Sharing tool definitions between XML files
by Peter
Hi all,
I'm wondering if there is any established way to share parameter
definitions between tool wrapper XML files?
For example, I am currently working on NCBI BLAST+ wrappers, and these
tools have a lot in common. For example, the output format option will
be a select parameter, and it will be the same for blastn, blastp,
tblastn, etc. I can just cut and paste the definition but this seems
inelegant and will be a long term maintenance burden if it ever needs
updating (lots of places would need to be updated the same way). I'd
like to have a shared XML snippet defining this parameter which I
could then reference/include from each tool wrapper than needs it.
I'm thinking of something like XML's <!ENTITY ...> might work. Is this possible?
Peter
11 years, 8 months
swap issue
by Isabelle Phan
Hello,
I am running galaxy, using a postgres backend.
The galaxy server systematically gets killed whenever I try uploading a bam file. The samtools process is still running.
This is the end of the log:
2010-08-26 18:08:11,371 INFO sqlalchemy.engine.threadlocal.TLEngine.0x...4610 {'param_1': 8}
sqlalchemy.engine.threadlocal.TLEngine.0x...4610 INFO 2010-08-26 18:08:11,371 {'param_1': 8}
2010-08-26 18:08:11,378 INFO sqlalchemy.pool.QueuePool.0x...4ed0 Connection <connection object at 0x567bf30; dsn: 'dbname=galaxy host=/var closed: 0> being returned to pool
sqlalchemy.pool.QueuePool.0x...4ed0 INFO 2010-08-26 18:08:11,378 Connection <connection object at 0x567bf30; dsn: 'dbname=galaxy host=/var closed: 0> being returned to pool
10.1.20.44 - - [26/Aug/2010:18:08:06 -0700] "POST /root/history_item_updates HTTP/1.1" 200 - "http://galaxy:8080/history" "Mozilla/5.0 (X1 (x86_64); en-US; rv:1.9.2.8) Gecko/20100722 Firefox/3.6.8"
Killed
I have the following options set in universe_wsgi.ini:
database_engine_option_server_side_cursors = True
database_engine_option_strategy = threadlocal
It seems to be running out of swap. I monitored memory usage with 'top' and galaxy died when available swap hit 0k free.
I am not superuser on the machine where galaxy is running and I have no other server available. Is there something I could do to prevent galaxy from dying?
Thanks,
Isabelle
--
Isabelle Phan, DPhil
Seattle Biomedical Research Institute
+1(206)256 7113
11 years, 10 months
Fastq_filter fails on large files
by Isabelle Phan
Hello,
The tool fastq_filter worked on 1M reads, but fails (hangs) on 15M reads. I had to kill the job after the user let it run for a whole day. The debug.txt file containing a python function "fastq_read_pass_filter" is created in the files/000/dataset_xxx_files directory. I am getting no error from the galaxy server.
I wonder what could cause fastq_filter to fail? The fastx equivalent tool works, but it misses all the options of fastq_filter.
I'd be grateful for any hints to help me get fastq_filter to work on large fastq files.
Thanks
Isabelle
12 years, 3 months
NCBI BLAST+ wrappers in Galaxy?
by Peter
Hi all,
Something I expect to find useful in several analysis pipelines is
a Galaxy wrapper for the NCBI BLAST+ tools (or even the old
NCBI "legacy" BLAST tools if such a wrapper exists).
I've been looking over the tools in galaxy-dist and galaxy-central and
the only NCBI BLAST wrapper I can see is for MEGABLAST, under
tools/metag_tools.
Is there some more general NCBI BLAST+ wrappers that I have
missed? Or is anyone already working on this?
Thanks,
Peter
12 years, 3 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
12 years, 4 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
12 years, 4 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
12 years, 4 months
