to run a second copy of local galaxy I just copied the whole directory
(cp -ra <old_dir> <new_dir>)
I then just edited the universe_wsgi.ini to use a different port. Now
when I start run.sh in <new_dir> I get following error:
galaxy.jobs INFO 2009-09-24 13:03:27,136 job stopper started
Traceback (most recent call last):
File "./scripts/paster.py", line 27, in <module>
line 78, in run
line 117, in invoke
line 212, in run
line 227, in command
line 250, in loadapp
line 193, in loadapp
line 214, in loadobj
line 606, in create
line 99, in invoke
line 57, in fix_call
File "<old_dir>/lib/galaxy/web/buildapp.py", line 68, in app_factory
File "<old_dir>/lib/galaxy/web/buildapp.py", line 38, in add_controllers
File "<new_dir>/lib/galaxy/web/controllers/page.py", line 9, in <module>
class PageListGrid( grids.Grid ):
NameError: name 'grids' is not defined
As you may notice there are some files in the stacktrace from old_dir.
Even more confusing is, that I renamed <old_dir> in the meantime. So
these files are nonexistant.
Where are these pathes hardcoded?
to reduce traffic when importing big dataset into our local galaxy we
would like to copy directly from the fileserver (which is accessible
from the galaxy server via NFS) into galaxy without moving through the
users desktop computer.
Is there already such a tool by chance? At a glance I could only find
import.py which imports only from a predefined set of files.
So if no such tool exist what would be the best starting point?
For security reasons I would restrict the import to a certain directory.
Anything else to keep in mind?
we just noticed a bug: we added a tag to history. Then we run a tool.
After that the list of datasets in the right pane just disappeared.
This is in rev 2690. Could not find any related update.
This question is more applicable to our galaxy-user list, so I am
redirecting it there. See the reply below.
What you are trying to do is, in fact, quite easy to perform with
1. Extend gene coordinates either direction with "Operate of Genomic
2. Join the newly extended genes with SNP dataset using "Operate of
3. Group by gene name and concatenate on SNP name using "Join,
Subtract and Group -> Join".
Please, see this history:
for an example. If you click on "rerun" link within history item (see
attached image), you will be able to see parameters I've used.
NOTE: There are two kind of join in Galaxy: relational join ("Join,
Subtract and Group->Join") and interval join ("Operate of Genomic
Intervals->Join"). Here we use interval join.
If have any trouble I will make a galactic quickie (short movie) for
On Sep 16, 2009, at 8:57 AM, Gerome Breen wrote:
> I am puzzled about how to generate something - can you help? I want to
> generate a file with hapmap or other sets of snps mapped to UCSC
> genes. I want to have one line per gene with the min start -20kb and
> max end +20kb and then a tab sperated list of hapmap SNPs in each
> gene. I have tried to do this but failed - the one line per gene is
> complicate by the fact that aggregate on column seems to discard the
> chr information and a join within two coordinates doesn't seem to be
> available but anyway would be very computationally intensive. Any
> solutions would be appreciated.
> The file format I am aiming at:
> chr start end gene_name snp1 snp2 snp3 etc.
> galaxy-bugs mailing list
i would like to nest different conditional statements in a tools xml file:
<param name="type1" type="select" label="input file format"
<option value="fasta" selected="true">FASTA</option>
<param name="type2" type="select" label="Paired end reads">
<option value="no" selected="true">No</option>
how do i access type2?
I have a problem saving workflows, every time I click the save button, the
dialog saying "Saving..." comes up but never disappears. I can't click on
anything, bu have to reload the page. When I then check the workflow,
nothing is saved. This happenes to me using Firefox3@Fedora10,
Firefox3.5(a)MacOsX10.5 and Safari(a)MacOsX10.5, both on the public Galaxy and
on our local copy. Has anyone else seen this?
I tried to update our local galaxy installation. I'm quite unexperienced
with Mercurial so I read up something on the web how to update. What I
After that I tried to restart but got an error message that I need to
run "sh manage_db.sh upgrade" which I did. So now it is running again.
But when I connect I see in the main screen: "Galaxy build: $Rev" which
is an old version. Does that mean something in my update failed? (I did
not get any messages that hinted at some problems beside the database
version.) Or was just some template not updated?