Dear Hans,
//galaxy_dist/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/schema.py,
line 42, in _load
data = list(result)[0]
IndexError: list index out of range
This error is because SQLAlchemy cannot load the controlled schema
version info from the DB, the result is empty, so
Dear Galaxy Dev,
Is there a way to set the genome build metadata on datasets
transferred from an external service in the sample tracking system?
-Leandro
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it is either malformed or otherwise incorrect.
Malformed LibraryFolder id ( 994debf9f6ab02b99d7cff57c04c6b7c )
specified, unable to decode
What could be the problem here? Any help would be appreciated.
regards,
Leandro
On Wed, Mar 28, 2012 at 1:15 PM, Leandro Hermida
soft...@leandrohermida.com wrote:
Dear
version from
last year and everything works ok during library folder association.
regards,
Leandro
On Wed, Mar 28, 2012 at 1:20 PM, Leandro Hermida
soft...@leandrohermida.com wrote:
Dear Galaxy Dev,
Now I have another problem with the Galaxy sample tracking data
transfer. Galaxy is not able
Dear all,
How do I get the new Galaxy look enabled that you see in
usegalaxy.org? I have two servers on the latest galaxy-dist.
regards,
Leandro
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Dear all,
Is it normal that the latest galaxy-dist creates a shed_tools
directory one directory up (and outside) from the server galaxy-dist
directory?
best,
Leandro
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Dear Galaxy Dev,
I've set up the Galaxy sample tracking system data transfer
functionality exactly as specified here
https://main.g2.bx.psu.edu/u/rkchak/p/data-transfer, but when I
attempt to transfer datasets it puts them into the queue and then
never seems to transfer anything.
The
in the second menu can be re-executed using the new file name as a
parameter then generating new options in this second menu?
regards,
Leandro
On Mar 21, 2012, at 9:27 AM, Leandro Hermida wrote:
Here's one example:
inputs
param type=data name=dataset refresh_on_change=true
label=Select a file
?
*Can you be more specific about what problems you're seeing and whether you
can reproduce with known tools?
Thanks,
J.
On Mar 20, 2012, at 9:28 AM, Leandro Hermida wrote:
Hi everyone,
Sorry to ping again, having the refresh_on_change functionality not
working in Galaxy has us making
,
seems like you are using jQuery to bind a custom Javascript
refresh_on_change function but when you look at that function it
doesn't do any form reloading, maybe just the feature is unfinished?
sincerely,
Leandro
On Wed, Feb 29, 2012 at 10:34 AM, Leandro Hermida
soft...@leandrohermida.com wrote
, Leandro Hermida wrote:
Hello,
If you have a form with an input like this:
param name=input1 type=select dynamic_options=get_options() /
And the options dynamically generated have integers as values, e.g.
options tuples like this:
[ One, 1, 1 ],
[ Two, 2, 0 ],
[ Three, 3, 0 ]
When you try
Hello,
We don't use the nginx module
kind regards,
Leandro
On Wed, Mar 7, 2012 at 4:42 PM, Jorrit Boekel
jorrit.boe...@scilifelab.se wrote:
Hi Nate,
I wasn't before, but I switched to nginx now. Non-uploading is still
happening in firefox (10.0.2 on ubuntu 11.10).
I can't be 100% sure
],
[ Three,3,False]
work?
Regards, Hans
On 02/29/2012 04:44 PM, Leandro Hermida wrote:
Hello,
If you have a form with an input like this:
param name=input1 type=select dynamic_options=get_options() /
And the options dynamically generated have integers as values, e.g
Hello,
If you have a form with an input like this:
param name=input1 type=select dynamic_options=get_options() /
And the options dynamically generated have integers as values, e.g.
options tuples like this:
[ One, 1, 1 ],
[ Two, 2, 0 ],
[ Three, 3, 0 ]
When you try to submit the galaxy form
Dear all,
Is there a way with the Galaxy sample tracking system to have the
dataset transfer feature copy data to a dataset library outside the
private Galaxy server data directory tree and then the dataset library
just link (like you can do with upload files feature when managing
data
Hi all,
We get the behavior mentioned some times too, its not reproducible
just like you mentioned. Some times it happens with small files, some
times with large files and again as you said it doesn't happen all the
time.
Now I haven't seen this yet on our Galaxy dev server which is the
latest
Hi everyone,
Does anyone have a typical external service type XML file for an
Illumina HiSeq 2000? I have created one but not sure if its correct
and there is no guide for creating the external service type XMLs
thanks,
Leandros
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Hi everyone,
It used to be in the previous or so galaxy-dist that if you wanted to
have a tool which displayed a web page from another web app in the
center Galaxy frame you simply did:
tool name=View External Web Page id=view_external_page version=1.0.0
descriptionfrom External
Hello,
In the latest galaxy-dist version when running the system cleanup commands
in the documented order I get an error when running the purge_datasets.sh
script:
sh delete_userless_histories.sh
sh purge_histories.sh
sh purge_libraries.sh
sh purge_folders.sh
sh delete_datasets.sh
sh
.
-Dannon
On Jan 20, 2012, at 11:07 AM, Leandro Hermida wrote:
Hi,
There seems to be a weird bug with the Input dataset workflow
control feature, hard to explain clearly but I'll try my best.
If you define a custom datatype that is a simple subclass of an
existing galaxy datatype
Hello,
We've created a new binary datatype for .fastq.gz files following the
same methodology as the BAM files since we don't want our fasta.gz
files to be gunzipped. I added the appropriate code in upload.py to
make sure of this. This new datatype and extension successfully does
not gunzip our
by specifying its own new datatype and extension
and changing binary.py to make sure it doesn't fall through to the
elsif where it tries to unzip stuff.
On Fri, Jan 20, 2012 at 2:25 PM, Peter Cock p.j.a.c...@googlemail.com wrote:
On Fri, Jan 20, 2012 at 12:42 PM, Leandro Hermida
soft
.
uploaded_dataset.data.dataset.purgable = False
trans.sa_session.add_all( ( uploaded_dataset.data,
uploaded_dataset.data.dataset ) )
trans.sa_session.flush()
return uploaded_dataset
Thanks!
Greg
On Jan 20, 2012, at 7:42 AM, Leandro Hermida wrote:
Hello,
We've created a new binary datatype
Hi,
There seems to be a weird bug with the Input dataset workflow
control feature, hard to explain clearly but I'll try my best.
If you define a custom datatype that is a simple subclass of an
existing galaxy datatype, e.g.:
datatype extension=myext type=galaxy.datatypes.data:Text
subclass=True
Hi all,
We tried to find something in the docs and mailing list no luck. We
created a new datatype the is a straight subclass of Binary and then
when we upload such a file in the Galaxy UI and check the checksums
between the original file and the file located in the Galaxy
database/files/...
this on my instance and the example you gave did give me the
correct string: Human (hg18). Do you still have this problem? If so, can you
provide an example where it still behaves incorrectly?
Thanks,
K
On Thu, Jul 14, 2011 at 4:16 AM, Leandro Hermida
soft...@leandrohermida.com wrote:
Hi
Hi,
I am trying to create a form where there are two select menus, both using
dynamic_options, where one is the parent menu that is chosen first and based
on the selection(s) there is a refresh and the second menu gets populated
based on the first menu's choice(s).
param name=names type=select
return value.id
AttributeError: 'list' object has no attribute 'id'
Is using multiple history items as a single input not currently supported,
or is there something else I'm doing wrong?
Cheers,
Kip
On Thu, Jun 9, 2011 at 7:05 AM, Leandro Hermida
soft...@leandrohermida.com wrote:
Hi
Having a very strange problem in the Galaxy web GUI that suddenly just
started happening yesterday, getting very strange behavior in the
history right panel.
- Most of the time when I click on something in the GUI like to go to
a tool page or to go to the Admin interface and come back suddenly
/galaxy_dist/static/robots.txt
[L]
RewriteRule ^(.*) http://galaxy.server.hostname:8080 [P]
On Fri, Jul 1, 2011 at 12:13 AM, Shantanu Pavgi pa...@uab.edu wrote:
On Jun 30, 2011, at 6:34 AM, Leandro Hermida wrote:
Hi Nate and Shantanu,
Thanks so much for the clear guidance, this works
1, 2011 at 10:36 AM, Leandro Hermida soft...@leandrohermida.com
wrote:
Hi Shantanu,
Thank you for your update, I've done my config a little differently and it
appears to work just the same. The relevant part looks like this:
Location /
## ActiveDirectory authentication
Hi - you can ignore this message, I figured out what the problem was and it
was caused by a change in my front end authentication setup
On Fri, Jul 1, 2011 at 10:21 AM, Leandro Hermida soft...@leandrohermida.com
wrote:
Having a very strange problem in the Galaxy web GUI that suddenly just
Hi Nate and Shantanu,
Thanks so much for the clear guidance, this works and sorry I didn't
read the Apache docs properly
best,
Leandro
On Thu, Jun 30, 2011 at 6:14 AM, Shantanu Pavgi pa...@uab.edu wrote:
On Jun 29, 2011, at 12:21 PM, Nate Coraor wrote:
Leandro Hermida wrote:
Hi Shantanu
Hi Shantanu,
In your Apache configuration exactly how did you set up an anonymous
REMOTE_USER just for specific locations like the /datasets/ path? I'm just
looking at the Apache docs and the RequestHeader directive has a context of
the entire VirtualHost and cannot be put into a Location
success setting dataset label/name and other attributes using
one of the custom code hook functions??
thanks,
leandro
On Thu, Jun 23, 2011 at 3:27 PM, Leandro Hermida soft...@leandrohermida.com
wrote:
Hi everyone,
Is it possible to change dataset labels in exec_after_process() ?
best,
Leandro
format=html name=html_file label=${out_prefix}.html/
/outputs
works for me and avoids the need to have a post execution hook code file.
On Fri, Jun 24, 2011 at 6:02 PM, Leandro Hermida
soft...@leandrohermida.com wrote:
Hi again,
Sorry that I didn't know before, it seems like the label
Hi,
In the last section of
https://bitbucket.org/galaxy/galaxy-central/wiki/ToolsMultipleOutput,
Number of output datasets cannot be determined until tool run, it should
be updated that the new additional datasets file format actually has a sixth
part at the end where you can set the database
Hi everyone,
Is it possible to change dataset labels in exec_after_process() ?
best,
Leandro
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Hi,
I've tried to do a simple test where I change the output dataset name
programmatically before it appears in the history using exec_before_job().
I just copied some example code:
def exec_before_job(inp_data, out_data, param_dict, tool):
for name, data in out_data.items():
, people's
email addresses are their usernames and email services work in Windows
as your username is your email nickname.
-L
On Thu, Jun 9, 2011 at 11:00 PM, Leandro Hermida
soft...@leandrohermida.com wrote:
Hi Nate,
Thank so much for the instructions :) , yes this is what I would want
to do
.
thank a lot,
Leandro
On Thu, Jun 9, 2011 at 6:54 PM, Nate Coraor n...@bx.psu.edu wrote:
Leandro Hermida wrote:
Hi,
Is it possible to tell Galaxy to use the bare username passed back by
external authentication as the email address without appending any
domain? It seems to complain
Thanks Galaxy Dev Team, the new galaxy-dist fixes multiple UI bugs with IE,
for e.g. the workflow editor works now works and the history expand/collapse
works! :)
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enough for some purposes, but will look much better than what you have been
using.
Sometime in the near future I hope to get a page like this
http://gmod.org/wiki/GMOD_Promotion up for Galaxy.
Thanks,
Dave C.
On Thu, May 19, 2011 at 12:15 PM, Leandro Hermida
soft...@leandrohermida.com wrote
have an answer for you, but when we're all back at work next week,
someone should be able to respond.
Thanks,
--nate
Leandro Hermida wrote:
Hi again,
Very sorry to ask again, just gotten no repsonse, but is this a Galaxy
bug
or does anyone have a functioning tool that takes multiple
See this page for the official installation instructions
https://bitbucket.org/galaxy/galaxy-central/wiki/GetGalaxy
2011/5/24 Björn Grüning bjoern.gruen...@pharmazie.uni-freiburg.de
Hi Jasmin,
at first you need to install mercurial. Under debian/ubuntu install it
with:
sudo apt-get
Not everything works correctly with checkbox booleans, the bug a couple
people and I reported long ago
https://bitbucket.org/galaxy/galaxy-central/issue/393/cant-use-checkbox-boolean-with-conditional
is still there.
2011/5/23 Peter Cock p.j.a.c...@googlemail.com
2011/5/23 Louise-Amélie
your subscriptions to this and other Galaxy lists,
please use the interface at:
http://lists.bx.psu.edu/
On 05/19/2011 12:03 PM, Leandro Hermida wrote:
Hi,
When Galaxy is configured to use the DRMAA job runner is there a way for a
tool to tell DRMAA the number of cores it would like
multithreaded tool, so it doesn't run a multithreaded job when
there's only one core available in the chosen node.
Hope that helps :)
Regards,
L-A
On 05/19/2011 03:05 PM, Leandro Hermida wrote:
Hi Louise-Amelie,
Thank you for the post reference, this is exactly what I was looking
I have the following tool input parameter:
param name=columns type=select multiple=true label=Select which
columns to output
optionSIZE/option
optionES/option
option selected=trueNES/option
optionNOM p-val/option
option selected=trueFDR q-val/option
optionFWER p-val/option
format=html and this works and displays
in Galaxy just fine. I would like to use multiple of these output datasets
in my history as the input for this other tool but something seems to be
wrong if you try to do this?
a bit lost,
Leandro
On Thu, May 19, 2011 at 3:30 PM, Leandro Hermida
soft
Hi all,
I enabled DRMAA on my test Galaxy server installation and in the server
startup output I get the following strange E #14ca [ 1.10] * wait
thread: 1002:Not enough memory. lines after loading the job manager:
...
galaxy.jobs.runners.local INFO 2011-05-18 17:10:23,025 starting workers
Hi,
Is there a way to increase the width of a select multiple menu for a param
tag type=data? Certain dataset labels I have are very informative :)
(i.e. long) and when used as an input to a tool you can't read what the
difference is between each item unless you look at the dataset number and
. I moved to the
previous version and everything is OK for me
Marina
On 18/05/2011 16:15, Leandro Hermida wrote:
Hi all,
I enabled DRMAA on my test Galaxy server installation and in the server
startup output I get the following strange E #14ca [ 1.10] * wait
thread: 1002:Not enough
Hi all,
In a tool XML I have a select menu param within/driving a conditional tag
and in the workflow editor it doesn't let me choose to allow the user to set
this select menu at runtime? Is this a bug?
best,
leandro
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Hi, how do you make float parameter types fully optional? optional=true
doesn't work.
-Leandro
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Hi everyone,
Has anyone actually properly implemented remote_user_logout_href in Galaxy
with external HTTP authentication? As probably those who have tried know,
it is rife there doesn't seem to be a clean and robust way to do this?
best,
Leandro
On Apr 27, 2011, at 9:40 AM, Leandro Hermida wrote:
Hi Dannon,
Thanks for your replies and advice, this leads me to a quesion... is it
possible to execute a tool job via the Galaxy API just like someone does via
the UI? Could I then have a tool script that wraps this programmatic
execution
Hi galaxy developers,
Just want to double-check, there is no way to import some kind of galaxy
tool context info into python code you are running for a tool?
best,
leandro
On Fri, Apr 15, 2011 at 8:03 PM, Leandro Hermida soft...@leandrohermida.com
wrote:
On Fri, Apr 15, 2011 at 7:27 PM
Hi,
For a tool select input parameter:
param name=input1 type=select
option value=hs33Homo sapiens/option
option value=mm19Mus musculus/option
option value=rn43Rattus norvegicus/option
/param
Is there an attribute for the variable $input1 that will give me the
displayed value (e.g.
On Thu, Apr 28, 2011 at 5:33 PM, Nate Coraor n...@bx.psu.edu wrote:
Pieter Neerincx wrote:
Hi Leandro,
On Apr 27, 2011, at 6:08 PM, Leandro Hermida wrote:
Hi Pieter,
cut
I have this *exact* same setup as you where I am authenticating with
the LDAP user ID and returning
On Thu, Apr 28, 2011 at 5:52 PM, Nate Coraor n...@bx.psu.edu wrote:
Leandro Hermida wrote:
Hi everyone,
Has anyone actually properly implemented remote_user_logout_href in
Galaxy
with external HTTP authentication? As probably those who have tried
know,
it is rife there doesn't seem
... is it
possible to execute a tool job via the Galaxy API just like someone does via
the UI? Could I then have a tool script that wraps this programmatic
execution of X tool jobs via the API?
regards,
Leandro
On Apr 21, 2011, at 7:49 AM, Leandro Hermida wrote:
Hi again,
Sorry
to Galaxy, if
anyone needs help with such an LDAP configuration please ask me I have it
working with Apache mod_authnz_ldap against Active Directory.
regards,
Leandro
On Fri, Apr 8, 2011 at 7:07 PM, Leandro Hermida
soft...@leandrohermida.comwrote:
Hello,
When returning REMOTE_USER env var from
Hi,
Just wondering if I got my setup right, I have Galaxy front-ended by Apache
doing the static caching, proxying and LDAP auth. What's nice is that
user's don't have to be created by an admin if the user authenticates and
authorizes properly against the LDAP config then Galaxy will
Hi Pieter,
On Wed, Apr 27, 2011 at 4:14 PM, Pieter Neerincx
pieter.neeri...@gmail.comwrote:
Hi Leandro,
On Apr 27, 2011, at 3:50 PM, Leandro Hermida wrote:
Hi,
Just wondering if I got my setup right, I have Galaxy front-ended by
Apache doing the static caching, proxying and LDAP auth
green from my perspective.
I think functionality like this built into the workflow editor would be
a
great addition.
Dave
On Apr 15, 2011, at 8:14 AM, Leandro Hermida wrote:
Hi everyone,
I was wondering what would be the way in Galaxy to program the
following:
- User clicks
Hi everyone,
I was wondering what would be the way in Galaxy to program the following:
- User clicks on a tool and form is displayed
- They use a select multi menu in the form to pick lets say X multiple
datasets from their history
- When they click submit the tool launches X number of jobs in
Hi all,
Sorry if this question has been asked before searched and couldn't find
anyone specifically talking about this. In the Galaxy wiki under
https://bitbucket.org/galaxy/galaxy-central/wiki/Config/ApacheProxy there
are instructions for setting up Galaxy behind a web server proxy. I
wondered
, I have seen
before configurations with mod_proxy and mod_rewrite directives together
doing the same thing I was wondering why! :)
best,
Leandro
On Fri, Apr 8, 2011 at 12:22 PM, Leandro Hermida soft...@leandrohermida.com
wrote:
Hi all,
Sorry if this question has been asked before searched
Hi,
It's built into mysqldump, just add the following option to your mysqldump
command:
--compatible=postgresql
-Leandro
On Wed, Mar 30, 2011 at 3:20 PM, SHAUN WEBB swe...@staffmail.ed.ac.ukwrote:
We are experiencing issues with workflows where jobs are running before the
previous step is
Hi everyone,
I posted a similar thread back in August
http://lists.bx.psu.edu/pipermail/galaxy-dev/2010-August/003224.html
There are a couple web UI issues with Galaxy when using IE, like as
mentioned in this thread in the history pane data items the link is missing
and you cannot expand them
H Nate,
Where can I find the wiki page which lists all of the attributes available
for tool objects? (e.g. input params, ouput, etc.)
best,
Leandro
On Thu, Jan 27, 2011 at 6:07 PM, Nate Coraor n...@bx.psu.edu wrote:
Leandro Hermida wrote:
Hello,
In your history where you have a piece
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