[galaxy-dev] Error in matplotlib

2016-01-19 Thread Shane Kelly 
Could anyone shed some light on this error please?
(Information from the Galaxy operator here who is having trouble
posting)


The error is for the dependency “package_matplotlib1_2”

The full error information is 

Name: matplotlib
Version: 1.2.1
Type: Package
Status: Error


Error: File
"/home/little_galaxy/galaxy/lib/tool_shed/galaxy_install/install_manager.py",
line 128, in install_and_build_package_via_fabric tool_dependency =
self.install_and_build_package( install_environment, tool_dependency,
actions_dict ) File
"/home/little_galaxy/galaxy/lib/tool_shed/galaxy_install/install_manager.py",
line 86, in install_and_build_package initial_download=True ) File
"/home/little_galaxy/galaxy/lib/tool_shed/galaxy_install/tool_dependencies/recipe/recipe_manager.py",
line 31, in execute_step initial_download=initial_download ) File
"/home/little_galaxy/galaxy/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py",
line 694, in execute_step dir = self.url_download( work_dir,
downloaded_filename, url, extract=True, checksums=checksums ) File
"/home/little_galaxy/galaxy/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py",
line 187, in url_download raise Exception( err_msg )

Error downloading from URL
https://github.com/matplotlib/matplotlib/archive/v1.2.1.tar.gz#md5#47ee56f51200b8760b98d97ee86f57c6:
HTTP Error 400: Bad Request
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Re: [galaxy-dev] tool development

2016-01-19 Thread Hans-Rudolf Hotz 

Hi Matthias

Have you considered "Data Libraries"?

A cron job can query your LIMS and use the API to create "Data 
Libraries". Then the user can select which datasets she/he wants to import.



And back to your original question: Yes, it is possible to create 
interactive tools. Check out the 'dynamic_options' examples on


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


Regards, Hans-Rudolf

On 01/19/2016 12:18 PM, Matthias De Smet wrote:

Hi All,

I would like to create a tool to import data from a sequencer on a networked 
share to a users history.
The ideal setup would be that a query can be submitted to a database which 
contains all metadata from the sequencer + the path of the sequencer output. 
The tool should then show the available datasets found in the database and 
provide checkboxes to select which data should be imported.

My question is: how do you guys propose I get started on this? Do I use the 
API? Is it even possible to get a tool to return some output without submitting 
it as a job, e.g. using it interactively?

Thanks for the help!

PS: I know the basics of tool development, but I haven’t got much experience, 
so all comments are welcome!

Matthias
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Re: [galaxy-dev] tool development

2016-01-19 Thread Matthias De Smet 
Hi Hans-Rudolf

Yes, we have considered using data libraries, but for this particular use case 
we would prefer an approach like this. Our users are notoriously bad at data 
management and we would like to limit the amount of data that gets loaded in 
Galaxy. The networked share does not store all data permanently, so we need 
something to query what is available so the users can load that into their 
history.

Ideally the datasets also shouldn’t be copied into Galaxy, but symlinked, if 
possible.

Thanks for the tip on ‘dynamic_options’. Hadn’t noticed it before.

Matthias


> Op 19 jan. 2016, om 13:40 heeft Hans-Rudolf Hotz  het volgende 
> geschreven:
> 
> Hi Matthias
> 
> Have you considered "Data Libraries"?
> 
> A cron job can query your LIMS and use the API to create "Data Libraries". 
> Then the user can select which datasets she/he wants to import.
> 
> 
> And back to your original question: Yes, it is possible to create interactive 
> tools. Check out the 'dynamic_options' examples on
> 
> https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax
> 
> 
> Regards, Hans-Rudolf
> 
> On 01/19/2016 12:18 PM, Matthias De Smet wrote:
>> Hi All,
>> 
>> I would like to create a tool to import data from a sequencer on a networked 
>> share to a users history.
>> The ideal setup would be that a query can be submitted to a database which 
>> contains all metadata from the sequencer + the path of the sequencer output. 
>> The tool should then show the available datasets found in the database and 
>> provide checkboxes to select which data should be imported.
>> 
>> My question is: how do you guys propose I get started on this? Do I use the 
>> API? Is it even possible to get a tool to return some output without 
>> submitting it as a job, e.g. using it interactively?
>> 
>> Thanks for the help!
>> 
>> PS: I know the basics of tool development, but I haven’t got much 
>> experience, so all comments are welcome!
>> 
>> Matthias
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>>   http://galaxyproject.org/search/mailinglists/
>> 

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Re: [galaxy-dev] CEAS error

2016-01-19 Thread Peter Briggs 

Hello Philipp

I'm assuming this is the 'ceas' tool from the toolshed which is owned by 
'pjbriggs' (that is me)?


If it is then from what you describe I'm not sure whether this is a 
problem with the specific tool or a more general issue with Galaxy's 
tool installation.


My own experiences of trying to debug tool dependency installation 
issues have been quite haphazard, and although I've seen this particular 
error (i.e the "database had no record") a few times with various tools, 
I've never been able to understand what has caused it.


First it may be worth trying the "Repair repository" option from the 
"Repository Actions" menu. If that doesn't help then I've also had some 
success in the past using the "Manage tool dependencies" option (which 
allows individual dependencies to be uninstalled and then re-installed). 
This might work if just one dependency is giving an error.


Beyond that I've found it necessary to start drilling into the Galaxy 
log files. Aside from the log of the actual Galaxy process (verbose but 
sometimes useful, I don't know how easy this is to find on your Docker 
instance - I don't have any experience of working with them), often the 
tool dependencies also create their own INSTALLATION.log files which are 
worth looking for/at.


The following recipe should allow you to access these from within Galaxy 
(this is for v15.10):


- Go to "Admin" -> "Manage installed tools"
- Click on the name of the tool of interest (e.g. 'ceas')
- Click on the name of an errored dependency under the "Missing tool 
dependencies" section
- In the list of dependencies, click on the name of the errored 
dependency again


This should take you to a page which includes a "folder browser" 
underneath the heading "Contents", where you can browse the contents of 
the installed tool dependency folder. Hopefully this will include a file 
called INSTALLATION.log, and if you click on it then the contents should 
be displayed and you can look to see if there are any error messages to 
indicate what went wrong.


Sometimes there is no INSTALLATION.log file however, in which case the 
main log file of the Galaxy process is probably the next place to look 
(if possible).


Sorry I don't have any more definitive answers - please let me know if 
any of the above helps.


Best wishes

Peter

On 17/01/16 18:36, Rathert, Philipp, Dr. wrote:

Dear All,


We are running a local docker-galaxy-stable instance on a Mac OS X
system. and observe a strange error:


CEAS
Description:
Revision:f411ce97a351

is not installing correctly.

After installing mysql-python in the container directly basically every
package is installed:

Installed tool dependencies/ - click the name to browse the dependency
installation directory/
NameVersion TypeInstallation status
R

3.1.2   package Installed
ucsc_fetchChromSizes

1.0 package Installed
python_mysqldb

1.2.5   package Installed
bx_python

0.7.1   package Installed


Missing tool dependencies/ - click the name to install the missing
dependency/
NameVersion TypeInstallation status
cistrome_ceas

1.0.2.d8c0751   package Error



cistrome_ceas

1.0.2.d8c0751   package Error
The installation directory for this tool dependency had contents but the 
database had no record. The installation log may show this tool dependency to 
be correctly installed, but due to the missing database record it is now being 
set to Error.



A reinstall results in the same error on different dependencies and it
looks like a random event.


Does anybody have an idea what could solve the issue?


I hope I provided enough information. In your answer please keep in mind
I am a newcomer to all this and a wet lab scientist.


Thank you for your help.


Cheers,


philipp



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--
Peter Briggs peter.bri...@manchester.ac.uk
Bioinformatics Core Facility University of Manchester
B.1083 Michael Smith Bldg Tel: (0161) 2751482
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Re: [galaxy-dev] python_mysqldb caused zip_safe flag not set

2016-01-19 Thread Peter Briggs 

Hello Mic

Apologies, I missed your post the first time around - I didn't pick up 
that it was related to my 'ceas' tool. However the error you reported 
sounds superficially similar to that reported by Philipp Rather. Did you 
manage to resolve the problem yourself?


If not (and if you're still interested in using the tool) then I'd first 
suggest trying to install the version from the main toolshed and seeing 
if you get the same error. (I don't think that the 'zip_safe flag not 
set' message in the INSTALLATION.log file is the problem as I also see 
this message in the STDERR section for successful installs.)


Best wishes

Peter

On 10/11/15 01:47, Mic wrote:

Hello,
I tried to install CEAS from testtoolshed, but I have recieved the below
error from python_mysqldb
(tool_dependency/python_mysqldb/1.2.5/pjbriggs/ceas/82df5af2995f)

The installation directory for this tool dependency had contents but the
database had no record. The installation log may show this tool
dependency to be correctly installed, but due to the missing database
record it is now being set to Error.

I installed MariaDB 10.1 on Ubuntu 14.04 in the following way:

apt-key adv --recv-keys --keyserver hkp://keyserver.ubuntu.com:80
 0xcbcb082a1bb943db
add-apt-repository 'deb [arch=amd64,i386]
http://mirror.aarnet.edu.au/pub/MariaDB/repo/10.1/ubuntu trusty main'
apt-get update
apt-get install mariadb-server libmariadbclient-dev

The INSTALLATION.log shows the following information:
...
byte-compiling build/bdist.linux-x86_64/egg/MySQLdb/cursors.py to
cursors.pyc
creating stub loader for _mysql.so
byte-compiling build/bdist.linux-x86_64/egg/_mysql.py to _mysql.pyc
creating build/bdist.linux-x86_64/egg/EGG-INFO
copying MySQL_python.egg-info/SOURCES.txt ->
build/bdist.linux-x86_64/egg/EGG-INFO
copying MySQL_python.egg-info/dependency_links.txt ->
build/bdist.linux-x86_64/egg/EGG-INFO
copying MySQL_python.egg-info/top_level.txt ->
build/bdist.linux-x86_64/egg/EGG-INFO
writing build/bdist.linux-x86_64/egg/EGG-INFO/native_libs.txt
creating dist
removing 'build/bdist.linux-x86_64/egg' (and everything under it)
Creating
/home/lorencm/galaxy/tool_dependency/python_mysqldb/1.2.5/pjbriggs/ceas/82df5af2995f/lib/python/site.py
Processing MySQL_python-1.2.5-py2.7-linux-x86_64.egg
Copying MySQL_python-1.2.5-py2.7-linux-x86_64.egg to
/home/lorencm/galaxy/tool_dependency/python_mysqldb/1.2.5/pjbriggs/ceas/82df5af2995f/lib/python
Adding MySQL-python 1.2.5 to easy-install.pth file

Installed
/home/lorencm/galaxy/tool_dependency/python_mysqldb/1.2.5/pjbriggs/ceas/82df5af2995f/lib/python/MySQL_python-1.2.5-py2.7-linux-x86_64.egg
Processing dependencies for MySQL-python==1.2.5
Finished processing dependencies for MySQL-python==1.2.5
#

#

  export
PYTHONPATH=$PYTHONPATH:/home/lorencm/galaxy/tool_dependency/python_mysqldb/1.2.5/pjbriggs/ceas/82df5af2995f/lib/python
&&
  python setup.py install --install-lib
/home/lorencm/galaxy/tool_dependency/python_mysqldb/1.2.5/pjbriggs/ceas/82df5af2995f/lib/python
--install-scripts
/home/lorencm/galaxy/tool_dependency/python_mysqldb/1.2.5/pjbriggs/ceas/82df5af2995f/bin
STDERR
zip_safe flag not set; analyzing archive contents...

What did I miss?

Thank you in advance.

Mic



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--
Peter Briggs peter.bri...@manchester.ac.uk
Bioinformatics Core Facility University of Manchester
B.1083 Michael Smith Bldg Tel: (0161) 2751482
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