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
3 years, 2 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/
>>
>
>
>
>
3 years, 10 months
error loading files into galaxy
by Hakeem Almabrazi
Hi,
I started getting the following error whenever I try to load a file into Galaxy local.
Traceback (most recent call last):
File "/usr/local/galaxy/galaxy-dist/tools/data_source/upload.py", line 8, in <module>
from galaxy import eggs
ImportError: cannot import name eggs
I will appreciate if someone can tell me what could happen to cause such issue and how to resolve it.
Regards,
4 years, 4 months
Upload issue in local installation
by Batsal Devkota
I installed galaxy locally in a linux server. However, I cannot upload the files (no matter how small, I have tried few kb size fasta files). When I try to upload, the link to the file shows up in the History and gets a new number (purple box). When I click on the link I get 'Dataset is uploading' forever.
In the terminal window where I start galaxy, I get the following error report:
92.17.41.13 - - [02/Aug/2012:15:33:32 -0400] "GET / HTTP/1.1" 200 - "-" "Mozilla/5.0 (Windows NT 5.2; rv:13.0) Gecko/20100101 Firefox/13.0.1"
92.17.41.13 - - [02/Aug/2012:15:33:32 -0400] "GET /root/tool_menu HTTP/1.1" 200 - "http://redhat:8080/" "Mozilla/5.0 (Windows NT 5.2; rv:13.0) Gecko/20100101 Firefox/13.0.1"
92.17.41.13 - - [02/Aug/2012:15:33:32 -0400] "GET /history HTTP/1.1" 200 - "http://redhat:8080/" "Mozilla/5.0 (Windows NT 5.2; rv:13.0) Gecko/20100101 Firefox/13.0.1"
92.17.41.13 - - [02/Aug/2012:15:33:33 -0400] "POST /root/user_get_usage HTTP/1.1" 200 - "http://redhat:8080/history" "Mozilla/5.0 (Windows NT 5.2; rv:13.0) Gecko/20100101 Firefox/13.0.1"
92.17.41.13 - - [02/Aug/2012:15:33:40 -0400] "GET /tool_runner?tool_id=upload1 HTTP/1.1" 200 - "http://redhat:8080/root/tool_menu" "Mozilla/5.0 (Windows NT 5.2; rv:13.0) Gecko/20100101 Firefox/13.0.1"
92.17.41.13 - - [02/Aug/2012:15:33:59 -0400] "POST /tool_runner/upload_async_create HTTP/1.1" 200 - "http://redhat:8080/" "Mozilla/5.0 (Windows NT 5.2; rv:13.0) Gecko/20100101 Firefox/13.0.1"
92.17.41.13 - - [02/Aug/2012:15:33:59 -0400] "GET /tool_runner/upload_async_message HTTP/1.1" 200 - "http://redhat:8080/" "Mozilla/5.0 (Windows NT 5.2; rv:13.0) Gecko/20100101 Firefox/13.0.1"
92.17.41.13 - - [02/Aug/2012:15:33:59 -0400] "GET /history HTTP/1.1" 200 - "http://redhat:8080/tool_runner/upload_async_message" "Mozilla/5.0 (Windows NT 5.2; rv:13.0) Gecko/20100101 Firefox/13.0.1"
92.17.41.13 - - [02/Aug/2012:15:33:59 -0400] "POST /root/user_get_usage HTTP/1.1" 200 - "http://redhat:8080/history" "Mozilla/5.0 (Windows NT 5.2; rv:13.0) Gecko/20100101 Firefox/13.0.1"
92.17.41.13 - - [02/Aug/2012:15:34:04 -0400] "POST /root/history_item_updates HTTP/1.1" 200 - "http://redhat:8080/history" "Mozilla/5.0 (Windows NT 5.2; rv:13.0) Gecko/20100101 Firefox/13.0.1"
92.17.41.13 - - [02/Aug/2012:15:34:08 -0400] "POST /root/history_item_updates HTTP/1.1" 200 - "http://redhat:8080/history" "Mozilla/5.0 (Windows NT 5.2; rv:13.0) Gecko/20100101 Firefox/13.0.1"
The last line keeps going for ever... writes new line every 4 secs.
I am stuck and don't know where to look. Please help.
Batsal.
4 years, 5 months
Rename output from a repeat
by Ulf Schaefer
Hi all
We frequently use the syntax below to rename outputs of workflows that
we run in batch. It is convenient to have sample names from fastqs
carried over to sams, bams, vcfs, etc.
#{input1 | basename}.bam
This does not seem to be working for inputs that are in repeats, e.g.
the VelvetOptimiser. Does anybody know if there is a syntax to make this
work, maybe
#{repeatname[0].input1 | basename}.bam ?
Thanks a lot for your help
Ulf
**************************************************************************
The information contained in the EMail and any attachments is confidential and intended solely and for the attention and use of the named addressee(s). It may not be disclosed to any other person without the express authority of Public Health England, or the intended recipient, or both. If you are not the intended recipient, you must not disclose, copy, distribute or retain this message or any part of it. This footnote also confirms that this EMail has been swept for computer viruses by Symantec.Cloud, but please re-sweep any attachments before opening or saving. http://www.gov.uk/PHE
**************************************************************************
4 years, 10 months
Object-Store, setting filetypes crashes Galaxy
by bjoern.gruening＠googlemail.com
Hi,
I have configured to use the hierarchical object store but as soon as I try
to reset the filetpye of a dataset Galaxy is crashing with:
galaxy.objectstore DEBUG 2014-06-12 14:39:21,180 Using preferred backend
'files3' for creation of MetadataFile 5963
132.230.153.57 - - [12/Jun/2014:14:39:20 +0200] "POST
/datasets/966f24627ef70c12/edit HTTP/1.1" 500 - "
http://galaxy.uni-freiburg.de/datasets/966f24627ef70c12/edit" "Mozilla/5.0
(X11; Linux x86_64; rv:29.0) Gecko/20100101 Fire
fox/29.0"
Error - <type 'exceptions.OSError'>: [Errno 2] No such file or directory:
'database/tmp/metadata_temp_file_1xnGcE'
URL: http://galaxy.uni-freiburg.de/datasets/966f24627ef70c12/edit
File
'/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/middleware/error.py',
line 149 in __call__
app_iter = self.application(environ, sr_checker)
File
'/usr/local/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/recursive.py',
line 84 in __call__
return self.application(environ, start_response)
File
'/usr/local/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpexceptions.py',
line 633 in __call__
return self.application(environ, start_response)
File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line
132 in __call__
return self.handle_request( environ, start_response )
File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line
190 in handle_request
body = method( trans, **kwargs )
File
'/usr/local/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/dataset.py',
line 295 in edit
trans.app.datatypes_registry.set_external_metadata_tool.tool_action.execute(
trans.app.datatypes_registry.set_external_metadata_tool, trans, incoming =
{ 'input1':data }, overwrite = False ) #overwrite is False as per existi
ng behavior
File '/usr/local/galaxy/galaxy-dist/lib/galaxy/tools/actions/metadata.py',
line 18 in execute
overwrite, history, job_params )
File '/usr/local/galaxy/galaxy-dist/lib/galaxy/tools/actions/metadata.py',
line 79 in execute_via_app
kwds = { 'overwrite' : overwrite } )
File '/usr/local/galaxy/galaxy-dist/lib/galaxy/datatypes/metadata.py', line
717 in setup_external_metadata
shutil.copy( dataset.metadata.get( meta_key, None ).file_name,
metadata_temp.file_name )
File '/usr/local/galaxy/galaxy-dist/lib/galaxy/datatypes/metadata.py', line
575 in file_name
self._filename = abspath( tempfile.NamedTemporaryFile( dir =
self.tmp_dir, prefix = "metadata_temp_file_" ).name )
File '/usr/local/python/2.7/lib/python2.7/tempfile.py', line 454 in
NamedTemporaryFile
(fd, name) = _mkstemp_inner(dir, prefix, suffix, flags)
File '/usr/local/python/2.7/lib/python2.7/tempfile.py', line 235 in
_mkstemp_inner
fd = _os.open(file, flags, 0600)
OSError: [Errno 2] No such file or directory:
'database/tmp/metadata_temp_file_1xnGcE'
I have attached my object_store_conf.xml file.
Thanks,
Bjoern
4 years, 11 months
Parallelism using metadata
by Marco Albuquerque
Hello Galaxy Dev,
I have a question regarding parallelism on a BAM file.
I have currently implemented 3 split options for the BAM datatype
1) by_rname -> splits the bam into files based on the chromosome
2) by_interval -> splits the bam into files based on a defined bp length,
and does so across the entire genome present in the BAM file
3) by_read -> splits the bam into files based on the number of reads
encountered (if multiple files, all other files match the interval as the
first)
Now, as you can imagine, reading and writing large BAM files is a pain, and
I personally think this is not the best solution for Galaxy.
What I was hoping to implement (but don't know how) is to create a new
metadata option in bam (bam.metadata.bam_interval) which would generate the
interval without creating a new file (essentially, I would create a symbolic
link to the old large file, and then update the metadata.bam_interval, this
would contain some string of the form chrom:start-end which could then be
used in a variety of tools which accept an interval as an option (for
example samtools view))
This would be far more efficient then my first implementation, but the thing
I don't know how to do is specify some kind of metadata at the split level.
I was hoping maybe you could direct me to an example that does this?
I have added the following to my metadata.py file:
class IntervalParameter( MetadataParamter )
def __init__( self, spec ):
MetadataParamter.__init__( self, spec ):
self.rname = self.spec.get( "rname" )
self.start = self.spec.get( "start" )
self.end = self.spec.get( "end" )
def to_string(self):
if self.rname = 'all':
return ''
else:
return ''.join([self.rname, ':', self.start, '-', self.end])
And the following to my binary.py file:
### UNDER THE BAM CLASS
MetadataElement( name="bam_interval", desc="BAM Interval",
param=metadata.IntervalParameter, rname="all", start="", end="",
visible=False, optional=True)
I somehow want rname="all" to be the default, but upon parallelism, I want
to be able to adjust this parameter in the split functions.
So,
<parallelism method="multi" split_inputs="normal,tumour"
split_mode="by_interval" split_size="50000000" merge_outputs="output"/>
Would actually change the metadata of each file, and not create sub-bams.
PLEASE HELP!!!
Marco
5 years
Strange repository dependency behavior with toolshed-installed naive_variant_caller
by Brian Claywell
First, I'm at a bit of a loss to even describe what's going on, so I
apologize in advance for a rambling bug report. Please bear with me!
The naive_variant_caller tool was failing on our instance with "Failed to
resolve dependency" errors on numpy, pyBamParser, and pyBamTools, despite
the tool dependencies and their respective dependency packages being
installed.
I attempted to use the "repair repository" action on naive_variant_caller
with no success. I then uninstalled naive_variant_caller,
package_numpy_1_7, package_pybamparser_0_0_1, and package_pybamtools_0_0_1
and attempted to reinstall naive_variant_caller from scratch, again
allowing Galaxy to manage the dependencies.
This time, the dependencies resolved (at least as far as the "Building
dependency shell command" messages were concerned), but
naive_variant_caller still failed, this time with an import error:
ImportError: No module named pyBamTools.genotyping.naive
Digging around a little I found that the env.sh that was sourced for
pyBamTools was looking for an env.sh in another pyBamTools revision
directory, but the revision it was looking for didn't exist.
Then I looked in the admin interface and saw that package_pybamtools_0_0_1
and package_pybamparser_0_0_1 were each installed twice; each had both the
most recent revision and an older revision with the "updates are available"
icon.
At this point I uninstalled naive_variant_caller and all of its dependency
packages again. I then installed naive_variant_caller from the toolshed
*without* dependency management, and manually installed the required
revisions of numpy, pybamparser, and pybamtools. Finally
naive_variant_caller started working.
However, naive_variant_caller is now shown in the admin interface as
"Installed, missing repository dependencies", and the installed repository
page shows that the dependencies are a very strange state (see attached
screenshot). That is, the same revision of numpy is listed as installed
twice, and the pybamparser and pybamtools dependencies are each listed as
simultaneously installed and uninstalled.
Can anyone shed some light on what could be happening and what to do about
it? Is there some external way to verify the consistency of a tool and its
dependencies?
Thanks!
Cheers,
Brian
--
Brian Claywell | programmer/analyst
Matsen Group | http://matsen.fredhutch.org <http://matsen.fhcrc.org/>
Fred Hutchinson Cancer Research Center
5 years
Announcement: Galaxy Docker Image 15.03
by Björn Grüning
Hi all!
We are proud to present you the next release of Galaxy Docker.
https://github.com/bgruening/docker-galaxy-stable
https://registry.hub.docker.com/u/bgruening/galaxy-stable/
A few highlights:
* based on Galaxy 15.03, with all it's new awesome features
* Docker image is now based on Ubuntu 14.04
* move all required Galaxy dependencies to toolshed/requirements
* use Ansible roles to build large parts of the image
* export the supervisord web-interface (port 9002)
* enable Galaxy reports webapp on GALAXY_URL/reports
* enable/disable services like FTP or Galaxy reports during start-up
The IPython integration was also updated and has a few new libraries to
make it more convenient for R users.
A big thanks to John Chilton for his enormous support and constant input.
The following new releases are available:
* docker pull bgruening/galaxy-stable:latest_2015.01.13
* docker pull bgruening/galaxy-stable:15.03
* docker pull bgruening/galaxy-stable (-> currently 15.03)
As usual feedback is more than welcome!
Cheers,
Bjoern
5 years, 2 months
Re: [galaxy-dev] Tool param type "library_data" (Dooley, Damion)
by Dooley, Damion
I was successful getting library dataset selection and form submission to happen within tool form tool form input <param type="library_data" ...> - Yay! But it appears one last fix (besides the "url: "/visualization/list_libraries",' bug) is needed to enable history tool item to be RERUN.
So if a galaxy dev can tackle this, great! Otherwise I'll have to drop this approach :<(
*****************
For others who may need...
tool form's param:
<param name="library_datasets" type="library_data" label="Reference Bin file" help="Select one reference bin at a time from the popup window's Reference Bin library."/>
<command> tag contents....
#if $library_datasets
-B "
#for $i, $dataset in enumerate($library_datasets)
#$dataset.get_file_name()
$dataset.id
#end for
"
#end if
Successfully submits either the full file path of selected dataset, or its id.
*****************
However trying to rerun this history tool item gets us an error (not related to the above <command> contents):
Error Traceback:
View as: Interactive | Text | XML (full)
⇝ AttributeError: 'int' object has no attribute 'id'
....
Module galaxy.tools.parameters.basic:146 in value_to_basic view
>> return self.to_string( value, app )
Module galaxy.tools.parameters.basic:2406 in to_string
app <galaxy.app.UniverseApplication object at 0x59a0710>
ldda 331
self <galaxy.tools.parameters.basic.LibraryDatasetToolParameter object at 0x7fced01d2090>
value [331]
>> return [ldda.id for ldda in value]
AttributeError: 'int' object has no attribute 'id'
which is in /lib/galaxy/tools/parameters/basic.py:
class LibraryDatasetToolParameter( ToolParameter ):
"""
Parameter that lets users select a LDDA from a modal window, then use it within the wrapper.
"""
...
def to_string( self, value, app ):
if not value:
return value
return [ldda.id for ldda in value]
"Value" is getting an array of dataset ids, whereas this method is expecting value to be a list of dataset objects. I tried changing ldda.id to just "id" but found other parts of LibraryDatasetTool code were broken as they too were expecting an object. Maybe this is related to the tool job's history detail link showing "Reference Bin file" as a string label of an object?:
Input Parameter Value Note for rerun
BLAST results as XML 240: megablast Pasted Entry vs 16SMicrobial.fasta
Reference Bin file [<galaxy.model.LibraryDatasetDatasetAssociation object at 0x7fcee04d4350>]
Tabular Report Column Labels Short name
HTML Report template templates.html_report
********************************
The other bug:
2) Tool_form.mako has a hardcoded url that doesn't work for galaxy installs that have a prefix so that needs adjustment:
$(".add-librarydataset").click(function() {
var link = $(this);
$.ajax({
url: "/visualization/list_libraries",
5 years, 2 months
