I am using the most recent version of Galaxy. There seems to
be a bug in viewing the current (active) history when I
use prefix in galaxy input file.
Here is the detail:
When I do not use prefix, e.g., in /config/galaxy.in :
prefix = /
cookie_path = /
and run galaxy server, I can upload a file and I can see my
uploaded file in the current history even after I refresh
the web browser (e.g., close and reopen the web browser) which
seems to be working fine. However when I use prefix, e.g. in
prefix = /galaxy-1/
cookie_path = /galaxy-1/
then after I upload a file and refresh the browser I do not
see the uploaded file in the current (or active) history. It
always shows me a new (clean history). This is a problem
because I get a error which seems to be related to the
history when I attempt to run any workflow.
Any idea where the problem should be?
Please note that I use external authentication but it
shouldn't be matter because it is working when the prefix
Thanks a lot,
Simon Fraser University
Burnaby, British Columbia
Canada V5A 1S6
phone: 778 782-8860
fax: 778 782-4242
I am trying to setup job submission to pbs server running on our
I have python 2.7 installed in /usr/local along with easy_install. But
when trying to compile pbs_python I am getting following error:
[galaxy@galaxy galaxy-dist]$ LIBTORQUE_DIR=/usr/lib python
scripts/scramble.py -e pbs_python
fetch_one(): Trying to fetch:
fetch_one(): Fetched to:
unpack_source(): Unpacked to:
copy_build_script(): Using build
run_scramble_script(): Beginning build
Traceback (most recent call last):
File "scramble.py", line 14, in <module>
from scramble_lib import *
File "../../../lib/scramble_lib.py", line 146, in <module>
from setuptools import *
File "build/bdist.linux-x86_64/egg/setuptools/__init__.py", line 11,
File "build/bdist.linux-x86_64/egg/setuptools/extension.py", line 8,
File "build/bdist.linux-x86_64/egg/setuptools/dist.py", line 21, in
AttributeError: 'module' object has no attribute 'packaging'
Traceback (most recent call last):
File "scripts/scramble.py", line 50, in <module>
File "/home/galaxy/galaxy-dist/lib/galaxy/eggs/scramble.py", line 57,
File "/home/galaxy/galaxy-dist/lib/galaxy/eggs/scramble.py", line 210,
raise ScrambleFailure( self, "%s(): Egg build failed for %s %s" %
( sys._getframe().f_code.co_name, self.name, self.version ) )
galaxy.eggs.scramble.ScrambleFailure: run_scramble_script(): Egg build
failed for pbs_python 4.3.5
I also tried setuptools-18.0.1 installed in user's local path but I am
still getting the same error.
It is Centos 6.6 OS. Any help would be appreciated.
Zuzanna K. Filutowska, HPC Systems Administrator
Poznan Supercomputing and Networking Center
Institute of Bioorganic Chemistry Polish Academy of Sciences
Seize the day boys! Make your lifes extraordinary! --John Keating
I just started setting up a galaxy instance and I'm a bit stuck with
user account activation without e-mail. Is it possible to run Galaxy
without an SMTP server set?
For example, for the administrator user, I set:
admin_users = <my e-mail>
in galaxy.ini . I'd also like to require login (i.e., require_login =
True) but it seems that I can't do that from the outset. That has to
be False and allow_user_creation has to be True.
Then I can create a user with the same account as above, who will then
become an administrator. But, the account has to be validated some
how and I can't seem to figure out how to do that without enabling an
Am I doing something that wasn't intended? Perhaps I must have an
SMTP server set? Or are there other steps I should do to activate the
administrator? The web page
https://wiki.galaxyproject.org/Admin/GetGalaxy makes it look easy...so
I am concerned I'm doing it all wrong...
Also, if this instance will be a production system some day, should I
start using a database (Postgres or MySQL) right away and not bother
with the default SQLite? Otherwise, I will have to port the data
over, which the documentation implies is not an easy thing to do...
I am trying to develop a tool to untar, unzip... an archive file in
order to obtain each file contained in the archive as a dataset in the
My problem is about the unknown various number of files contained within
the archive file.
I was thinking about having an output variable in my .xml that would be
fed by my wrapper and returned in order to filter the number of outputs
in my .xml ; but the <output> section in the .xml can only get "files"
not numbers, right?
In my tool, I ask the user to fill the number of files he wants from the
in .xml I have put 10 outputs for files contained in the archive (out1,
out2...) precised in my command and in the output section (for now I can
retrieve maximum 10 outputs from my archive).
In the output section, I would like to use <filter> tag in order to
select only the output number inferior than the number specified by the
<filter>num_uncompressed_files >= "2"</filter>
It does not seem to work well. Could you please tell me if it is
possible to use the filter tag as such? If so, how?
Would you have a better idea to implement that tool?
Thanks in advance,
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I am trying to config a cluster galaxy server using PBS torque. I have
gone through the documentation but it is not clear to me how the
job_conf.xml should be set up. Are there detailed documents on how
galaxy works with the resource manger and how galaxy submits jobs?
My current problem jobs can be created and submitted but within the
history tab I have "this job is waiting to run". The job never gets
submitted to PBS torque queue and cannot be seen using qstat. My
job_conf.xml is shown below. If anyone can give a sample to a working
configuration file for job_conf.xml using PBS torque that will be most
<!-- A sample job config that explicitly configures job running the way
it is configured by default (if there is no explicit config). -->
<plugin id="pbs" type="runner"
<destination id="Core2" runner="pbs">
I have been tasked with getting a Galaxy server up and running
for a group at work.
1. No-one can tell me how many users (concurrent or otherwise)
there will be
2. Most of the analyses will be NGS.
3. Tools will be developed in-house but we will use public
domain tools also.
4. There will be a guy running the server/developing tools
pretty much full time.
I have two favoured solutions at the moment:
1. A pipeline processor ( 64 Core, 512G Ram, with DAS of about 150TB ),
and a Web server to act as frontend and database server, and another,
smaller box for a total install of galaxy, but doing only the
2. An all-in-one server with 128 Cores, 1TB ram, DAS storage of 150TB,
and development work done on a VM.
Any input would be hepfull.
I'm running the bgruening/galaxy-stable docker image. After making some
changes to the tools, I can no longer upload workflows. How do I debug?
What I get from the server is
Internal Server Error Galaxy was unable to successfully complete your
An error occurred.
This may be an intermittent problem due to load or other unpredictable
factors, reloading the page may address the problem.
*The error has been logged to our team.*
Since I am 'our team', I'd like to find out how to see the log! None of the
logs under /home/galaxy indicate a problem (that I notice), but uwsgi.log
does list a GET command for the workflow:
[28/Jul/2015:16:31:50 +0000] "GET /api/datatypes?extension_only=False&
HTTP/1.1" 200 - "http://22.214.171.124:8080/workflow/import_workflow"
"Mozilla/5.0 (Windows NT 6.1; WOW64; rv:39.0) Gecko/20100101 Firefox/39.0"
I figured it was an issue with the workflow, so I created a simple workflow
on the same galaxy instance. When I tried to download the workflow file, I
got the exact same error.
Restarting the instance (several times) didn't help.
How do I get more info on these errors?
I'm sorry your' having problems with the htseq-count tool. Could you
elaborate a bit on an error messages you see for the missing tool
dependencies? You should be able to click on those repositories that
show missing dependencies and see which ones are not properly installed
and then clicking on those get to an error message.
I know there has been an issue with the freetype_2_4 package, at least
for me, I am unable to download the file from sourceforge at the moment.
Also, there has been a bug that can cause some fairly tough to trace
errors during installation that was recently patched:
I've also copied this message to the galaxy-dev mailing list in case
anyone there has additional insight.
> Garcia Escudero, Ramon <mailto:firstname.lastname@example.org>
> July 28, 2015 at 7:17 AM
> Dear Lance,
> I'm having problems installing "htseq-count wrapper for Galaxy" in my
> local galaxy from the Galaxy Toolshed at
> Main problems include missing tool dependencies for
> package freetype
> package imaging
> package matplotlib
> I'm runing ubuntu 14.04 LTS
> Coul you help me with this problem?
> Many thanks
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Lance Parsons - Scientific Programmer
134 Carl C. Icahn Laboratory
Lewis-Sigler Institute for Integrative Genomics
We are thinking of putting our galaxy instance in a new more powerful
environment. Galaxy is now on a single server containing a psql database
which is migrated from mysql a few years ago.
The new environment already houses a really nice backupped highly available
as galaxy admin I am quite reluctant of migrating back to mysql, the system
admin is quite reluctant of installing this psql database with the same
grade of backup and availability just for galaxy.
I could only come up with the line "*PostgreSQL is much preferred since
we've found it works better with our DB abstraction layer, SQLAlchemy
<http://www.sqlalchemy.org/>.*" from the galaxy wiki, which is a rather
My question now is.
Is Postgres still the preferred database or is Mysql now also a safe bet.
For mysql we would have to migrate back, system management would have a lot
of experience tuning databases and a high quality instance is already
For Psql a new database instance would have to be installed, less knowledge
of the database system is available but it is the preferred database.
Could someone point out some more pros and cons in this question?
Central Veterinary Institute of Wageningen UR (CVI)
Department of Infection Biology
PO box 65, 8200 AB Lelystad, NL
Visiting address: ASG, Edelhertweg 15, 8219 PH Lelystad
Maybe someone can help with a question I posted at biostars about a week
ago but have no solution yet..
Its about a bwa mem index builder error.
If anyone could help me out on this...!