I have a script that outputs around 20 files with fixed names. Ideally I
would like to have as output a page with links to these 20 files. From the
wiki I understand that Composite Datatypes should be the way to go, somehow
putting all the output files in a folder.
I've tried to use the AutoPrimaryComposite example but I don't manage to
make it work.
- How do I register the new data type?
- How do I tell the data type to look for the output files in the newly
*Andreu Alibés, PhD
**Bioinformatics Core & EMBL-CRG Systems Biology Unit
Center for Genomic Regulation*
C/ Dr. Aiguader 88, 08003 Barcelona, Spain
Phone: +34 93 316 0202
I have some skilled end users that would like to download multiple files from our local galaxy data library with command line utilities (i.e. they would like to "wget" some files from histories).
One way to do this is to copy the item link within the history and paste as wget argument. Unfortunately, this has to be done for every item.
Another way is to select all files from the Data Library and download as archive (but you can't copy the link...) and it takes so much time when you have to download BAM files (or any other huge one)...
I was looking at the source code wondering how difficult would be to add a functionality for the data library that is:
For selected items "get the public link"
that saves a text file with all the public links (or copies them to pasteboard, or simply displays them in another window....) so that one can use that info to script the download somewhere else (and at any time)...
Any suggestion is welcome! :-)
Cogentech - Consortium for Genomic Technologies
via adamello, 16
Jobs on our galaxy server are not being run. When a new workflow is run,
only a single job in the workflow is executed. All later jobs are not run.
If the server is restarted, then the 2nd job in the workflow will be
executed, but all later jobs will not be run.
I am logging at the debug level and see the following error message repeated
many times in the logs
UnboundExecutionError: Instance <Job at 0x5203290> is not bound to a
Session; attribute refresh operation cannot proceed
galaxy.jobs ERROR 2010-09-09 13:36:03,985 Exception in monitor_step
Traceback (most recent call last):
File "/labkey/galaxy/galaxy_dist/lib/galaxy/jobs/__init__.py", line 138,
File "/labkey/galaxy/galaxy_dist/lib/galaxy/jobs/__init__.py", line 212,
log.exception( "failure running job %d" % job.id )
line 158, in __get__
return self.impl.get(instance_state(instance), instance_dict(instance))
line 377, in get
value = callable_()
line 185, in __call__
attr.impl.key in unmodified
line 1863, in _load_scalar_attributes
"attribute refresh operation cannot proceed" % (state_str(state)))
I have not been able to successfully completely run a workflow yet on this
server (this is a new install)
Specifics about the server are
- Galaxy version: changeset: 4246:f09915c8da94
- Operating System: Ubuntu 10.04
- Python version: 2.6.5
- Database: postgres 8.4
Has anyone seen an error like this before. I have searched the mailing lists
and the wiki and could not find a reference.
Thank you in advance for the assistance.
I've just started looking at installing a local copy of Galaxy, and have
registered with the mailing list.
First one quick question - is there an easy way to search the Galaxy
wiki (or documentation in general)? Perhaps my questions are
already discussed if I knew where to look...
I understand that to install Galaxy locally we just clone the mercurial
repository (either galaxy-central or galaxy-dist) and then use hg to
periodically update this to the latest code. i.e. There are no formal
releases with a version number that come as a tar ball or similar.
Naturally, once I have a copy of Galaxy, I will be making some
changes to it - in particular configuration changes, for example
to use PostgreSQL.
Is the the workflow described here the recommend approach?
(I found this presentation via a Google search)
If I understand it, the idea is that we rename tool_conf.xml.sample to
tool_conf.xml (and remove it from the .hgignore file) so that any
changes made to the sample configuration will be merged into our
Alternatively, we could just take a copy and leave tool_conf.xml in
the ignore file. We would then have to manually apply any changes
made to the tool_conf.xml.sample on a case by case basis.
Also do you recommend I make my own changes on a branch?
September 8, 2010 Galaxy Development News Brief
Here are the highlights of what you will get if you perform the
hg pull -u -r f09915c8da94
New Multiple Sample Tracking Features
* UI enhancements: checkboxes to select samples & select field to
* State change mechanism added for multiple samples and removed for
individual samples in the sample_events page.
* Enhanced sample searching implemented. Uses sample name, barcode and
dataset name with menu items in masthead and admin menu.
o Example of usage: new wild-card searches.
New Custom Sorting in Grid Framework
* Enhance grid framework to enable custom column sorting (default
* Sort criteria are now mapped to a column, and the column defines the
sorting to be done on the grid query.
o Examples of usage: (a) case-insensitive sorting of text fields and
(b) case-insensitive sorting for user names in published-item grids.
New Data Format Conversion Tools
* NGS: SAM Tools => BAM-to-SAM converts BAM format to SAM format
* Convert Formats => Wig to bigWig converter
New GFF Format Filtering Tools
* Filter and Sort => GFF => Extract features from GFF file, Filter GFF
file by attribute using simple expressions, Filter GFF file by feature
count using simple expressions.
* New Filter GFF file by feature count filters a GFF file using
conditions based on transcripts' features counts.
o Example of usage: filter for transcripts that have a minimum number
of exons or transcripts that have 3' UTRs.
Updated & Improved
* Added support for the AddressField, CheckboxField, SelectField and
WorkflowField form field types (in addition to the previously supported
TextArea and TextField) to data library templates.
* Inherited template fields now also inherit any field contents from the
immediate "parent" of the current item (folder or dataset).
* The information in our data library templates wiki at
has been updated to reflect the new features and behavior.
Sample Tracking: Email notifications
* Notification of specific sample state changes.
* Changes made to barcode scan AMQP handler to update sample state to
also send email when required.
* Notification to multiple recipients.
* Request events history records notifications.
* UI enhancements:
o "edit request" page to allow users to change notification
o "request" page to show the request type state, user & notification
Jobs & related
* Improved handling of metadata to optimize job processing. Includes a
new user prompt to set metadata manually or retry auto-detection
externally when using 'set_metadata_externally = True' .
* Enhance wig datatype to only use first 100 data lines to determine
column type metadata if dataset filesize exceeds
max_optional_metadata_filesize as configured in datatypes_conf.xml.
* Add 'NullToolOutputActionOption' to tool output dataset actions. This
action option is used implicitly when no ToolOutputActionOption(s) have
o Example of usage: a metadata value can be set to a static value on a
per Tool Output basis.
Installation and Management
* Added support for installing Galaxy on systems without direct access
to the Internet. Updated Galaxy Installation wiki (see section "How to
get eggs: If your Galaxy server does not have Internet access"
* When viewing library dataset information as an administrator, add a
field that displays the path to the actual disk file that underlies the
* Each track now has an Overview checkbox that will set the initial
* Visualizations that users own or are shared with can now be cloned.
* New go-to feature allows users to redirect quickly to a specified
chromosome or position.
o Example of usage: "chr1:1-100,000,000".
* Drag-zoom activated when a chromosomal position is clicked on.
* Line tracks display mode can also now be activated inline.
* Changing display mode from "Auto" now fetches additional detail data
and displays features. Displays error messages in canvas elements if
present. This also limits the number of features displayed per tile.
* Slight makeover to Galaxy tabs: (a) added published item links to
'Shared Data' tab; (b) standardized personal item lists as 'Saved XXXs';
and (c) added defaults action for Visualization tab.
* Minor grid refactoring.
* Don't re-sort BAM files on upload if already sorted (adapted from Brad
* Use image_path for Workflows and now display modal instead of relative
Galaxy Project Team
This project is supported in part by NSF, NHGRI, and the Huck Institutes
of the Life Sciences, and The Institute for CyberScience at Penn State.
Hi all, I'm trying to share some histories with other users. I've added annotations to items in histories. When users import my histories, the annotation field is blank...
Cogentech - Consortium for Genomic Technologies
via adamello, 16
Using the run.sh script, and the default 'log_level = DEBUG'
universe_wsgi.ini file setting gives a huge amount of output.
Changing the ini to either log_level = INFO, WARNING or ERROR and i
get the same output, including the INFO messages every second.
I assumed that WARNING or ERROR would not give the INFO messages; is
there some way to not see these?
Queensland Facility for Advanced Bioinformatics
Level 6, QBP
University of Queensland, QLD 4072
T: +61 (0)7 3346 2070
F: +61 (0)7 3346 2101
I've been setting up data libraries for researchers with their data as
provided on USB drives, and the workflow is great, except that I'm doing
something wrong with data library permissions and can't figure out just
>From the admin interface I'll select "Manage data libraries" from the
left bar, pick a library, and then from "library actions" select "edit
On that "Manage library permissions on library xxxxxx" screen the four
associated/not-associated sections have only the role that I initially
associated with the data library on import, and it's always the sole
item in associated, and 'not-associated' is empty.
How do I add other roles to associated if not-associated is empty, and
more importantly how do I let the researcher who has 'manage library
permissions' pick new ones when "roles not associated" is empty for them
The workaround I've found is to remove every role from "roles
associated" in "access library", which briefly makes every role in the
system show in "roles not associated", and then I can multi-select and
re-add the removed roles and the new ones.
I gather from Greg's write-ups that the right usage includes smarter use
of groups and non-user roles, but is it really the case that I can't
associate new roles to a library's "access library" right w/o first
removing all those already there?
Also, is there a way for researchers to be able to add users to their
group/non-user-role without and administrator having to do it for them?
Ry4an Brase 612-626-6575
University of Minnesota Supercomputing Institute
for Advanced Computational Research http://www.msi.umn.edu
I'm trying to integrate genomeview as a display application. The
configuration of the display applications seems to be pretty
straightforward, but genomeview needs multiple input files.
I can of course write a cgi file that will take a bunch of get
parameters and use these as input files for the java applet. so on the
side of genomeview, there's not really a big problem.
however, to integrate it with galaxy, i don't see how to send multiple
datasets to genomeview. you can only add the "view with genomeview" link
to one dataset (or to all, but all will be viewed seperately).
so i came up with the idea of a new datatype, .gvl, the genomeview list.
in it, basically, a list of links to the datasets, so galaxy can work
with them. i could make a tool, gvl creator, to take several datasets as
input and then create a really simple textfile containing one url per
line, for each dataset.
i think this is the way to go (if anyone has better suggestions, please
tell!) but now come the real questions:
how do i get the public url of my datasets? all other tools use the
filesystem path, can't really find an example.
any idea how i could maybe take a dynamic number of inputs? i suppose
that's not possible. this is not that big a problem. i could combine
multiple gvl creators and then a gvl merger or something, no biggie!
all help really appreciated. and of course i'll be happy to share
everything with whoever is interested afterwards :-)
with kind regards,
Tel:+32 (0)9 331 36 95 fax:+32 (0)9 3313809
VIB Department of Plant Systems Biology, Ghent University
Technologiepark 927, 9052 Gent, BELGIUM
"If you type google into google, you can break the internet"