. The following download_by_url 
action should work:


type="download_by_url">http://downloads.sourceforge.net/project/transpose/transpose/transpose-2.0/2.0/transpose-2.0.zip 



   --Dave B.

On 09/30/2013 08:45 AM, Joachim Jacob | VIB | wrote:

Hi all,


Not fixed yet. Somehow the download does not work: I have escaped the
ampersands and the hyphens. The download seems to have to proceed, since
I receive no error from the download step. The next step in the
dependencies file gives an error: mv: cannot stat transpose.zip': No
such file or directory



Cheers,
J


Joachim Jacob
Contact details: http://www.bits.vib.be/index.php/about/80-team


On 09/30/2013 02:06 PM, Peter Cock wrote:

You must escape any ampersand in the XML as & and then it should
work.

Peter

On Mon, Sep 30, 2013 at 12:51 PM, Joachim Jacob | VIB |
 wrote:

Hi all,


The download URL seems not to be accepted in tool_dependencies.xml.
It is an
URL from sourceforge, the direct link to a package.

The error upon uploading the tool to my toolshed:
**
Metadata may have been defined for some items in revision
'5665a799775d'.
Correct the following problems if necessary and reset metadata.
tool_dependencies.xml - Exception attempting to parse
/mnt/toolsheddb/database/000/repo_26/tool_dependencies.xml: not
well-formed
(invalid token): line 6, column 149
**

The tool_dependencies.xml file:
**
1 
2 
3 
4
5 
6 http://downloads.sourceforge.net/project/transpose/transpose/transpose-2.0/2.0/transpose-2.0.zip?r=&ts=1380535239&use_mirror=surfnet

7mkdir bin
8  unzip
transpose-2.0.zip
 cd
transpose-2.0/src
 gcc transpose.c -o
transpose
 
$INSTALL_DIR/transpose-2.0/src/transpose
$INSTALL_DIR/bin
 
 chmod +x
$INSTALL_DIR/bin/transpose
 
 $INSTALL_DIR/bin
 
 
 
 
 Compiling transpose and putting in the path.
 


**


Cheers,
Joachim

--
Joachim Jacob
Contact details: http://www.bits.vib.be/index.php/about/80-team


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Re: [galaxy-dev] Messed up a tool installation from a local toolshed


See attachment.

Joachim Jacob
Contact details: http://www.bits.vib.be/index.php/about/80-team


On 09/30/2013 02:15 PM, Peter Cock wrote:

On Mon, Sep 30, 2013 at 1:05 PM, Joachim Jacob | VIB |
 wrote:

Hi Greg,


Sorry to dig up this unsolved thread from a few months back.

Recap of the bug: I have developed a small tool. I have put it in my local
Toolshed, and installed it. After applying some changes to the tool, I 'hg
push'ed the changes to my repository on my toolshed. I uninstalled the tool,
and reinstalled it. Since I work with job handlers, I have to restart
Galaxy. Since I had about ~4 committed changes, I have repeated these steps
about 4 times.

The bug: the tool appears multiple times in the tool management window. 2
times as new, and 1 time as uninstalled (since I uninstalled it). The tool
is still available in the toolbox, although it should not. The 2 installed
tools have an option 'install', but when I click this I get an internal
server error 500.

Galaxy version:
*
[galaxy@galaxy galaxy-dist]$ hg tip
changeset:   10411:c42567f43aa7
tag: tip
user:greg
date:Mon Aug 19 13:19:56 2013 -0400
summary: Filter invalid objects when generating the list of
repository_dependencies objects that are associated with a tool shed
repository installed into Galaxy.
*

As per your request: the web log of this internal server error.


193.191.128.2 - - [30/Sep/2013:13:15:19 +0200] "GET
/admin_toolshed/prepare_for_install?tool_shed_url=http://toolshed.bits.vib.be/&repository_ids=968205d9ed31733d&changeset_revisions=e08a6d9e97a3
HTTP/1.1" 500 -
"http://galaxy.bits.vib.be/admin_toolshed/browse_repositories"; "Mozilla/5.0
(X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Ubuntu
Chromium/28.0.1500.71 Chrome/28.0.1500.71 Safari/537.36"
Debug at: http://galaxy.bits.vib.be/_debug/view/1380535486


The postgres database shows:


galaxydb=>  select id, tool_shed, name, owner,
installed_changeset_revision, status, error_message from
tool_shed_repository where name = 'transpose';
  id |  tool_shed   |   name|  owner  |
installed_changeset_revision |   status| error_message
+--+---+-+--+-+---
  45 | toolshed.bits.vib.be | transpose | joachim | cee0157acee1
| Uninstalled |
  44 | toolshed.bits.vib.be | transpose | joachim | 2fa0462b9303
| New |
  43 | toolshed.bits.vib.be | transpose | joachim | e08a6d9e97a3
| New |
(3 rows)

How should I proceed ?


This is the second time I experience this. On a last note: I have noted also
that I managed to get a repository with different branches in this tool shed
repository, by mixing 'hg push' and uploading a tarball. There seems no easy
way to fixing this.


Kind regards,
Joachim

Hmm - do these "New" entries show up in white on the
"Manage installed tool shed repositories" admin page?

It sounds like a case of what was nicknamed "white ghosts",
some causes of which have been fixed - but I don't think there
was any automated removal of old "white ghosts" (I still have
two on my test system).

Peter




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Re: [galaxy-dev] Download URL not accepted in tool_dependencies.xml


Hi all,


Not fixed yet. Somehow the download does not work: I have escaped the 
ampersands and the hyphens. The download seems to have to proceed, since 
I receive no error from the download step. The next step in the 
dependencies file gives an error: 
mv: cannot stat transpose.zip': No such file or directory




Cheers,
J


Joachim Jacob
Contact details: http://www.bits.vib.be/index.php/about/80-team


On 09/30/2013 02:06 PM, Peter Cock wrote:

You must escape any ampersand in the XML as & and then it should work.

Peter

On Mon, Sep 30, 2013 at 12:51 PM, Joachim Jacob | VIB |
 wrote:

Hi all,


The download URL seems not to be accepted in tool_dependencies.xml. It is an
URL from sourceforge, the direct link to a package.

The error upon uploading the tool to my toolshed:
**
Metadata may have been defined for some items in revision '5665a799775d'.
Correct the following problems if necessary and reset metadata.
tool_dependencies.xml - Exception attempting to parse
/mnt/toolsheddb/database/000/repo_26/tool_dependencies.xml: not well-formed
(invalid token): line 6, column 149
**

The tool_dependencies.xml file:
**
1 
2 
3 
4
5 
6 http://downloads.sourceforge.net/project/transpose/transpose/transpose-2.0/2.0/transpose-2.0.zip?r=&ts=1380535239&use_mirror=surfnet
7mkdir bin
8  unzip transpose-2.0.zip
 cd transpose-2.0/src
 gcc transpose.c -o
transpose
 
$INSTALL_DIR/transpose-2.0/src/transpose
$INSTALL_DIR/bin
 
 chmod +x
$INSTALL_DIR/bin/transpose
 
 $INSTALL_DIR/bin
 
 
 
 
 Compiling transpose and putting in the path.
 


**


Cheers,
Joachim

--
Joachim Jacob
Contact details: http://www.bits.vib.be/index.php/about/80-team


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___
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Re: [galaxy-dev] Messed up a tool installation from a local toolshed

2013-09-30 Thread Greg Von Kuster

Hello Joachim,

What version of Galaxy / Tool Shed code are you using?  

On Sep 30, 2013, at 8:05 AM, Joachim Jacob | VIB |  wrote:

> Hi Greg,
> 
> 
> Sorry to dig up this unsolved thread from a few months back.
> 
> Recap of the bug: I have developed a small tool. I have put it in my local 
> Toolshed, and installed it. After applying some changes to the tool, I 'hg 
> push'ed the changes to my repository on my toolshed. I uninstalled the tool, 
> and reinstalled it. Since I work with job handlers, I have to restart Galaxy. 
> Since I had about ~4 committed changes, I have repeated these steps about 4 
> times.
> 
What process do you use for "applying some changes to the tool"?  Do you make 
these changes in a separate development repository and push them to your 
repository in your tool shed?  Or are you making changes to the installed 
repository in your Galaxy instance and attempting to push them back to the 
repository in your Tool Shed?


> The bug: the tool appears multiple times in the tool management window. 2 
> times as new, and 1 time as uninstalled (since I uninstalled it). The tool is 
> still available in the toolbox, although it should not. The 2 installed tools 
> have an option 'install', but when I click this I get an internal server 
> error 500.
> 
> Galaxy version:
> *
> [galaxy@galaxy galaxy-dist]$ hg tip
> changeset:   10411:c42567f43aa7
> tag: tip
> user:greg
> date:Mon Aug 19 13:19:56 2013 -0400
> summary: Filter invalid objects when generating the list of 
> repository_dependencies objects that are associated with a tool shed 
> repository installed into Galaxy.
> *
> 
> As per your request: the web log of this internal server error.
> 
> 
> 193.191.128.2 - - [30/Sep/2013:13:15:19 +0200] "GET 
> /admin_toolshed/prepare_for_install?tool_shed_url=http://toolshed.bits.vib.be/&repository_ids=968205d9ed31733d&changeset_revisions=e08a6d9e97a3
>  HTTP/1.1" 500 - 
> "http://galaxy.bits.vib.be/admin_toolshed/browse_repositories"; "Mozilla/5.0 
> (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Ubuntu 
> Chromium/28.0.1500.71 Chrome/28.0.1500.71 Safari/537.36"
> Debug at: http://galaxy.bits.vib.be/_debug/view/1380535486


When you point your browser to the above "Debug URL", what is the stack trace 
that is displayed?


> 
> 
> The postgres database shows:
> 
> 
> galaxydb=>  select id, tool_shed, name, owner, 
> installed_changeset_revision, status, error_message from tool_shed_repository 
> where name = 'transpose';
> id |  tool_shed   |   name|  owner  | 
> installed_changeset_revision |   status| error_message
> +--+---+-+--+-+---
> 45 | toolshed.bits.vib.be | transpose | joachim | cee0157acee1
>  | Uninstalled |
> 44 | toolshed.bits.vib.be | transpose | joachim | 2fa0462b9303
>  | New |
> 43 | toolshed.bits.vib.be | transpose | joachim | e08a6d9e97a3
>  | New |
> (3 rows)
> 


These repositories in the "New" state look like the so-called "white ghosts" 
that cropped up for a time.  The issues that resulted in their creation have 
been resolved, but some of the fixes will not be available in the distribution 
until the next Galaxy release, which is not yet scheduled.


> How should I proceed ?

You'll undoubtedly need to manually fix your database with sql - delete these 
records in the "New" state and all associated recoirds defined by foreign keys.


> 
> 
> This is the second time I experience this. On a last note: I have noted also 
> that I managed to get a repository with different branches in this tool shed 
> repository, by mixing 'hg push' and uploading a tarball. There seems no easy 
> way to fixing this.
> 
> 
> Kind regards,
> Joachim
> 
> Joachim Jacob
> Contact details: http://www.bits.vib.be/index.php/about/80-team
> 
> 
> On 06/14/2013 04:15 PM, Greg Von Kuster wrote:
>> Hello Joachim,
>> 
>> What version of Galaxy are your running?
>> 
>> What does the tool shed paster go show for the 500 Internal Server Error?
>> 
>> Also, run the following sql manually in your Galaxy database and send the 
>> results.
>> 
>> select id, tool_shed, name, owner, installed_changeset_revision, status, 
>> error_message from tool_shed_repository;
>> 
>> Thanks,
>> 
>> Greg Von Kuster
>> 
>> 
>> On Jun 14, 2013, at 3:41 AM, Joachim Jacob > > wrote:
>> 
>>> Hi all,
>>> 
>>> I have developed a tool in our local Galaxy, and imported it in a local 
>>> toolshed. I next removed the 'dev' version of the tool in Galaxy, and 
>>> installed it now via het Tool Shed Manager.
>>> 
>>> I got an error that the dependencies could not be installed. If figured it 
>>> out that it (needed to add an extra shell_command in the tool_dependencies) 
>>> (and

Re: [galaxy-dev] Messed up a tool installation from a local toolshed

On Mon, Sep 30, 2013 at 1:05 PM, Joachim Jacob | VIB |
 wrote:
> Hi Greg,
>
>
> Sorry to dig up this unsolved thread from a few months back.
>
> Recap of the bug: I have developed a small tool. I have put it in my local
> Toolshed, and installed it. After applying some changes to the tool, I 'hg
> push'ed the changes to my repository on my toolshed. I uninstalled the tool,
> and reinstalled it. Since I work with job handlers, I have to restart
> Galaxy. Since I had about ~4 committed changes, I have repeated these steps
> about 4 times.
>
> The bug: the tool appears multiple times in the tool management window. 2
> times as new, and 1 time as uninstalled (since I uninstalled it). The tool
> is still available in the toolbox, although it should not. The 2 installed
> tools have an option 'install', but when I click this I get an internal
> server error 500.
>
> Galaxy version:
> *
> [galaxy@galaxy galaxy-dist]$ hg tip
> changeset:   10411:c42567f43aa7
> tag: tip
> user:greg
> date:Mon Aug 19 13:19:56 2013 -0400
> summary: Filter invalid objects when generating the list of
> repository_dependencies objects that are associated with a tool shed
> repository installed into Galaxy.
> *
>
> As per your request: the web log of this internal server error.
>
> 
> 193.191.128.2 - - [30/Sep/2013:13:15:19 +0200] "GET
> /admin_toolshed/prepare_for_install?tool_shed_url=http://toolshed.bits.vib.be/&repository_ids=968205d9ed31733d&changeset_revisions=e08a6d9e97a3
> HTTP/1.1" 500 -
> "http://galaxy.bits.vib.be/admin_toolshed/browse_repositories"; "Mozilla/5.0
> (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Ubuntu
> Chromium/28.0.1500.71 Chrome/28.0.1500.71 Safari/537.36"
> Debug at: http://galaxy.bits.vib.be/_debug/view/1380535486
> 
>
> The postgres database shows:
>
> 
> galaxydb=>  select id, tool_shed, name, owner,
> installed_changeset_revision, status, error_message from
> tool_shed_repository where name = 'transpose';
>  id |  tool_shed   |   name|  owner  |
> installed_changeset_revision |   status| error_message
> +--+---+-+--+-+---
>  45 | toolshed.bits.vib.be | transpose | joachim | cee0157acee1
> | Uninstalled |
>  44 | toolshed.bits.vib.be | transpose | joachim | 2fa0462b9303
> | New |
>  43 | toolshed.bits.vib.be | transpose | joachim | e08a6d9e97a3
> | New |
> (3 rows)
> 
> How should I proceed ?
>
>
> This is the second time I experience this. On a last note: I have noted also
> that I managed to get a repository with different branches in this tool shed
> repository, by mixing 'hg push' and uploading a tarball. There seems no easy
> way to fixing this.
>
>
> Kind regards,
> Joachim

Hmm - do these "New" entries show up in white on the
"Manage installed tool shed repositories" admin page?

It sounds like a case of what was nicknamed "white ghosts",
some causes of which have been fixed - but I don't think there
was any automated removal of old "white ghosts" (I still have
two on my test system).

Peter
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Re: [galaxy-dev] Download URL not accepted in tool_dependencies.xml

You must escape any ampersand in the XML as & and then it should work.

Peter

On Mon, Sep 30, 2013 at 12:51 PM, Joachim Jacob | VIB |
 wrote:
> Hi all,
>
>
> The download URL seems not to be accepted in tool_dependencies.xml. It is an
> URL from sourceforge, the direct link to a package.
>
> The error upon uploading the tool to my toolshed:
> **
> Metadata may have been defined for some items in revision '5665a799775d'.
> Correct the following problems if necessary and reset metadata.
> tool_dependencies.xml - Exception attempting to parse
> /mnt/toolsheddb/database/000/repo_26/tool_dependencies.xml: not well-formed
> (invalid token): line 6, column 149
> **
>
> The tool_dependencies.xml file:
> **
> 1 
> 2 
> 3 
> 4
> 5 
> 6  type="download_by_url">http://downloads.sourceforge.net/project/transpose/transpose/transpose-2.0/2.0/transpose-2.0.zip?r=&ts=1380535239&use_mirror=surfnet
> 7mkdir bin
> 8  unzip transpose-2.0.zip
> cd transpose-2.0/src
> gcc transpose.c -o
> transpose
> 
> $INSTALL_DIR/transpose-2.0/src/transpose
> $INSTALL_DIR/bin
> 
> chmod +x
> $INSTALL_DIR/bin/transpose
> 
>  action="prepend_to">$INSTALL_DIR/bin
> 
> 
> 
> 
> Compiling transpose and putting in the path.
> 
> 
> 
> **
>
>
> Cheers,
> Joachim
>
> --
> Joachim Jacob
> Contact details: http://www.bits.vib.be/index.php/about/80-team
>
>
> ___
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> 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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Re: [galaxy-dev] Test Toolshed Biopython package dependency & NumPy

On Mon, Sep 30, 2013 at 12:23 PM, Bjoern Gruening
 wrote:
> Hi,
>
> it does not mean anything, but for me its working locally on a Fedora
> (stable) machine.
>
> If I can anything do to fix that, please let me know.
> Bjoern

Thanks Bjoern - I'm pretty sure this is a Tool Shed issue,
rather than the Biopython or NumPy package definitions
themselves.

Peter
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Re: [galaxy-dev] Messed up a tool installation from a local toolshed

Hi Greg,

Sorry to dig up this unsolved thread from a few months back.

Recap of the bug: I have developed a small tool. I have put it in my 
local Toolshed, and installed it. After applying some changes to the 
tool, I 'hg push'ed the changes to my repository on my toolshed. I 
uninstalled the tool, and reinstalled it. Since I work with job 
handlers, I have to restart Galaxy. Since I had about ~4 committed 
changes, I have repeated these steps about 4 times.

The bug: the tool appears multiple times in the tool management window. 
2 times as new, and 1 time as uninstalled (since I uninstalled it). The 
tool is still available in the toolbox, although it should not. The 2 
installed tools have an option 'install', but when I click this I get an 
internal server error 500.

Galaxy version:
*
[galaxy@galaxy galaxy-dist]$ hg tip
changeset:   10411:c42567f43aa7
tag: tip
user:greg
date:Mon Aug 19 13:19:56 2013 -0400
summary: Filter invalid objects when generating the list of 
repository_dependencies objects that are associated with a tool shed 
repository installed into Galaxy.

*

As per your request: the web log of this internal server error.

193.191.128.2 - - [30/Sep/2013:13:15:19 +0200] "GET 
/admin_toolshed/prepare_for_install?tool_shed_url=http://toolshed.bits.vib.be/&repository_ids=968205d9ed31733d&changeset_revisions=e08a6d9e97a3 
HTTP/1.1" 500 - 
"http://galaxy.bits.vib.be/admin_toolshed/browse_repositories"; 
"Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) 
Ubuntu Chromium/28.0.1500.71 Chrome/28.0.1500.71 Safari/537.36"

Debug at: http://galaxy.bits.vib.be/_debug/view/1380535486

The postgres database shows:

galaxydb=>  select id, tool_shed, name, owner, 
installed_changeset_revision, status, error_message from 
tool_shed_repository where name = 'transpose';
 id |  tool_shed   |   name|  owner  | 
installed_changeset_revision |   status| error_message

+--+---+-+--+-+---
 45 | toolshed.bits.vib.be | transpose | joachim | 
cee0157acee1 | Uninstalled |
 44 | toolshed.bits.vib.be | transpose | joachim | 
2fa0462b9303 | New |
 43 | toolshed.bits.vib.be | transpose | joachim | 
e08a6d9e97a3 | New |

(3 rows)

How should I proceed ?

This is the second time I experience this. On a last note: I have noted 
also that I managed to get a repository with different branches in this 
tool shed repository, by mixing 'hg push' and uploading a tarball. There 
seems no easy way to fixing this.

Kind regards,
Joachim

Joachim Jacob
Contact details: http://www.bits.vib.be/index.php/about/80-team

On 06/14/2013 04:15 PM, Greg Von Kuster wrote:

Hello Joachim,

What version of Galaxy are your running?

What does the tool shed paster go show for the 500 Internal Server Error?

Also, run the following sql manually in your Galaxy database and send 
the results.

select id, tool_shed, name, owner, installed_changeset_revision, 
status, error_message from tool_shed_repository;

Thanks,

Greg Von Kuster

On Jun 14, 2013, at 3:41 AM, Joachim Jacob > wrote:

Hi all,

I have developed a tool in our local Galaxy, and imported it in a 
local toolshed. I next removed the 'dev' version of the tool in 
Galaxy, and installed it now via het Tool Shed Manager.

I got an error that the dependencies could not be installed. If 
figured it out that it (needed to add an extra shell_command in the 
tool_dependencies) (and the mount point on my system needs to have 
exec permissions of course).

So I updated the tool in the toolshed. BUT, then I uninstalled the 
tool from Galaxy, and reinstalled it from the Tool Shed ... instead 
of just updating. Anyway, it has happened.

Now I have the tool listed in my 'Install Tool Shed Repositories', 
and when I click on it, it says 'this tool is not installed'. The 
only action I can apply on this installed tool shed repository is 
'Install' (...). But clicking on that 'install' button, leads me to 
an error page (http error 500).

**
URL: 
http://localhost/admin_toolshed/prepare_for_install?tool_shed_url=http://localhost:9009/&repository_ids=84cbaf0b6bf7a1a9&changeset_revisions=fc2339abcab7 

Module weberror.evalexception.middleware:364 in respond view
>>  app_iter = self.application(environ, detect_start_response)
Module paste.recursive:84 in __call__  view
>>  return self.application(environ, start_response)
Module paste.httpexceptions:633 in __call__ view
>>  return self.application(environ, start_response)
Module galaxy.web.framework.base:132 in __call__  view
>>  return self.handle_request( environ, start_response )
Module galaxy.web.framework.base:190 in handle_reques

Re: [galaxy-dev] Download URL not accepted in tool_dependencies.xml

Hi Joachim,

try to remove the last part '?r=&ts=1380535239&use_mirror=surfnet'

Cheers,
Bjoern

> Hi all,
> 
> 
> The download URL seems not to be accepted in tool_dependencies.xml. It 
> is an URL from sourceforge, the direct link to a package.
> 
> The error upon uploading the tool to my toolshed:
> **
> Metadata may have been defined for some items in revision 
> '5665a799775d'. Correct the following problems if necessary and reset 
> metadata.
> tool_dependencies.xml - Exception attempting to parse 
> /mnt/toolsheddb/database/000/repo_26/tool_dependencies.xml: not 
> well-formed (invalid token): line 6, column 149
> **
> 
> The tool_dependencies.xml file:
> **
> 1 
> 2 
> 3 
> 4
> 5 
> 6  type="download_by_url">http://downloads.sourceforge.net/project/transpose/transpose/transpose-2.0/2.0/transpose-2.0.zip?r=&ts=1380535239&use_mirror=surfnet
> 7mkdir bin
> 8  unzip 
> transpose-2.0.zip
>  cd transpose-2.0/src
>  gcc transpose.c -o 
> transpose
>  
> $INSTALL_DIR/transpose-2.0/src/transpose
> $INSTALL_DIR/bin
>  
>  chmod +x 
> $INSTALL_DIR/bin/transpose
>  
>   action="prepend_to">$INSTALL_DIR/bin
>  
>  
>  
>  
>  Compiling transpose and putting in the path.
>  
> 
> 
> **
> 
> 
> Cheers,
> Joachim
> 



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Re: [galaxy-dev] Download URL not accepted in tool_dependencies.xml

2013-09-30 Thread Nicola Soranzo

This problem is probably due to the 2 ampersands '&', which are not
allowed in XML. Try substituting them with '&'.

Nicola

Il giorno lun, 30/09/2013 alle 13.51 +0200, Joachim Jacob | VIB | ha
scritto: 
> Hi all,
> 
> 
> The download URL seems not to be accepted in tool_dependencies.xml. It 
> is an URL from sourceforge, the direct link to a package.
> 
> The error upon uploading the tool to my toolshed:
> **
> Metadata may have been defined for some items in revision 
> '5665a799775d'. Correct the following problems if necessary and reset 
> metadata.
> tool_dependencies.xml - Exception attempting to parse 
> /mnt/toolsheddb/database/000/repo_26/tool_dependencies.xml: not 
> well-formed (invalid token): line 6, column 149
> **
> 
> The tool_dependencies.xml file:
> **
> 1 
> 2 
> 3 
> 4
> 5 
> 6  type="download_by_url">http://downloads.sourceforge.net/project/transpose/transpose/transpose-2.0/2.0/transpose-2.0.zip?r=&ts=1380535239&use_mirror=surfnet
> 7mkdir bin
> 8  unzip 
> transpose-2.0.zip
>  cd transpose-2.0/src
>  gcc transpose.c -o 
> transpose
>  
> $INSTALL_DIR/transpose-2.0/src/transpose
> $INSTALL_DIR/bin
>  
>  chmod +x 
> $INSTALL_DIR/bin/transpose
>  
>   action="prepend_to">$INSTALL_DIR/bin
>  
>  
>  
>  
>  Compiling transpose and putting in the path.
>  
> 
> 
> **
> 
> 
> Cheers,
> Joachim
> 


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[galaxy-dev] Download URL not accepted in tool_dependencies.xml


Hi all,


The download URL seems not to be accepted in tool_dependencies.xml. It 
is an URL from sourceforge, the direct link to a package.


The error upon uploading the tool to my toolshed:
**
Metadata may have been defined for some items in revision 
'5665a799775d'. Correct the following problems if necessary and reset 
metadata.
tool_dependencies.xml - Exception attempting to parse 
/mnt/toolsheddb/database/000/repo_26/tool_dependencies.xml: not 
well-formed (invalid token): line 6, column 149

**

The tool_dependencies.xml file:
**
1 
2 
3 
4
5 
6 type="download_by_url">http://downloads.sourceforge.net/project/transpose/transpose/transpose-2.0/2.0/transpose-2.0.zip?r=&ts=1380535239&use_mirror=surfnet

7mkdir bin
8  unzip 
transpose-2.0.zip

cd transpose-2.0/src
gcc transpose.c -o 
transpose


$INSTALL_DIR/transpose-2.0/src/transpose
$INSTALL_DIR/bin

chmod +x 
$INSTALL_DIR/bin/transpose


action="prepend_to">$INSTALL_DIR/bin





Compiling transpose and putting in the path.



**


Cheers,
Joachim

--
Joachim Jacob
Contact details: http://www.bits.vib.be/index.php/about/80-team


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Re: [galaxy-dev] Test Toolshed Biopython package dependency & NumPy

Hi,

it does not mean anything, but for me its working locally on a Fedora
(stable) machine.

If I can anything do to fix that, please let me know.
Bjoern

> On Sun, Sep 29, 2013 at 1:17 PM, Björn Grüning wrote:
> > I updated R, numpy, scipy, scikit and removed the atlas dependency. It
> > seems to work fine for the ChemicalToolBox. I do not remove the lapack
> > dependency, because I did not get any complains until now.
> 
> I'm seeing problems on the Test Tool Shed with NumPy :(
> 
> The updated no-ATLAS numpy is revision f0490401cfff
> http://testtoolshed.g2.bx.psu.edu/view/iuc/package_numpy_1_7
> 
> My tools using NumPy via Biopython 1.62 do seem to be
> picking up this new NumPy package, which is good.
> 
> However, the install of NumPy seems to be failing in strange
> and *different* ways - which I suspect points to a Tool Shed
> test framework bug, perhaps in sharing the dependencies
> between tools?
> 
> --
> 
> http://testtoolshed.g2.bx.psu.edu/view/peterjc/seq_select_by_id /9e9e3b860aa0
> Looks like partial NumPy install?
> 
> Installation errors - no functional tests were run for any tools in
> this changeset revision
> Tool dependencies
> TypeNameVersion
> biopython package 1.62
> Error
> Traceback (most recent call last): File "setup.py", line 463, in
>  setup(**setup_args) File
> "/usr/lib/python2.7/distutils/core.py", line 152, in setup
> dist.run_commands() File "/usr/lib/python2.7/distutils/dist.py", line
> 953, in run_commands self.run_command(cmd) File
> "/usr/lib/python2.7/distutils/dist.py", line 972, in run_command
> cmd_obj.run() File "setup.py", line 216, in run if
> check_dependencies_once(): File "setup.py", line 123, in
> check_dependencies_once _CHECKED = check_dependencies() File
> "setup.py", line 163, in check_dependencies if is_Numpy_installed():
> File "setup.py", line 282, in is_Numpy_installed return
> bool(can_import("numpy")) File "setup.py", line 274, in can_import
> return __import__(module_name) File
> "/ToolDependencies/numpy/1.7.1/iuc/package_numpy_1_7/f0490401cfff/lib/python/numpy/__init__.py",
> line 137, in  import add_newdocs File
> "/ToolDependencies/numpy/1.7.1/iuc/package_numpy_1_7/f0490401cfff/lib/python/numpy/add_newdocs.py",
> line 9, in  from numpy.lib import add_newdoc File
> "/ToolDependencies/numpy/1.7.1/iuc/package_numpy_1_7/f0490401cfff/lib/python/numpy/lib/__init__.py",
> line 13, in  from polynomial import * File
> "/ToolDependencies/numpy/1.7.1/iuc/package_numpy_1_7/f0490401cfff/lib/python/numpy/lib/polynomial.py",
> line 11, in  import numpy.core.numeric as NX AttributeError:
> 'module' object has no attribute 'core'
> 
> --
> 
> http://testtoolshed.g2.bx.psu.edu/view/peterjc/seq_select_by_id/9e9e3b860aa0
> Apparently the same error:
> 
> Installation errors - no functional tests were run for any tools in
> this changeset revision
> Tool dependencies
> TypeNameVersion
> biopython package 1.62
> Error
> Traceback (most recent call last): File "setup.py", line 463, in
>  setup(**setup_args) File
> "/usr/lib/python2.7/distutils/core.py", line 152, in setup
> dist.run_commands() File "/usr/lib/python2.7/distutils/dist.py", line
> 953, in run_commands self.run_command(cmd) File
> "/usr/lib/python2.7/distutils/dist.py", line 972, in run_command
> cmd_obj.run() File "setup.py", line 216, in run if
> check_dependencies_once(): File "setup.py", line 123, in
> check_dependencies_once _CHECKED = check_dependencies() File
> "setup.py", line 163, in check_dependencies if is_Numpy_installed():
> File "setup.py", line 282, in is_Numpy_installed return
> bool(can_import("numpy")) File "setup.py", line 274, in can_import
> return __import__(module_name) File
> "/ToolDependencies/numpy/1.7.1/iuc/package_numpy_1_7/f0490401cfff/lib/python/numpy/__init__.py",
> line 137, in  import add_newdocs File
> "/ToolDependencies/numpy/1.7.1/iuc/package_numpy_1_7/f0490401cfff/lib/python/numpy/add_newdocs.py",
> line 9, in  from numpy.lib import add_newdoc File
> "/ToolDependencies/numpy/1.7.1/iuc/package_numpy_1_7/f0490401cfff/lib/python/numpy/lib/__init__.py",
> line 13, in  from polynomial import * File
> "/ToolDependencies/numpy/1.7.1/iuc/package_numpy_1_7/f0490401cfff/lib/python/numpy/lib/polynomial.py",
> line 11, in  import numpy.core.numeric as NX AttributeError:
> 'module' object has no attribute 'core'
> 
> --
> 
> http://testtoolshed.g2.bx.psu.edu/view/peterjc/seq_rename/d08767ae73ce
> Looks like a different partial NumPy install?
> 
> Installation errors - no functional tests were run for any tools in
> this changeset revision
> Tool dependencies
> TypeNameVersion
> biopython package 1.62
> Error
> Traceback (most recent call last): File "setup.py", line 393, in
>  if is_Numpy_installed(): File "setup.py", line 282, in
> is_Numpy_installed return bool(can_import("numpy")) File "setup.py",
> line 274, in can_import return __import__(module_name) File
> "/ToolDependencies/numpy/1.7.1/iuc/package_numpy_1_7/f04

Re: [galaxy-dev] puzzle: tool result always "set dataset state to ERROR"

On Mon, Sep 30, 2013 at 7:07 AM, ruiwang.sz  wrote:
> Hi Peter,
>
> Thanks! I got it working by putting a suppressMessages() around the function
> call.

Great, but what I meant was just add this to your XML file to tell Galaxy
to ignore the stderr and only use the return code for deciding if there
was an error. This way you get to see any warnings from your tool:

> I might have some questions on how to generate output file names on the
> fly...let me make some attempts
> first. :-)
>
> Best,
> Rui

Please read this thread first - there are already lots of people working on
wrapping deseq2 into Galaxy,
http://lists.bx.psu.edu/pipermail/galaxy-dev/2013-September/016444.html

Peter
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[galaxy-dev] Test Toolshed Biopython package dependency & NumPy