you specify username, password and email in the body (payload) of the POST
as Key:Value pairs.
Code from the API method: (
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).
On Sun, Dec 29, 2013 at 11:22 PM, xlwang <xlwang_0903(a)163.com> wrote:
> 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:
> to create a user through API you send a POST request to /api/users
> More information about User API here:
> On Fri, Dec 27, 2013 at 5:11 AM, xlwang <xlwang_0903(a)163.com> wrote:
>> I want to create users through Galaxy API.For example, I can get users
>> information through url like this(use postman):
>> 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:
>> To search Galaxy mailing lists use the unified search at:
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.
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:
18.104.22.168 - - [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"
22.214.171.124 - - [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"
126.96.36.199 - - [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"
188.8.131.52 - - [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"
184.108.40.206 - - [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"
220.127.116.11 - - [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"
18.104.22.168 - - [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"
22.214.171.124 - - [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"
126.96.36.199 - - [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"
188.8.131.52 - - [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"
184.108.40.206 - - [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.
> From: Cristian Alejandro Rojas <alejandro.0317(a)gmail.com>
> Date: December 26, 2013 2:37 AM
> To: galaxy-dev(a)lists.bx.psu.edu
> Subject: [galaxy-dev] Some plugin for digital normalization
> Hello all,
> I've been searching in tool sheds(main and test) for a plugin to do
digital normalization of reads, for example Trinity has one script to do
this (./util/normalize_by_kmer_coverage.pl), diginorm is another
> Do you know if there is a galaxy tool ready for this work or should I
develop my own?
I am actively working on a wrapper for normalize-by-median.py and the other
tools in the khmer suite.
It requires some changes on our end which you can track here:
You can install this branch of khmer via pip
pip install -e email@example.com:ged-lab/khmer.git@output_naming1#egg=khmer
or if you don't have a github account:
pip install -e git+
(Instructions on installing using a virtualenv or on OS X are at:
https://khmer.readthedocs.org/en/latest/install.html just substitute in the
pertinent pip line from above)
I haven't tested it much; doing so is the top of my to-do list for the rest
of this week. If you or anyone else is feeling adventurous I would be happy
to have the feedback.
Michael R. Crusoe: Software Engineer and Bioinformatician mcrusoe(a)msu.edu
@ the Genomics, Evolution, and Development lab; Michigan State University
I have a tool wrapper with a <param> of type="data".
Currently, this renders as a text box with a drop down list that has
52 items in it (the number of things I have in my history, I guess).
I'd like to filter this list so that only some items in the history
(in my case any item whose name ends with '.rda') are shown in this
It seems like maybe the 'format' parameter to the 'param' tag is what
I want, but:
1) I tried format="rda" and that didn't seem to change anything.
2) "rda" is not in the datatypes.conf file which the documentation
suggests is required?
(.rda is an extension used for serialized R objects.)
The tool I'm working on only accepts rda files as input and the reason
I'm asking for this is that it is all too easy to accidentally feed it
a file of some other type. If the dropdown could be filtered so that
only items which will work with the tool are shown, that would be
Is there a way to do that?
Looking for pointers on what might be causing this problem:
A user had a moderately complicated workflow that when run under certain parameter values results in a traceback that ends:
Module workflow_run_mako:232 in render_body
>> for ic in oc.input_step.module.get_data_inputs():
AttributeError: 'WorkflowStep' object has no attribute 'module'
After some puzzling, I realized one of the parameters was outside the allowed range (a max on an integer param) and that Galaxy was trying to render "run.mako" flagging up the error but erroring out. Why Galaxy tries to call this non-existent member is unclear to me. Any insight or places I should start exploring?
Galaxy version: various (started with an 6-month old one, upgraded to latest production to see if it would fix error, it didn't)
Hosting OS: CentOS 6
Paul Agapow (paul-michael.agapow(a)hpa.org.uk)
Bioinformatics, Health Protection Agency (UK)
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I would like to use bioblend to export the result of a galaxy workflow.
To do that, we want to use an implemented tool called export_data; which
enables the copy of a result file from galaxy arborescence to a local
directory which belong to the user making the analysis and the export.
We tried to launch this tool using the run_tool function but it doesn't
I get an error message which is very long and attached to this email.
Please help me on that it is the final step of several ones using bioblend.
Have a nice day,
Olivia Doppelt-Azeroual, PhD
Tel: 92 15
CIB - Institut Pasteur
Thank you for your answer and for trying to help. This is greatly
I didn't really made any progress in tracking down this error, and
hopefully this weird behaviour will not happen anymore with the November
But here are my answers to your questions, in case it would ring a bell:
Has this behaviour been reported with any other workflow?
It has been reported with 2 different workflows as of now. These 2
workflows doesn't have anything in common, except that they are huge (one
of them has 37 steps, producing a total of about 110 datasets).
Are you running Galaxy as a single process or multiple processes? If
multiple processes, how many web, handler and manager processes do you
have and are they all on the same machine?
We are running Galaxy in multiple processes with 5 web servers, 3 job
handlers and no manager (I believe the manager was rendered obsolete in
one of the latest Galaxy distributions). All these processes are run on
the same machine.
Have you made any modifications to Galaxy that could result in this
What is the value of track_jobs_in_database in your universe_wsgi.ini
We never touched this part of the configuration file and the line still
reads: "#track_jobs_in_database = None".
After reading your answer, I've decided to modify this line to:
"track_jobs_in_database = True"
Unfortunately, running one of the faulty workflows several times (5x), I
noticed that one of them was still showing this strange behaviour where
some jobs were executed before their inputs were ready.
Do you think this issue could be related to the fact that we are using
Galaxy with the multiple processes configuration? We implemented this
configuration some time ago because some of our users were complaining
about the slow responsiveness of the web interface.
Would you recommend using Galaxy without the multiple processes
configuration? (Lets say if updating to November 4th distribution doesn't
fix this issue)
I guess you are probably using the multiple processes configuration as
well on Galaxy main?
Thanks again for your help!
Posted by John Chilton on Nov 09, 2013; 2:50pm
Have you made any progress tracking down this error? This appears very
serious, but to tell you the truth I have no clue what could cause it. The
distribution you are using is pretty old at this point I feel like if it
was a bug the exhibited under relatively standard parameter combinations
someone else would have reported it by now.
Can you tell me some things: has this been reported with any other
workflows? Is there anything special about this workflow? Can you rebuild
the workflow and see if the error occurs again?
Additional questions if the problem is not restricted to the workflow:
are you running Galaxy as a single process or multiple processes? If
multiple processes, how many web, handler, and manager processes do you
have? Are they all on the same machine? Have you made any modifications to
Galaxy that could result in this behavior? What is the value of
track_jobs_in_database in your universe_wsgi.ini configuration file?
On Thu, Nov 7, 2013 at 10:34 AM, Jean-Francois Payotte <[hidden email]>
Dear Galaxy mailing-list,
Once again I come seeking for your help. I hope someone already had this
issue or will have an idea on where to look to solve it. :)
One of our users reported having workflows failing because some steps were
executed before all their inputs where ready.
You can find a screenshot attached, where we can see that step (42) "Sort
on data 39" has been executed while step (39) is still waiting to run
This behaviour has been reproduced with at least two different Galaxy
tools (one custom, and the sort tool which comes standard with Galaxy).
This behaviour seems to be a little bit random, as running two times a
workflow where this issue occurs, only one time did some steps were
executed in the wrong order.
I could be wrong, but I don't think this issue is grid-related as, from my
understanding, Galaxy is not using SGE job dependencies functionality.
I believe all jobs stays in some internal queues (within Galaxy) until all
input files are ready, and only then the job is submitted to the cluster.
Any help or any hint on what to look at to solve this issue would be
We have updated our Galaxy instance to August 12th distribution on October
1st, and I believe we never experienced this issue before the update.
Many thanks for your help,
I think one of the aspects where Galaxy is a bit soft is the ability to do
distributed tasks. The current system of split/replicate/merge tasks based
on file type is a bit limited and hard for tool developers to expand upon.
Distributed computing is a non-trival thing to implement and I think it
would be a better use of our time to use an already existing framework. And
it would also mean one less API for tool writers to have to develop for.
I was wondering if anybody has looked at Mesos (
http://mesos.apache.org/). You can see an overview of the Mesos
The important thing about Mesos is that it provides an API for C/C++,
Java/Scala and Python to write distributed frameworks. There are already
implementations of frameworks for common parallel programming systems such
- Hadoop (https://github.com/mesos/hadoop)
- MPI (
- Spark (http://spark-project.org)
And you can find example Python framework at
Integration with Galaxy would have three parts:
1) Add a system config variable to Galaxy called 'MESOS_URL' that is then
passed to tool wrappers and allows them to contact the local mesos
infrastructure (assuming the system has been configured) or pass a null if
the system isn't available.
2) Write a tool runner that works as a mesos framework to executes single
cpu jobs on the distributed system.
3) For instances where mesos is not available at a system wide level (say
they only have access to an SGE based cluster), but the user wants to run
distributed jobs, write a wrapper that can create a mesos cluster using the
existing queueing system. For example, right now I run a Mesos system under
the SGE queue system.
I'm curious to see what other people think.