From: John Chilton [jmchil...@gmail.com]
Sent: Wednesday, November 19, 2014 6:39 AM
To: Dooley, Damion
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] master_api_key currently doesn't benefit from a real
admin's key?!
If you already have an admin key
I made the erroneous assumption that if I put my own admin user API key into
the galaxy configuration master_api_key field, it would accept that and run all
the api functions that needed a key connected to a user. It took fair bit of
debugging to realize that the master_api_key field chops off
From: John Chilton [jmchil...@gmail.com]
Sent: Wednesday, October 22, 2014 6:42 PM
To: Dooley, Damion
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] Determining galaxy api path automatically from a tool
via dynamic_options?
Well host is probably not enough - it doesn't seem like a good
After uploading my beta status tool to our test toolshed, I tried installing it
on another of our galaxy servers but it wasn't able to find the api endpoint
url. Is there a way to automatically do this within tool forms? I was hoping
to avoid hardcoding this as part of the tool installation
To: Dooley, Damion
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] Tool development: Is it possible to pass a user's id
in dynamic_options() parameter?
Hi Damion,
Text fields are not currently able to be populated by dynamic_options, but in a
dynamic_options select list you could access
This was asked a few years ago but no takers: Galaxy Tool Development:
(http://dev.list.galaxyproject.org/Reading-user-id-before-the-execution-of-the-tool-td4490324.html)
Seems like this isn't possible, unless there's a way to plant user's name in a
text field on the tool's form, so that a
Chilton [jmchil...@gmail.com]
Sent: Thursday, October 02, 2014 9:42 AM
To: Dooley, Damion
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] Simple standard for API use of a global user/key that
all loaded tools can draw upon?
Okay - revisiting this because I was not nearly cautious enough
I see Galaxy API has a feature to import a history dataset into the library (in
copy_hda_to_ldda() fn from GCC2013 training day course). Is this available as
well via Bioblend? Latest docs don't seem to include this feature. It would
be the opposite of Bioblend's
Do any of you see the need to establish a way for tools to use a global
(current site) API url/key combination? From a security perspective I'm
assuming this is basically ok since tools run under the galaxy user anyways
(and can directly read and write files to their heart's content). I
Well well, thanks very much for that reference! I can see how your system to
enable a workflow to process delta (diff) data (and merge the results back with
a previous run's output) would greatly lighten the processing power for keeping
results current. Interesting choice of technologies too.
Earlier on in the project analysis I was pursuing a Git solution because it
seemed all its features would work with documents/code/files of any kind and so
would be perfect for scientific reproducibility. But its ability to
efficiently archive non-documents is quite hit and miss, and the file
this go along with people's expectations?
Cheers,
Damion
From: Björn Grüning [bjoern.gruen...@gmail.com]
Sent: Monday, September 01, 2014 12:47 PM
To: Dooley, Damion; Björn Grüning; galaxy-dev@lists.bx.psu.edu
Cc: Hsiao, William
Subject: Re: [galaxy-dev
, August 23, 2014 12:17 AM
To: Dooley, Damion; galaxy-dev@lists.bx.psu.edu
Cc: Hsiao, William
Subject: Re: [galaxy-dev] Concept for a Galaxy Versioned Fasta Data Retrieval
Tool
Hi Damion,
the idea sounds fantastic!
Can we go a step further and use a specific datatype that keeps entire
fasta files
: Saturday, August 23, 2014 2:25 AM
To: Dooley, Damion
Cc: galaxy-dev@lists.bx.psu.edu; Hsiao, William
Subject: Re: [galaxy-dev] Concept for a Galaxy Versioned Fasta Data Retrieval
Tool
I also think that this a great idea, and as you described it I think it's
feasible as a stand-alone galaxy tool
We are about to implement a fasta database (file) versioning system as a Galaxy
tool. I wanted to get interested people's feedback first before we roll ahead
with the prototype implementation. The versioning system aims to:
* Enable reproducible research: To recreate a search result at a
Does this apply to all past galaxy installs? I have an older galaxy site I've
been wanting to phase out rather than upgrade. For now I'd like to use a patch
but site version (parent: 7148:17d57db9a7c0 ) predates any of the tags. I
presume I'd have to just implement the patch by hand?
Hi folks,
Having a difficult time with coding the configure step in this new
tool_dependency.xml file, namely that an error /bin/sh: configure: command not
found results when I try to install my beta development tool from a local test
toolshed (which is downloading and installing other tools
To: Dooley, Damion
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] Toolshed tool_dependency.xml git archive configure
issue
Hey Damion,
You should be able to do ./configure --disable-gui ... to get it to work (that
is, make sure the full path to the configure command is given). At least I
A little more info:
action type=shell_commandls -a/action
#
ls -a
STDOUT
.
..
#
#
ls -a
STDERR
so I guess the .git archive is being unpackaged somewhere
From: Aaron Petkau [aaron.pet...@gmail.com]
Sent: Friday, August 01, 2014 12:26 PM
To: Dooley, Damion
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] Toolshed tool_dependency.xml git archive configure
issue
Hmmm... you know what. I tested this out and it looks like Galaxy expects
Hi folks,
In Upload files to a data library form, seems like whatever valid path I
enter for linking to data on the server, even with galaxy as user and r
permissions on the folder and files - I get the invalid paths message after
submitting? The basic form info:
p.s. I do have allow_library_path_paste = True set in universe_wsgi.ini
Damion
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Solved. It was actually a file permissions thing on an ancestral folder. I
will add a trello card to suggest slightly better error reporting on this
though.
Regards,
Damion
Hsiao lab, BC Public Health Microbiology Reference Laboratory, BC Centre for
Disease Control
655 West 12th Avenue,
Hello, Eric,
If the dynamic filters approach doesn't work out I can send you an approach
that worked for me. It involves creating a tool-generated html report that
contains a form which provides selection choices; and the form is set to submit
to a 2nd tool of your choice tool (it contains
To: Dooley, Damion
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] Inform tool interface with data specific to selected
dataset
Hi Damion,
Would you mind sharing your approach with us all?
Thanks!
Igor
On May 9, 2014 1:51 PM, Dooley, Damion
damion.doo...@bccdc.camailto:damion.doo
I tried upgrading a local galaxy test site to the stable or default codebases.
Most of galaxy seemed to work fine - and I can start and stop it. But the
local toolshed I had running under it seems now to be jammed in an error state:
Internal Server Error
Galaxy was unable to
I'll try to keep this short! I'm wondering why on a fresh install of galaxy
via a setup script into a python virtualenv, my custom toolshed tool's .loc
files don't seem to be loading, i.e. the tool's tool_data_table_conf.xml file
isn't loading. All the other parts of the tool (and other
One further piece of the mystery I see now:
The View Data tables Registry shows my tool's loc files, but has odd stuff
for Tool data path and Missing index file columns, for example:
blast_reporting_fields [tab]
So I see this now in main.log:
galaxy.tools.data WARNING 2014-05-07 16:40:29,613 Line 3 in tool data table
'blast_reporting_fields' is invalid (HINT: 'TAB' characters must be used to
separate fields):
length numeric int 1 1 1
Alignment length
The
Well Galaxians, I have to eat humble pie, kind of. Mismatches between the
tool's tool_data_table_conf.xml and the actual tabular data were responsible
for the disappearing act, which log rather indirectly alluded to. Something
that didn't show itself on the dev server.
I'll push for some
For those who need it in the future, found the solution, so now the html
report/form can trigger the given tool to run. Turns out the tool_state value
wasn't the problem. It was the input type=hidden name=input
value=%(dataset_selection_id)s / value that was wrong. Solution: the xml
tool
To: Dooley, Damion damion.doo...@bccdc.ca
Cc: galaxy-dev@lists.bx.psu.edu galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] Can a tool upload a .loc file that is then
... RENAME: custom galaxy tool python modules
Message-ID:
CANwbokfAJCLWH7afNk-s7yZXKcz6pWYVq4Ttn0Q=uezvfxt
Hi Galaxians,
I've got a nice html report of blast results by query, and tabular subject
result listing a handful of columns. It was set up so that checkboxes by each
row and a submit button for each subject sent form data to another tool we
have. I'd tricked the other tool's form into
Python code in galaxy tools can import all sorts of modules. Is there a way to
add an extra path to the sys.path so that I can include some other python
modules that way? I.e. in some galaxy python config file?
I'd like to say in my tool code
HTMLReportModule = __import__(html_template)
Hey folks! I'm trying to revise a tool that allows the user to select from an
extendable list of template files for generating blast report output. The idea
is that if some reporting needs aren't covered by a generic template, then they
can develop their own template which can then show up on
Oh, great! I'd assumed new tool versions would overwrite them so they could
implement changes. But what you say is simpler and more straightforward!
Thanks,
D.
From: Peter Cock [p.j.a.c...@googlemail.com]
Sent: Monday, April 07, 2014 2:23 PM
To: Dooley
After following some of the links that this thread referenced (since it is
totally related to the one I put in on friday), I found the rollback
solution, to disable pbkdf2 authentication. I did attempt pbkdf2 for a while,
but openssl upgrade and pbkdf2 recompile issues have led me to drop
I think this is a follow-up to last june's
http://dev.list.galaxyproject.org/proftpd-setting-tt4660329.html question.
I was trying a new test install of galaxy (following instructions on galaxy
website for a local install from galaxy-dist hg source), sitting on a server
with two existing
I'm stumped: Can tools that are destined for the toolshed use options
from_data_table=... ... ?
In a blast_reporting.xml tool script I have
param name=filter_column type=select label=Col
options from_data_table=blast_reporting_fields
filter
?
From: Greg Von Kuster [g...@bx.psu.edu]
Sent: Monday, January 20, 2014 1:21 PM
To: Dooley, Damion
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] Toolshed throwing error when reading tool's XML
Hello Damion,
Tool Shed repositories that contain tools that include dynamically
back into galaxy without having to stop/restart the server.
Hoping an extension to the tool_data_tables class could do this too.
Regards,
Damion
--
Message: 1
Date: Fri, 10 Jan 2014 16:56:56 -0800
From: Dooley, Damion
I've seen
$__app__.tool_data_tables[ 'all_fasta' ].get_fields() )[0][-1]
in tool xml templates. Is there a way I can access the tool_data_tables
structure from python code too?
I see all the initialization stuff happening in
From: Greg Von Kuster [g...@bx.psu.edu]
Sent: Friday, January 03, 2014 3:48 PM
To: Dooley, Damion
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] Small icon bug in local galaxy install
Hello Damion,
I believe this issue was corrected in
https://bitbucket.org/galaxy/galaxy
A few of our local galaxy installs have a relative folder path (i.e. in
universe_wsgi.ini, prefix = /galaxylab) . In the Admin tab, Manage
installed tool shed repositories, the icons in the legend below aren't showing
because they have an absolute url:
img
Hi folks,
Has someone seen this behaviour? I'm trying to do a once-over maintenance
cleanup of our galaxy installs. The galaxy account is getting emailed nightly
with an error which is happening when it gets to delete_datasets.sh cron task,
basically:
AttributeError: 'NoneType' object
I'm doing a 1 step generic reporting tool along the lines of the BLAST XML to
tabular script by Peter. I was just about to ask about this line, which
looked pretty much like a bug:
sallseqid = ;.join(name.split(None,1)[0] for name in hit_def.split(
))
Then I found the patch from Nov
Woops - I realize now findtext() must be unescaping all gt;, so Peter was
trying to address other non-splitting occurances of as per his patch
notes. But perhaps a stop_err() isn't merrited in this case?
So ignore my test for gt; comment.
Regards,
Damion
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