Dear Galaxy developer community,
Galaxy tool developers attending ISMB are encouraged to sign up for the
Bioinformatics Interoperability SIG to be held on Friday, June 13. The SIG
will include presentations on Galaxy and other interoperability
environments and will feature a hackathon where tool developers can add
their tools to Galaxy or another environment.
For more information about the SIG please see the BSI SIG Web
Information about ISMB and how to register is at
BSI SIG Committee
Michael Reich <mreich(a)broadinstitute.org>
Director of Cancer Informatics Development
Broad Institute of MIT and Harvard
7 Cambridge Center, Cambridge, MA 02142, USA (617) 714-7467
After I update galaxy-dist to the latest version, I got the following error
message when I run run.sh command:
galaxy.tool_shed.tool_shed_registry DEBUG 2012-06-01 09:57:15,503 Loaded
reference to tool shed: Galaxy test tool shed
Traceback (most recent call last):
File "/home/galaxy/galaxy-dist/lib/galaxy/web/buildapp.py", line 82, in
app = UniverseApplication( global_conf = global_conf, **kwargs )
File "/home/galaxy/galaxy-dist/lib/galaxy/app.py", line 64, in __init__
File "/home/galaxy/galaxy-dist/lib/galaxy/tool_shed/__init__.py", line
26, in load_proprietary_datatypes
load_datatype_items( self.app, tool_shed_repository,
File "/home/galaxy/galaxy-dist/lib/galaxy/util/shed_util.py", line 1024,
converter_path, display_path =
alter_config_and_load_prorietary_datatypes( app, datatypes_config,
relative_install_dir, deactivate=deactivate )
File "/home/galaxy/galaxy-dist/lib/galaxy/util/shed_util.py", line 236,
TypeError: load_datatypes() got an unexpected keyword argument 'override'
Our lab's proteomics data is frequently outputted into >50 files
containing different fractions of proteins. The files are locally stored
and not present on the Galaxy server. We've planned to somehow (inside
galaxy) merge these files and split them into tasks so they can be run
on the cluster. We would either merge/split the files by concatenation,
or untar/tar files at every job, depending on filetype and tool. No
problems so far.
However, I have been looking around for a way to upload >50 files
simultaneously to galaxy and convert to one dataset, and this does not
seem to be supported. Before starting to create a hack to make this
work, which doesn't seem especially trivial to me, I'd like to know if I
should instead use libraries. From what I've seen, libraries are not
treated as datasets in Galaxy but rather contain datasets. If there was
a "tar all sets in library and import to history" I'd be using that, but
I've only encountered "tar/zip sets and download locally" which would be
a bit of a workaround.
I haven't found much on this subject in the mailing list, has this
functionality been requested before?
I've got a problem with PBS when I want to submit a job to our cluster with Galaxy.
Every time, PBS says me "pbs_submit failed, PBS error 15023: Bad user - no password entry".
Indeed, Galaxy uses my email address (used in Galaxy) as user by default !
But, before, when I used SGE on my previous lab, Galaxy used the galaxy owner user and not my email…
Is it possible to set the owner user as previous Galaxy version ? (I found the "drmaa_external_*" session in universe but I don't really understand how to configure this part…).
Thanks a lot,
I have been trying to run a quick test using the tool_dependency_dir
configuration option to prove out how it works ... but unfortunately I
can't get it to function right. I was hoping someone could point out my
error. I have written a simple tool in galaxy, version_test, that will
just echo out a version number to a text file so I could test out tool
dependencies and install locations. But my required package is not
getting resolved by galaxy....
Snippet from my configuration file:
# Directory which contains dependent tool binaries or a env.sh to set
env vars in order to find specific versions.
tool_dependency_dir = /opt
My simple tool:
<tool id="version_test" name="version_test" version="1.0.0">
<description>provides simple stats on BAM files</description>
<param name="input1" type="data" format="tabular,binary" label="Holder
for input file - not used." />
<data name="output1" format="txt" />
[galaxy@galaxy-0-4:galaxy-dist]$ ls -lat /opt/galaxy_test/
drwxr-xr-x 3 root root 4096 May 16 14:10 2.0
drwxr-xr-x 3 root root 4096 May 16 14:09 1.0
drwxr-xr-x 4 root root 4096 May 16 14:05 .
-rw-r--r-- 1 root root 50 May 16 14:05 env.sh
drwxr-xr-x 72 root root 4096 May 16 14:04 ..
My env file:
Galaxy log messages when invoking my test tool:
galaxy.tools DEBUG 2012-05-31 21:59:17,349 Dependency galaxy_test
galaxy.tools WARNING 2012-05-31 21:59:17,349 Failed to resolve
dependency on 'galaxy_test', ignoring
If I manually source the env.sh file , my test.sh is found and executes
Where am I going wrong?