Running jobs as real user and extra_file_path
by Louise-Amélie Schmitt
Hi everyone,
I just wanted to ask how the extra_file_path is handled in case of job
running as the real user since the file_path is only writable by the
galaxy user. Any clue?
Thanks,
L-A
2 years, 2 months
Python script can't can't import BioPython modules in Galaxy 16.01
by Makis Ladoukakis
Hello everyone,
I've recently upgraded to Galaxy 16.01 and i have some issues with a python wrapper from a tool. When I run it via Galaxy I get the following error:
Traceback (most recent call last):
File "/home/galaxy_user/galaxy/tools/myTools/know_parser/know_parser.py", line 12, in <module>
from Bio import SeqIO
ImportError: No module named Bio
However when I click on the "view details" icon to copy the command from the tool and run it on my command line the tool works perfectly. In addition this issue occurs while I already have installed BioPython.
When I type Python and write "from Bio import SeqIO" I get no error.
Can this be an issue related to the virtual environment that is initialized each time Galaxy starts?
Thank you in advance,
Makis Ladoukakis
2 years, 6 months
Python ValueError: too many values to unpack
by Matthias De Smet
Hi all,
I’m trying to develop a tool that lets you select a file on the server. I’m using the dynamic_options setting to let Galaxy render a dropdown list of available file.
However, when I try to test the tool in its current form, I get the following error:
<pre>
galaxy.web.framework.decorators ERROR 2016-01-26 13:08:35,649 Uncaught exception in exposed API method:
Traceback (most recent call last):
File "lib/galaxy/web/framework/decorators.py", line 260, in decorator
rval = func( self, trans, *args, **kwargs)
File "lib/galaxy/webapps/galaxy/api/tools.py", line 98, in build
return tool.to_json(trans, kwd.get('inputs', kwd))
File "lib/galaxy/tools/__init__.py", line 2602, in to_json
populate_state(trans, self.inputs, state_inputs, state_errors, params.__dict__)
File "lib/galaxy/tools/__init__.py", line 2471, in populate_state
state[input.name] = input.get_initial_value(trans, context, history=history)
File "lib/galaxy/tools/parameters/basic.py", line 984, in get_initial_value
value = [ optval for _, optval, selected in options if selected ]
ValueError: too many values to unpack
</pre>
My tool xml looks like this:
<pre>
<tool id="archivetolibrary" name="Copy files" version="0.1.0">
<description>from the archive to a data library</description>
<code file="list_files.py"/>
<command interpreter="bash">
test.sh > $log
</command>
<inputs>
<param name="archive_source" type="select" display="radio" label="Choose source archive">
<options from_file="archives.loc">
<column name="name" index="0"/>
<column name="value" index="1"/>
</options>
</param>
<param name="query" type="text" label="Search for files"/>
<param name="selected_file" type="select" label="Choose your file" dynamic_options="list_files(archive_source,query)"/>
</inputs>
<outputs>
<data name="log" format="txt" label="${tool.name} on ${on_string}"></data>
</outputs>
<tests>
<test>
</test>
</tests>
<help>
This tool copies data from and archive folder to your history. Keep in mind this folder MUST be readable by Galaxy in order for this tool to work.
</help>
</tool>
</pre>
and the script called in the “code” tag looks like this
<pre>
def list_files(dir,query): listing=[]
for fname in listdir(dir):
fullpath = path.join(dir, fname) #only select datafiles, not md5 checksums
if path.isfile(fullpath) and not fullpath.endswith(".md5"):
listing.append( fname )
return listing
</pre>
This script should return a list with filenames that should be displayed in the dropdown list.
I’m tracking Galaxy release 15.10, running on a Ubuntu 14.04.3 server
Thanks for your help!
Matthias
2 years, 9 months
workflow import error
by Tony Schreiner
We have 2 galaxy instances running
one is
v15.05-74-gf6b894a
the other is
v15.10-30-g6a47d2d
a user is trying to import a workflow file, it works on the older one, but
raises an error on the newer one.
URL: http://redacted.edu:8080/workflow/import_workflow
<http://prince.bc.edu:8080/workflow/import_workflow>
File '/cluster/home/galaxy/galaxy/lib/galaxy/web/framework/middleware/error.py',
line 151 in __call__
app_iter = self.application(environ, sr_checker)
File '/cluster/home/galaxy/galaxy/eggs/Paste-1.7.5.1-py2.7.egg/paste/recursive.py',
line 84 in __call__
return self.application(environ, start_response)
File '/cluster/home/galaxy/galaxy/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpexceptions.py',
line 633 in __call__
return self.application(environ, start_response)
File '/cluster/home/galaxy/galaxy/lib/galaxy/web/framework/base.py', line
133 in __call__
return self.handle_request( environ, start_response )
File '/cluster/home/galaxy/galaxy/lib/galaxy/web/framework/base.py', line
191 in handle_request
body = method( trans, **kwargs )
File '/cluster/home/galaxy/galaxy/lib/galaxy/webapps/galaxy/controllers/workflow.py',
line 921 in import_workflow
workflow, missing_tool_tups = self._workflow_from_dict( trans, data,
source=src, add_to_menu=add_to_menu )
File '/cluster/home/galaxy/galaxy/lib/galaxy/web/base/controller.py', line
1111 in _workflow_from_dict
publish=publish
File '/cluster/home/galaxy/galaxy/lib/galaxy/managers/workflows.py', line
159 in build_workflow_from_dict
module, step = self.__module_from_dict( trans, step_dict, secure=False )
File '/cluster/home/galaxy/galaxy/lib/galaxy/managers/workflows.py', line
605 in __module_from_dict
module.save_to_step( step )
File '/cluster/home/galaxy/galaxy/lib/galaxy/workflow/modules.py', line 592
in save_to_step
step.tool_inputs = self.tool.params_to_strings( self.state.inputs,
self.trans.app )
File '/cluster/home/galaxy/galaxy/lib/galaxy/tools/__init__.py', line 1980
in params_to_strings
return params_to_strings( self.inputs, params, app )
File '/cluster/home/galaxy/galaxy/lib/galaxy/tools/parameters/__init__.py',
line 92 in params_to_strings
value = params[ key ].value_to_basic( value, app )
File '/cluster/home/galaxy/galaxy/lib/galaxy/tools/parameters/grouping.py',
line 574 in value_to_basic
rval[ self.test_param.name ] = self.test_param.value_to_basic( value[
self.test_param.name ], app )
KeyError: 'uncol'
i'm not able conclude much from this dump. Can anyone suggest some steps to
debug this.
Cheers
Tony Schreiner
2 years, 9 months
Re: [galaxy-dev] how to create users through Galaxy API?
by Martin Čech
Hi,
you specify username, password and email in the body (payload) of the POST
as Key:Value pairs.
Code from the API method: (
https://galaxy-central.readthedocs.org/en/latest/_modules/galaxy/webapps/...)
username = payload[ 'username' ] email = payload[ 'email' ] password =
payload[ 'password' ]
There are also other conditions that need to be fulfilled (e.g. user
creation has to be turned on in the configuration) - you will find these
when you look at the source code of the method (because the documentation
is not perfect yet, sorry).
M.
On Sun, Dec 29, 2013 at 11:22 PM, xlwang <xlwang_0903(a)163.com> wrote:
> hi,
> I still have some confusion.
> post /api/users , when i use postman, it seems like this:
>
>
> No other parameters? How to confirm the new user's information?Such as
> user name, password.
> Can you give me a example please?Thank you!
>
> At 2013-12-30 06:04:15,"Martin Čech" <marten(a)bx.psu.edu> wrote:
>
> Hello,
>
> to create a user through API you send a POST request to /api/users
>
> More information about User API here:
>
>
> https://galaxy-central.readthedocs.org/en/latest/lib/galaxy.webapps.galax...
>
> Martin
>
>
> On Fri, Dec 27, 2013 at 5:11 AM, xlwang <xlwang_0903(a)163.com> wrote:
>
>> hello,
>> I want to create users through Galaxy API.For example, I can get users
>> information through url like this(use postman):
>> http://localhost:8080/api/users?key=my_key
>> But how to create a user?
>>
>>
>>
>> ___________________________________________________________
>> 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/
>>
>
>
>
>
2 years, 10 months
Error running JBrowse
by Raymond Wan
Dear all,
I'm trying to run the JBrowse tool within Galaxy. The installation
was fine (I think), but when I run the tool, I get this error:
Fatal error: Exit code 1 () Traceback (most recent call last): File
"/d15/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/d022577ff9cf/jbrowse/jbrowse.py",
line 11, in <module> from Bio.Data import CodonTable ImportError: No
module named
Does this mean I'm missing something?
In the history, if I click the "(i)" icon for the incomplete job (in
red), everything looks fine, except that it says:
Tool Version: python: can't open file 'jbrowse.py': [Errno 2] No such
file or directory
However, "jbrowse.py" does exist in the path above. Any idea what
could be wrong?
Thank you!
Ray
2 years, 11 months
Amazon Instance Types for Galaxy
by Lapointe, David
Are there instance types which will not work for Galaxy/Cloudman on AWS? EBS volumes for example.
Thanks,
David
--
David Lapointe Ph.D.
Sr. Bioinformatics Specialist
Research Technology (RT)
Tufts Technology Services (TTS)
16 Dearborn Road
Somerville MA 02144
Phone: 617-627-5319
Fax: 617-627-3667
http://it.tufts.edu
3 years
Python tool wrapper with multiple input and output files
by Marco Tangaro
Dear experts,
my name is Marco and I'm working to port our python tool to the Galaxy
framework.
The main script needs a rna.bam file as input, a reference fasta file, both
mandatory. Finally, you can add a dna.bam file, but this is optional.
Therefore an example command is:
script.py -i rna.bam -f reference.fa -j dna.bam
The outout is a tabular.
Again the -j dna.bam option is completely optional.
So quite soon it turned out that I had to use a python wrapper to parse our
script. Now the wrapper works fine.
The next step is to run the tool over multiple input file and we would like
to avoid to use a workflow.
The idea is that to each input file corresponds an output file. The
reference is still the same.
For instance, we have:
rna_1.bam + dna_1.bam -> output_1.txt
rna_2.bam + dna_2.bam -> output_2.txt
rna_3.bam + dna_3.bam -> output_3.txt
...
and so on.
But I don't know the best strategy to give to my wrapper multiple input
files.
Moreover I have to be sure, when the dna_xyz.bam files are uploaded, that
they correspond to the right rna_xyz.bam file.
I would like to have as output a page which is showing as results the link
to the single output files as suggested here.
https://wiki.galaxyproject.org/Admin/Tools/Multiple%20Output%20Files
planning to integrate a javascript interface.
I've browsed a lot, but on multiple input file the posts are old.
I'm using the last galaxy release (16_04).
I'm quite new to the galaxy world...
Thanks a lot for your suggestions,
Marco
3 years
Auto detection of output format Galaxy custom tool
by Katherine Beaulieu
Hi everyone,
I am looking to auto-detect the file format of a file outputted by a python
tool I have written. Does anyone have any idea how to do this? I have tried
setting the format attribute to "auto" with no luck. Let me know if you
would like to see my tool config file.
Cheers,
Katherine
3 years
Implementing iRODS with Galaxy
by Yip, Miu ki
Hello Galaxy Team,
We're from the Bioinformatics Shared Resources (BSR) at Cold Spring Harbor Labs and we're looking to implement irods on a newly installed version of Galaxy.
We want to incorporate iRODS (http://irods.org/). Is there a recommended way to do this, or no?
Thanks in advance for the advice.
Best,
Miuki Yip
3 years
