Help with Summary Statistics
by D. A. Cowart
Hello,
I am attempting to use Galaxy to calculate the mean sequence read
length and identify the range of read lengths for my 454 data. The
data has already been organized and sorted by species. The format of
the data is as follows:
>HD4AU5D01BHBCQCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC
>HD4AU5D01A093MCTCTGTCGCTCTGTCTCTCTTCTCTCTCTCTCTCTCT
etc...for each species
I have attempted to use the "Summary Statistics" button, however it
appears to only be for numerical data and not sequence data. Is this
tool/task available
via Galaxy?
Thank you,
Dominique Cowart
User name: dac330
8 years
from Galaxy to Megan
by Judith van Bleijswijk
Dear Galaxy users that also use Megan,
I hope you can help me combining Galaxy with Megan4. I followed the Galaxy metagenome workflow (author aun1) on shotgun DNA 454 sequences of two samples that I would like to compare. The results are two nice trees and tables with the lowest taxonomic ranks for the two samples.
Besides the taxonomy I am also interested in the functions and I would like to use Megan4 (with SEED and KEGG classification) for this purpose. I tried to import a Galaxy file (.tabular) with c1 =high quality segment name and c2-c13 =blasthit results and a Galaxy fasta file with the high quality segment names and sequences. This does not work and I receive the message parsing failed, no reads found.
I am interested to know how you solved this issue and which files in the Galaxy metagenome workflow you use to import into Megan4.
Or maybe there is other software that you use to compare suits of functional genes in your metagenome datasets?
Regards,
Judith van Bleijswijk
9 years, 7 months
Why doesn't bowtie in galaxy accepting colorspace reads directly?
by Praveen Raj Somarajan
Hi All,
I'm wondering why the Bowtie version in (even latest) Galaxy does NOT support .csfasta/.qual input files directly, though it is mentioned under "Map with Bowtie for SOLiD". This is the case of "BWA for SOLiD" as well. One would expect direct support on colorspace files. Do you have any plans of implementing this?I see this would be a great support to SOLiD users.
Look forward to your comments
Thanks,
Raj
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9 years, 7 months
GeneTrack server error
by Doo Yang
Hi,
I can't connect the GeneTrack server.
This is the error message.
I tried this a couple times in different days but keeps failing.
Firefox can't establish a connection to the server at
genetrack.g2.bx.psu.edu.
Thank you,
9 years, 7 months
FTP Upload Error
by Amanda Jones
I'm having trouble uploading via FTP to my Galaxy account. I've been
receiving the following error message: 503 Sorry, the maximum number of
clients(3) for this user are already connected. I've ensured that I'm
only using a single connection to upload. Any clue what's going on? I
still have available space in my Galaxy account for the upload and I've
previously uploaded similarly sized files with no problems.
9 years, 7 months
igenome error
by Paul Brady
I try to download the human hg19 from igenomes in galaxy.
I use 'shared data' > 'data libraries' > 'igenomes' > select hg19, but this persistently downloads the mm9 mouse genome not the human genome.
Any suggestions?
Paul Brady
Afdeling CME-UZ,
O&N I Herestraat 49 - bus 602,
3000 Leuven,
Belgium.
Tel: +32 16 345902
e-mail: Paul.Brady(a)med.kuleuven.be
9 years, 7 months
Errors during database migration after updating galaxy
by Joel Rosenberg
My cloud galaxy cluster can't boot up after attempting a bitbucket update due to a 502 HTTP error when trying to update the DB. Here's the log:
/mnt/galaxyTools/galaxy-central/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.6-linux-x86_64-ucs4.egg/pysam/__init__.py:1: RuntimeWarning: __builtin__.file size changed, may indicate binary incompatibility
from csamtools import *
python path is: /mnt/galaxyTools/galaxy-central/eggs/numpy-1.6.0-py2.6-linux-x86_64-ucs4.egg, /mnt/galaxyTools/galaxy-central/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.6-linux-x86_64-ucs4.egg, /mnt/galaxyTools/galaxy-central/eggs/boto-2.5.2-py2.6.egg, /mnt/galaxyTools/galaxy-central/eggs/mercurial-2.2.3-py2.6-linux-x86_64-ucs4.egg, /mnt/galaxyTools/galaxy-central/eggs/Fabric-1.4.2-py2.6.egg, /mnt/galaxyTools/galaxy-central/eggs/ssh-1.7.14-py2.6.egg, /mnt/galaxyTools/galaxy-central/eggs/Whoosh-0.3.18-py2.6.egg, /mnt/galaxyTools/galaxy-central/eggs/pycrypto-2.5-py2.6-linux-x86_64-ucs4.egg, /mnt/galaxyTools/galaxy-central/eggs/python_lzo-1.08_2.03_static-py2.6-linux-x86_64-ucs4.egg, /mnt/galaxyTools/galaxy-central/eggs/bx_python-0.7.1_7b95ff194725-py2.6-linux-x86_64-ucs4.egg, /mnt/galaxyTools/galaxy-central/eggs/amqplib-0.6.1-py2.6.egg, /mnt/galaxyTools/galaxy-central/eggs/pexpect-2.4-py2.6.egg, /mnt/galaxyTools/galaxy-central/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg, /mnt/galaxyTools/galaxy-central/eggs/Babel-0.9.4-py2.6.egg, /mnt/galaxyTools/galaxy-central/eggs/MarkupSafe-0.12-py2.6-linux-x86_64-ucs4.egg, /mnt/galaxyTools/galaxy-central/eggs/Mako-0.4.1-py2.6.egg, /mnt/galaxyTools/galaxy-central/eggs/WebHelpers-0.2-py2.6.egg, /mnt/galaxyTools/galaxy-central/eggs/simplejson-2.1.1-py2.6-linux-x86_64-ucs4.egg, /mnt/galaxyTools/galaxy-central/eggs/wchartype-0.1-py2.6.egg, /mnt/galaxyTools/galaxy-central/eggs/elementtree-1.2.6_20050316-py2.6.egg, /mnt/galaxyTools/galaxy-central/eggs/docutils-0.7-py2.6.egg, /mnt/galaxyTools/galaxy-central/eggs/WebOb-0.8.5-py2.6.egg, /mnt/galaxyTools/galaxy-central/eggs/Routes-1.12.3-py2.6.egg, /mnt/galaxyTools/galaxy-central/eggs/Cheetah-2.2.2-py2.6-linux-x86_64-ucs4.egg, /mnt/galaxyTools/galaxy-central/eggs/PasteDeploy-1.3.3-py2.6.egg, /mnt/galaxyTools/galaxy-central/eggs/PasteScript-1.7.3-py2.6.egg, /mnt/galaxyTools/galaxy-central/eggs/Paste-1.6-py2.6.egg, /mnt/galaxyTools/galaxy-central/lib, /usr/lib/python2.6/, /usr/lib/python2.6/plat-linux2, /usr/lib/python2.6/lib-tk, /usr/lib/python2.6/lib-old, /usr/lib/python2.6/lib-dynload
galaxy.tool_shed.tool_shed_registry DEBUG 2012-09-30 21:13:18,317 Loading references to tool sheds from tool_sheds_conf.xml
galaxy.tool_shed.tool_shed_registry DEBUG 2012-09-30 21:13:18,317 Loaded reference to tool shed: Galaxy main tool shed
galaxy.tool_shed.tool_shed_registry DEBUG 2012-09-30 21:13:18,318 Loaded reference to tool shed: Galaxy test tool shed
galaxy.model.migrate.check DEBUG 2012-09-30 21:13:18,344 psycopg2 egg successfully loaded for postgres dialect
galaxy.model.migrate.check INFO 2012-09-30 21:13:18,610 At database version 107
galaxy.tool_shed.migrate.check DEBUG 2012-09-30 21:13:18,620 psycopg2 egg successfully loaded for postgres dialect
Traceback (most recent call last):
File "/mnt/galaxyTools/galaxy-central/lib/galaxy/webapps/galaxy/buildapp.py", line 36, in app_factory
app = UniverseApplication( global_conf = global_conf, **kwargs )
File "/mnt/galaxyTools/galaxy-central/lib/galaxy/app.py", line 47, in __init__
verify_tools( self, db_url, kwargs.get( 'global_conf', {} ).get( '__file__', None ), self.config.database_engine_options )
File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tool_shed/migrate/check.py", line 54, in verify_tools
missing_tool_configs_dict = check_for_missing_tools( app, tool_panel_configs, latest_tool_migration_script_number )
File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tool_shed/migrate/common.py", line 33, in check_for_missing_tools
response = urllib2.urlopen( url )
File "/usr/lib/python2.6/urllib2.py", line 126, in urlopen
return _opener.open(url, data, timeout)
File "/usr/lib/python2.6/urllib2.py", line 397, in open
response = meth(req, response)
File "/usr/lib/python2.6/urllib2.py", line 510, in http_response
'http', request, response, code, msg, hdrs)
File "/usr/lib/python2.6/urllib2.py", line 435, in error
return self._call_chain(*args)
File "/usr/lib/python2.6/urllib2.py", line 369, in _call_chain
result = func(*args)
File "/usr/lib/python2.6/urllib2.py", line 518, in http_error_default
raise HTTPError(req.get_full_url(), code, msg, hdrs, fp)
HTTPError: HTTP Error 502: Bad Gateway
Removing PID file paster.pid
9 years, 7 months
server down?
by DEDRICK＠pitt.edu
I am using Galaxy main and my jobs aren't running. They are still grey
colored, indicating that they haven't started. I used Galaxy main
yesterday just fine. Is something wrong with the server?
I tried re-running the jobs, still no progress.
--
Rebekah Dedrick, Ph.D.
University of Pittsburgh
Hatfull Laboratory
376 Crawford Hall
4249 Fifth Avenue
Pittsburgh, PA 15260
9 years, 7 months
Training
by Ryan Peters
To whom it may concern,
Can you tell me about how I can schedule a training for Galaxy and any Galaxy trainings that are coming up in the East Coast which I can attend. I would be willing to travel.
Thanks
9 years, 7 months
FreeBayes repeated error
by Dalgard, Clifton
Dear Team and Galaxy Users,
I have been running FreeBayes on BAM output generated from pooled
sequencing of 30 haploid yeast genomes with a total of 90 million reads. I
am observing an inconsistent but repeated error using FreeBayes which
states:
An error occurred running this job:*terminate called after throwing an
instance of 'std::out_of_range'
what(): vector<bool>::_M_range_check
Aborted*
*
*
Interestingly, I can view partial output of the tool run and after running
the tool repeated with the same data and parameters, I have noticed that
the partial output has different lengths (and thus suggests it is not data
dependent).
Is there any insight to why FreeBayes won't complete?
Thank you,
Clifton
9 years, 7 months
