megablast installation in Galaxy
by Eric Enns
Hi
I am implementing a local installation of galaxy and am stuck on the
megablast portion. I installed blast 2.2.24 which includes formatdb and
megablast. The installation guide says to use BLAST+, but that does not have
megablast or formatdb in it. The megablast installation I have does not
output in the correct format. How do I install BLAST+ so that it will work
in galaxy.
-Eric
10 years, 9 months
Setting default entry in select parameter
by Peter
Hi all,
I'm trying to setup a select parameter where I want to pre-select an entry as
the default (rather than just the first entry). To that end, I have
set the value
attribute as implied by the wiki documentation:
http://bitbucket.org/galaxy/galaxy-central/wiki/ToolConfigSyntax
e.g.
<param name="matrix" type="select" value="BLOSUM62" label="Scoring matrix">
<option value="BLOSUM80">BLOSUM80</option>
<option value="BLOSUM62">BLOSUM62 (default)</option>
<option value="BLOSUM50">BLOSUM50</option>
<option value="BLOSUM45">BLOSUM45</option>
<option value="PAM250">PAM250</option>
<option value="BLOSUM90">BLOSUM90</option>
<option value="PAM30">PAM30</option>
<option value="PAM70">PAM70</option>
</param>
This does not work - Galaxy (in Firefox at least) always defaults to the first
entry as the default. This also happens if I set display="radio". Is this a bug,
is setting a default for select parameters done in another way, or is this a
missing feature?
For now I have just put the default at the top, breaking the alphabetic order:
<param name="matrix" type="select" label="Scoring matrix">
<option value="BLOSUM62">BLOSUM62 (default)</option>
<option value="BLOSUM80">BLOSUM80</option>
<option value="BLOSUM50">BLOSUM50</option>
<option value="BLOSUM45">BLOSUM45</option>
<option value="PAM250">PAM250</option>
<option value="BLOSUM90">BLOSUM90</option>
<option value="PAM30">PAM30</option>
<option value="PAM70">PAM70</option>
</param>
Regards,
Peter
10 years, 9 months
Managing galaxy-central in a local svn repo
by Branden Timm
Hello,
I am trying to figure out the best way to use subversion to track both
galaxy-central and our local tool integration work. We are standardized
on subversion, so I'd like to use it if possible. What I've done so far:
Downloaded the latest galaxy-central 'hg clone
https://bitbucket.org/galaxy/galaxy-central'
Copied galaxy-central, including mercurial info, into the /trunk
subdirectory of my repo.
My plan is that when future revisions to galaxy-central are available, I
can create a new branch, use hg pull to update the codebase, test, and
finally merge that branch back into /trunk.
I noticed that just the size of the galaxy-central mercurial repo is
about 230M. Is this because back-versions are being included? If so,
should I just do a clone to the most recent revision and then use 'hg
pull' to apply future revisions?
Cheers
--
Branden Timm
University of Wisconsin
Great Lakes Bioenergy Research Center
btimm(a)glbrc.wisc.edu
10 years, 9 months
Using rsyslog for logging from Galaxy
by Peter
Hi all,
For our production server we are using rsyslog for centralised logging,
http://www.rsyslog.com/
Galaxy is using "import logging" which can output to rsyslog, using
SysLogHandler rather than StreamHandler or FileHandler. Based
on grep'ing the source code Galaxy doesn't support this yet. I
could probably add it but it isn't clear to me where this would be
done... functions configure_logging() in lib/galaxy/config.py and
in lib/galaxy/webapps/community/config.py look like strong
possibilities but both allow for some global_conf_parser override
(and I'm not sure what that does).
Has anyone looked at modifying this area before, or could offer
some tips?
Thanks,
Peter
10 years, 9 months
Re: [galaxy-dev] [galaxy-user] Undocumented tags for tool configuration
by Kelly Vincent
Jelle,
(I've copied this to galaxy-dev since it's more appropriate to that one)
The data table approach is fairly new, so there aren't too many
examples yet, although more tools are being converted and will be
available soon in the distribution. Basically, there are 3 steps to
using it:
1. Modify tool_data_table_conf.xml to specify:
- the bowtie data table
- the column types in the loc file
- It should look something like this:
<table name="bowtie_indexes">
<columns>name, value</columns>
<file path="tool-data/bowtie_indices.loc" />
</table>
2. Create/modify the loc file to correspond with the column types
specified in tool_data_table_conf.xml (in this example, the loc file
doesn't have to be changed), though we are going to be changing the
specification to <columns>value, dbkey, name, path</columns>
3. Modify the Bowtie wrapper to use the data table instead of the loc
file directly, replacing this:
<options from_file="bowtie_indices.loc">
<column name="value" index="1" />
<column name="name" index="0" />
</options>
- with this:
<options from_data_table="bowtie_indexes"/>
The <actions> in the Bowtie wrapper is used in lieu of the deprecated
<code> tag to set the dbkey of the output dataset. In
bowtie_wrapper.xml, according to the first action block, if the
refGenomeSource.genomeSource is "indexed" (not "history"), then it
will assign the dbkey of the output file to be the same as that of the
reference file. It does this by looking at through the loc file and
finding the line that has the value that's been selected in the index
dropdown box as column 1 of the loc file entry and using the dbkey, in
column 0 (ignoring comment lines (starting with #) along the way).
If refGenomeSource.genomeSource is "history", it resorts to default
behavior for Galaxy, which is that the output is assigned the same
value as the first input that has a dbkey specified.
The second block would not be needed for most cases--it is required
here to handle the specific case of a small reference file we use for
functional testing. It says that if the dbkey has been set to
"equCab2chrM" (that's what the <filter type="metadata_value"...
column="1" /> tag) does then it should be changed to "equCab2" (the
<option type="from_param" ... column="0" ...> tag does).
If you need more information than this, let us know.
Regards,
Kelly
On Oct 1, 2010, at 4:22 AM, Jelle Scholtalbers wrote:
> Hey,
>
> I was looking through the bowtie_wrapper.xml to get some information
> about how to use the tool_data_table_conf.xml. There I also noticed
> in the output section the tag <actions>.
> Is there any information on this tag as is does seem to be used a lot?
>
> Cheers,
> Jelle
> _______________________________________________
> galaxy-user mailing list
> galaxy-user(a)lists.bx.psu.edu
> http://lists.bx.psu.edu/listinfo/galaxy-user
10 years, 10 months
target in links
by Belinda M. Giardine
Am I missing something or is it not possible to set the target in the
links from reStructuredText? It would be nice to be able to open help
links in a separate window.
Belinda
10 years, 10 months
Error running workflow
by Branden Timm
Hello,
I seem to be having database-related issues when running my workflow.
galaxy.jobs DEBUG 2010-09-09 21:14:48,967 dispatching job 180 to local runner
galaxy.jobs INFO 2010-09-09 21:14:49,058 job 180 dispatched
galaxy.jobs.runners.local DEBUG 2010-09-09 21:14:49,697 executing: soap -a /home/galaxy/galaxy_dist/database/files/000/dataset_400.dat -D /home/galaxy/galaxy_dist/soap_indices/ecoli_U00096.fasta.index -o /home/galaxy/galaxy_dist/database/files/000/dataset_431.dat -u None -r 1 -n 5 -v 2 -M 4 2>&1
galaxy.jobs ERROR 2010-09-09 21:14:50,209 failure running job 181
Traceback (most recent call last):
File "/home/galaxy/galaxy_dist/lib/galaxy/jobs/__init__.py", line 185, in __monitor_step
self.sa_session.refresh( job )
File "/home/galaxy/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.4.egg/sqlalchemy/orm/scoping.py", line 127, in do
return getattr(self.registry(), name)(*args, **kwargs)
File "/home/galaxy/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.4.egg/sqlalchemy/orm/session.py", line 926, in refresh
self._validate_persistent(state)
File "/home/galaxy/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.4.egg/sqlalchemy/orm/session.py", line 1234, in _validate_persistent
raise sa_exc.InvalidRequestError(
InvalidRequestError: Instance '<Job at 0x1a4074d0>' is not persistent within this Session
146.151.211.150 - - [09/Sep/2010:21:14:48 -0500] "POST /workflow/run?id=f597429621d6eb2b HTTP/1.1" 200 - "http://galaxy.glbrc.wisc.edu/workflow/run?id=f597429621d6eb2b" "Mozilla/5.0 (Macintosh; U; Intel Mac OS X 10_6_4; en-us) AppleWebKit/533.17.8 (KHTML, like Gecko) Version/5.0.1 Safari/533.17.8"
galaxy.jobs ERROR 2010-09-09 21:14:51,219 failure running job 182
Traceback (most recent call last):
File "/home/galaxy/galaxy_dist/lib/galaxy/jobs/__init__.py", line 185, in __monitor_step
self.sa_session.refresh( job )
File "/home/galaxy/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.4.egg/sqlalchemy/orm/scoping.py", line 127, in do
return getattr(self.registry(), name)(*args, **kwargs)
File "/home/galaxy/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.4.egg/sqlalchemy/orm/session.py", line 926, in refresh
self._validate_persistent(state)
File "/home/galaxy/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.4.egg/sqlalchemy/orm/session.py", line 1234, in _validate_persistent
raise sa_exc.InvalidRequestError(
InvalidRequestError: Instance '<Job at 0x2aaab001acd0>' is not persistent within this Session
galaxy.jobs.runners.local DEBUG 2010-09-09 21:14:52,460 execution finished: soap -a /home/galaxy/galaxy_dist/database/files/000/dataset_400.dat -D /home/galaxy/galaxy_dist/soap_indices/ecoli_U00096.fasta.index -o /home/galaxy/galaxy_dist/database/files/000/dataset_431.dat -u None -r 1 -n 5 -v 2 -M 4 2>&1
In Galaxy itself, the SOAP tool returns its results and the rest of the jobs just wait to run. Why am I having these errors?
Cheers
--
Branden Timm
btimm(a)glbrc.wisc.edu
10 years, 10 months
user interface aspects don't show up right or look right in IE 7
by Leandro Hermida
Hello,
I just had a look and see initially that certain aspects of the Galaxy
UI don't show up or don't look right in IE 7, e.g. in the history pane
the underlying link on the name of each data object to expand it isn't
there.
Is IE 7 supported? I dislike IE and don't use it otherwise but am
forced to use it in my environment as it's part of there standard
client image and it is almost impossible to get another browser like
Firefox installed for every user that will use Galaxy.
best,
Leandro
10 years, 10 months
