Pull request for bowtie_wrappers tool
by Nicola Soranzo
Dear Galaxy DevTeam,
I have made a few updates to the bowtie_wrappers tool from the Tool
Shed, may someone please pull from:
https://bitbucket.org/nsoranzo/bowtie_wrappers/
for the following changes:
- Add fields for --nofw and --norc options also for single-end reads
- Remove field for --cutoff option of bowtie-build
- Do not show fields for --best and --strata options for paired-end
reads
- Add control to choose between -a and -k options
- Show fields for --pairtries and --maxbts options only when noTryHard
- Add control to choose between Maq- and SOAP-like alignment
- Add range validators to all integer parameters
I am not sure this mailing list is the correct place for such pull
requests, if not please advise me!
Thanks,
Nicola
--
Nicola Soranzo, Ph.D.
CRS4
Bioinformatics Program
Loc. Piscina Manna
09010 Pula (CA), Italy
http://www.bioinformatica.crs4.it/
9 years, 3 months
Uploading large files as Admin Still slow!
by Jackie Lighten
Hi,
I am trying to upload 2x 2.5GB files to my data libraries (in Admin on a
local instance) but it has so far been running over night and not completed.
How can I speed this up?
Can I upload compressed files?
Can I not just copy these files directly in to
$galaxy-dist/database/files/000 ?
Thanks,
Jack
9 years, 3 months
Selecting Intermediary Files in a Workflow
by Kolby Chien
Hello,
I've been working with a local installation of Galaxy and my question is
about how Galaxy chooses which file to use in the next step of the
workflow.
I have created a custom file type called "cub" which is required for my
custom tools and I have added this custom file type into the extension
list. When I run the first step of my workflow, Galaxy will create an
intermediate cub file called dataset_51.dat.cub containing my processed
data, but also an empty intermediate dat file as well of the same name sans
cub extension (dataset_51.dat) . The next tool in the workflow requires a
cub file type input, but instead of using the cub file, it chooses to
process the empty .dat file instead, causing the tool to process
incorrectly.
I've looked over some settings and double checked that my tool xml files
specify cub as the output file type and as the input file type for the next
tool, but now I am at a loss. Is there anyway to specify to Galaxy that
the cub file should be used in the next step of the workflow instead of the
dat file?
Thank you very much for your help,
Kolby
9 years, 3 months
lwr job runner error.
by Luobin Yang
Hi,
I checked out a refresh copy of latest galaxy-dist, but I found the
following error in the log file after I ran Galaxy:
galaxy.jobs.handler ERROR 2013-01-27 10:10:19,168 Job runner is not
loadable: galaxy.jobs.runners.lwr
Traceback (most recent call last):
File "/home/galaxy/galaxy-dist/lib/galaxy/jobs/handler.py", line 447, in
_load_plugin
module = __import__( module_name )
File "/home/galaxy/galaxy-dist/lib/galaxy/jobs/runners/lwr.py", line 232
worker = threading.Thread( ( name="LwrJobRunner.thread-%d" % i ),
target=self.run_next )
^
SyntaxError: invalid syntax
Luobin
9 years, 3 months
galaxy.json?
by Luobin Yang
Hi,
When I run a job in my locally installed Galaxy, there is always an error
message showing in the log file:
Error opening galaxy.json file: [Errno 2] No such file or directory:
'/home/galaxy/galaxy-dist/database/job_working_directory/005/5797/galaxy.json
Any clue how to get rid of it?
Thanks,
Luobin
9 years, 3 months
ce10
by Alfonso Garrido-Lecca
Hello,
Could somebody please help me uploading the C. elegans genome (Ce10) into
galaxy on the cloud?
thanks
alfonso
9 years, 3 months
Tool metadata of Flexbar
by Johannes Röhr
Recently, I updated the Flexbar tool definition in the Galaxy Tool Shed repository flexbar to work with a new version of the program. I changed the version of the tool definition from 2.3 to 2.31, adjusted requirements and uploaded files. However, the Flexbar tool in the repo still shows the old tool version and requirements, whereas the tool command seems to be updated.
Furthermore, the change log shows that new repository metadata is associated with the latest change set, but bizarrely the initial metadata is now associated with commit 11 instead of 12, which was the last bugfix commit before the update (commit 13). The update took place more than a week ago.
Any suggestions why that is the case? Thanks!
9 years, 3 months
Blank history panel / Error in history API at listing contents
by Peter Cock
Hello all,
I've noticed on my test setup (tracking galaxy-central) a problem with
some histories not displaying. If I click on saved histories, I am show
a list. Some will load (slower than I recall), but others result in a blank
right hand pane - with the following error from run.sh
galaxy.webapps.galaxy.api.history_contents ERROR 2013-01-16
15:24:22,726 Error in history API at listing contents: <type
'exceptions.TypeError'>, cannot concatenate 'str' and 'NoneType'
objects
The same error and blank pane happens if I click on the reload
history icon. A screenshot is attached.
This error is coming from HistoryContentsController in file
lib/galaxy/webapps/galaxy/api/history_contents.py - specifically
in the call to get_hda_dict. I tried modifying this for loop so that
any individual transaction with an error is ignored (but a debug
message logged), and I could then load the rest of the problem
histories.
The error from get_hda_dict is from the first line, which takes
the galaxy.model.HistoryDatasetAssociation object and asks:
hda_dict = hda.get_api_value( view='element' )
That takes us to lib/galaxy/model/__init__.py and the root of
the problem: I am seeing entries where both name and val
are None, meaning this line fails with the TypeError above:
rval['metadata_' + name] = val
Clearly some of my histories now have some 'bad' data in them,
and currently Galaxy is failing to cope. Based on the ID numbers
this has been happening for a while, so not a recent regression.
Here is a patch which seems to help.
Peter
$ hg diff lib/galaxy/model/__init__.py
diff -r 81c3b8a6a621 lib/galaxy/model/__init__.py
--- a/lib/galaxy/model/__init__.py Wed Jan 16 15:14:04 2013 +0000
+++ b/lib/galaxy/model/__init__.py Wed Jan 16 16:26:28 2013 +0000
@@ -1530,7 +1530,11 @@
val = val.file_name
elif isinstance( val, list ):
val = ', '.join( [str(v) for v in val] )
- rval['metadata_' + name] = val
+ if name is None:
+ log.debug("get_api_value(view=%r) : name %r, val %r"
% (view, name, val))
+ assert val is None, "get_api_value(view=%r) : name
%r, val %r" % (view, name, val)
+ else:
+ rval['metadata_' + name] = val
return rval
class HistoryDatasetAssociationDisplayAtAuthorization( object ):
9 years, 3 months
Galaxy is hiring Software Engineers and Post-Docs
by Dave Clements
Hello all,
The Galaxy Project is once again expanding and we are looking for
highly-motivated, seeking-a-challenge, computationally-savvy,
biologically-aware software engineers and post-docs to work on the project.
See http://bit.ly/gxyhiring for details.
Really, it's a great project with a great community. If you or someone you
know would be interested in working with this thriving community on a
rapidly evolving high performance platform that is used by thousands of
researchers around the world every day, then please consider joining the
team.
As always, please let me, or any of us (
http://wiki.galaxyproject.org/GalaxyTeam), know if you have any questions.
Thanks,
Dave Clements
Galaxy Training and Outreach
--
<http://galaxyproject.org/wiki/GCC2012>http://galaxyproject.org/
http://getgalaxy.org/
http://usegalaxy.org/
http://wiki.galaxyproject.org/
9 years, 3 months
Galaxy with Univa Grid Engine (UGE) instead of SGE?
by Peter Cock
Hello all,
Our local Galaxy server had been running happily under SGE, using
one of the last free releases (not sure exactly which - I could ask).
Due to concerns about long term maintenance, the SysAdmin has
moved us to an SGE compatible setup - Univa Grid Engine (UGE).
However, in at least one respect this is not a drop in replacement,
while other cluster usage appears to be working fine our Galaxy
installation is not, e.g.
galaxy.jobs.runners.drmaa DEBUG 2013-01-15 17:14:33,660 (331:842)
submitting file
/mnt/galaxy/galaxy-central/database/pbs/galaxy_331:842.sh
galaxy.jobs.runners.drmaa DEBUG 2013-01-15 17:14:33,661 (331:842)
command is: /mnt/galaxy/galaxy-central/extract_dataset_parts.sh
/mnt/galaxy/galaxy-central/database/job_working_directory/000/331/task_0;
blastp -query "/mnt/galaxy/galaxy-central/database/job_working_directory/000/331/task_0/dataset_344.dat"
-db "/var/local/blast/ncbi/nr" -task blastp -evalue 0.001 -out
/mnt/galaxy/galaxy-central/database/job_working_directory/000/331/task_0/dataset_373.dat
-outfmt 5 -num_threads 8
galaxy.jobs.runners.drmaa ERROR 2013-01-15 17:14:33,666 Uncaught
exception queueing job
Traceback (most recent call last):
File "/mnt/galaxy/galaxy-central/lib/galaxy/jobs/runners/drmaa.py",
line 146, in run_next
self.queue_job( obj )
File "/mnt/galaxy/galaxy-central/lib/galaxy/jobs/runners/drmaa.py",
line 234, in queue_job
job_id = self.ds.runJob(jt)
File "/mnt/galaxy/galaxy-central/eggs/drmaa-0.4b3-py2.6.egg/drmaa/__init__.py",
line 331, in runJob
_h.c(_w.drmaa_run_job, jid, _ct.sizeof(jid), jobTemplate)
File "/mnt/galaxy/galaxy-central/eggs/drmaa-0.4b3-py2.6.egg/drmaa/helpers.py",
line 213, in c
return f(*(args + (error_buffer, sizeof(error_buffer))))
File "/mnt/galaxy/galaxy-central/eggs/drmaa-0.4b3-py2.6.egg/drmaa/errors.py",
line 90, in error_check
raise _ERRORS[code-1]("code %s: %s" % (code, error_buffer.value))
DeniedByDrmException: code 17: error: no suitable queues
Debugging this by attempting a manual submission,
$ qsub /mnt/galaxy/galaxy-central/database/pbs/galaxy_331:842.sh
Unable to run job: Colon (':') not allowed in objectname.
Exiting.
Renaming the file to replace the colon with (say) an underscore allows
a manual qsub to work fine with UGE. I've edited Galaxy to avoid the
colons (patch below) but the submission still fails.
Additionally removing the SGE specific settings in universe_wsgi.ini did
allow the job to be submitted I am still having problems. Perhaps I need
to fix all the other filenames too (e.g. stdout, stderr, error code), or do that
in one go by removing the colon in the job name?
Has anyone else tried Galaxy under UGE, and do you have any advice?
Thanks,
Peter
--
Quick filename hack to avoid colons in job script filenames - might
be better to avoid this in the job name itself?
$ hg diff
diff -r 1bfe2768026a lib/galaxy/jobs/runners/drmaa.py
--- a/lib/galaxy/jobs/runners/drmaa.py Mon Jan 14 17:21:25 2013 +0000
+++ b/lib/galaxy/jobs/runners/drmaa.py Tue Jan 15 18:44:31 2013 +0000
@@ -191,7 +191,7 @@
job_name = ''.join( map( lambda x: x if x in ( string.letters
+ string.digits + '_' ) else '_', job_name ) )
jt = self.ds.createJobTemplate()
- jt.remoteCommand = "%s/galaxy_%s.sh" %
(self.app.config.cluster_files_directory, job_wrapper.get_id_tag())
+ jt.remoteCommand = ("%s/galaxy_%s.sh" %
(self.app.config.cluster_files_directory,
job_wrapper.get_id_tag())).replace(":", "_")
jt.jobName = job_name
jt.outputPath = ":%s" % ofile
jt.errorPath = ":%s" % efile
@@ -229,6 +229,7 @@
log.debug("(%s) submitting file %s" % ( galaxy_id_tag,
jt.remoteCommand ) )
log.debug("(%s) command is: %s" % ( galaxy_id_tag, command_line ) )
+ log.debug("(%s) spec: %s" % ( galaxy_id_tag, native_spec))
# runJob will raise if there's a submit problem
if self.external_runJob_script is None:
job_id = self.ds.runJob(jt)
@@ -423,7 +424,7 @@
drm_job_state.ofile = "%s.drmout" % os.path.join(os.getcwd(),
job_wrapper.working_directory, job_wrapper.get_id_tag())
drm_job_state.efile = "%s.drmerr" % os.path.join(os.getcwd(),
job_wrapper.working_directory, job_wrapper.get_id_tag())
drm_job_state.ecfile = "%s.drmec" % os.path.join(os.getcwd(),
job_wrapper.working_directory, job_wrapper.get_id_tag())
- drm_job_state.job_file = "%s/galaxy_%s.sh" %
(self.app.config.cluster_files_directory, job.get_id())
+ drm_job_state.job_file = ("%s/galaxy_%s.sh" %
(self.app.config.cluster_files_directory, job.get_id())).replace(":",
"_")
drm_job_state.job_id = str( job_id )
drm_job_state.runner_url = job_wrapper.get_job_runner_url()
job_wrapper.command_line = job.get_command_line()
9 years, 3 months
