Re: [galaxy-dev] (no subject)
by Vidya .H.K
Hi,
Actually I am not computer expert as well. I have just started to work in
this area. so I am not able to figure out how to solve this problem. I
request you to elaborate on what you meant in your previous mail.
Thanks in advance
> As I wrote in my previous e-mail: "Please send all follow-up with a cc
to the mailing list ("reply-all")."
> In order to debug you situation you need to simulate a complete
> commandline, the same Galaxy is doing.
> Regards, Hans
> On 01/23/2012 05:35 AM, Vidya .H.K wrote:
>> Hi,
>> Sorry for delayed reply. When I execute "macs_wrapper.py" on command line,
>> I get the following error.
>> python macs_wrapper.py
>> File "<stdin>", line 1
>> python macs_wrapper.py
>> Thanks in advance
>>> On 01/10/2012 06:31 AM, Vidya .H.K wrote:
>>>> Hi,
>>>> I think macs is exceutable with galaxy user.
>>> what happens if you execute "macs_wrapper.py" on the command line?
Regards, Hans
>>> PS: Please send all follow-up with a cc to the mailing list
>>> ("reply-all").
>>>>> On 01/09/2012 05:04 AM, Vidya .H.K wrote:
>>>>>> Hi,
>>>>>> I am new user to galaxy. I have installed galaxy on the Linux local
server
>>>>>> for ChIP-seq analysis. While running MACS, an error is flagged
>>>>>> "An error occurred running this job: /bin/sh: macs: not found"
.
>>>>>> I have set the path for macs in /bin. But still the error persists. It
>>>>>> would be great if any one help me resolve this problem.
>>>>> Hi Vidya
>>>>> Is macs executable for the galaxy user (ie the user the galaxy
server
>>>>> is
>>>>> running as) ?
>>>>> Regards, Hans
>>>>>> Thanks in advance.
>>>>>> Regards
>>>>>> vidya
>>>>>> ___________________________________________________________ Please
keep all replies on the list by using "reply all"
>>>>>> in your mail client. To manage your subscriptions to this
>>>>>> and other Galaxy lists, please use the interface at:
>>>>>> http://lists.bx.psu.edu/
>>>>
10 years, 4 months
CloudMan Autoscaling Question
by Jesse Erdmann
Hi,
We're in the planning phases of implementing an Amazon cluster for a
particular workflow. We think volume will be such that it will make
sense to have at least a the manager and a worker node running working
all of the time and will be albe to reduce costs by using the reserved
instance pricing. However, we have some questions about how auto
scaling works with regards to stopping vs. terminating worker nodes.
In my brief experience working with CloudMan I've been able to
determine that allocating instances that use EBS volumes accrues
charges. With the 15GB EBS volume currently allocated by the CloudMan
AMI, starting a new worker node costs $1.50. So if I start a worker
node, terminate it and start another one I get charged $3.00.
However, if I start an instance, stop it and restart it I only get
charged $1.50 for the initial allocation and I do not get charged for
restarting it. Also, to my understanding (help me if I'm wrong here
because my experience is limited) I don't get charged for the time
where the volume is still mounted on EBS, but the instance is not
running. I have a few questions regarding this.
1) For those with more experience with Amazon's pricing, is my scenario correct?
2) Will the autoscaling of nodes terminate unused nodes or simply stop them?
3) If autoscaling terminates nodes, is it possible to stop and restart
nodes within the cluster and not terminate them and still have
CloudMan utilize them in the cluster appropriately?
Thanks!
--
Jesse Erdmann
Bioinformatics Analyst
Masonic Cancer Center
University of Minnesota
jerdmann(a)umn.edu
612-626-3123
10 years, 4 months
unit tests failures
by Anne Pajon
Hello,
I've installed recently galaxy on one of our test server with python2.7 and I am running out of ideas on how to solve the issue related to this unit test failure: galaxy.objectstore.DiskObjectStore. Here is the output when running sh run_unit_tests.sh.
[webapp@uk-cri-lbio08 galaxy-dist]$ sh run_unit_tests.sh
Data (galaxy.datatypes.data)
Doctest: galaxy.datatypes.data.Data ... ok
sniff (galaxy.datatypes.images.Html)
Doctest: galaxy.datatypes.images.Html.sniff ... ok
sniff (galaxy.datatypes.interval.Bed)
Doctest: galaxy.datatypes.interval.Bed.sniff ... ok
sniff (galaxy.datatypes.interval.CustomTrack)
Doctest: galaxy.datatypes.interval.CustomTrack.sniff ... ok
sniff (galaxy.datatypes.interval.Gff)
Doctest: galaxy.datatypes.interval.Gff.sniff ... ok
sniff (galaxy.datatypes.interval.Gff3)
Doctest: galaxy.datatypes.interval.Gff3.sniff ... ok
sniff (galaxy.datatypes.interval.Gtf)
Doctest: galaxy.datatypes.interval.Gtf.sniff ... ok
sniff (galaxy.datatypes.interval.Interval)
Doctest: galaxy.datatypes.interval.Interval.sniff ... ok
sniff (galaxy.datatypes.interval.Wiggle)
Doctest: galaxy.datatypes.interval.Wiggle.sniff ... ok
sniff (galaxy.datatypes.qualityscore.QualityScore454)
Doctest: galaxy.datatypes.qualityscore.QualityScore454.sniff ... ok
sniff (galaxy.datatypes.qualityscore.QualityScoreSOLiD)
Doctest: galaxy.datatypes.qualityscore.QualityScoreSOLiD.sniff ... ok
sniff (galaxy.datatypes.sequence.Axt)
Doctest: galaxy.datatypes.sequence.Axt.sniff ... ok
sniff (galaxy.datatypes.sequence.Fasta)
Doctest: galaxy.datatypes.sequence.Fasta.sniff ... ok
sniff (galaxy.datatypes.sequence.Fastq)
Doctest: galaxy.datatypes.sequence.Fastq.sniff ... ok
sniff (galaxy.datatypes.sequence.Lav)
Doctest: galaxy.datatypes.sequence.Lav.sniff ... ok
sniff (galaxy.datatypes.sequence.Maf)
Doctest: galaxy.datatypes.sequence.Maf.sniff ... ok
get_split_commands_sequential (galaxy.datatypes.sequence.Sequence)
Doctest: galaxy.datatypes.sequence.Sequence.get_split_commands_sequential ... ok
get_split_commands_with_toc (galaxy.datatypes.sequence.Sequence)
Doctest: galaxy.datatypes.sequence.Sequence.get_split_commands_with_toc ... ok
sniff (galaxy.datatypes.sequence.csFasta)
Doctest: galaxy.datatypes.sequence.csFasta.sniff ... ok
convert_newlines (galaxy.datatypes.sniff)
Doctest: galaxy.datatypes.sniff.convert_newlines ... ok
convert_newlines_sep2tabs (galaxy.datatypes.sniff)
Doctest: galaxy.datatypes.sniff.convert_newlines_sep2tabs ... ok
get_headers (galaxy.datatypes.sniff)
Doctest: galaxy.datatypes.sniff.get_headers ... ok
guess_ext (galaxy.datatypes.sniff)
Doctest: galaxy.datatypes.sniff.guess_ext ... ok
is_column_based (galaxy.datatypes.sniff)
Doctest: galaxy.datatypes.sniff.is_column_based ... ok
sep2tabs (galaxy.datatypes.sniff)
Doctest: galaxy.datatypes.sniff.sep2tabs ... ok
sniff (galaxy.datatypes.tabular.Pileup)
Doctest: galaxy.datatypes.tabular.Pileup.sniff ... ok
sniff (galaxy.datatypes.tabular.Sam)
Doctest: galaxy.datatypes.tabular.Sam.sniff ... ok
sniff (galaxy.datatypes.xml.BlastXml)
Doctest: galaxy.datatypes.xml.BlastXml.sniff ... ok
sniff (galaxy.datatypes.xml.GenericXml)
Doctest: galaxy.datatypes.xml.GenericXml.sniff ... ok
test_basic (galaxy.model.mapping_tests.MappingTests) ... ok
DiskObjectStore (galaxy.objectstore)
Doctest: galaxy.objectstore.DiskObjectStore ... FAIL
galaxy.tools.deps.tests.test
galaxy.tools.deps.tests.test ... ok
BooleanToolParameter (galaxy.tools.parameters.basic)
Doctest: galaxy.tools.parameters.basic.BooleanToolParameter ... ok
ColumnListParameter (galaxy.tools.parameters.basic)
Doctest: galaxy.tools.parameters.basic.ColumnListParameter ... ok
DrillDownSelectToolParameter (galaxy.tools.parameters.basic)
Doctest: galaxy.tools.parameters.basic.DrillDownSelectToolParameter ... ok
FileToolParameter (galaxy.tools.parameters.basic)
Doctest: galaxy.tools.parameters.basic.FileToolParameter ... ok
FloatToolParameter (galaxy.tools.parameters.basic)
Doctest: galaxy.tools.parameters.basic.FloatToolParameter ... ok
GenomeBuildParameter (galaxy.tools.parameters.basic)
Doctest: galaxy.tools.parameters.basic.GenomeBuildParameter ... ok
HiddenToolParameter (galaxy.tools.parameters.basic)
Doctest: galaxy.tools.parameters.basic.HiddenToolParameter ... ok
IntegerToolParameter (galaxy.tools.parameters.basic)
Doctest: galaxy.tools.parameters.basic.IntegerToolParameter ... ok
SelectToolParameter (galaxy.tools.parameters.basic)
Doctest: galaxy.tools.parameters.basic.SelectToolParameter ... ok
TextToolParameter (galaxy.tools.parameters.basic)
Doctest: galaxy.tools.parameters.basic.TextToolParameter ... ok
ToolInputTranslator (galaxy.tools.parameters.input_translation)
Doctest: galaxy.tools.parameters.input_translation.ToolInputTranslator ... ok
ToolParameterSanitizer (galaxy.tools.parameters.sanitize)
Doctest: galaxy.tools.parameters.sanitize.ToolParameterSanitizer ... ok
ExpressionValidator (galaxy.tools.parameters.validation)
Doctest: galaxy.tools.parameters.validation.ExpressionValidator ... ok
InRangeValidator (galaxy.tools.parameters.validation)
Doctest: galaxy.tools.parameters.validation.InRangeValidator ... ok
LengthValidator (galaxy.tools.parameters.validation)
Doctest: galaxy.tools.parameters.validation.LengthValidator ... ok
RegexValidator (galaxy.tools.parameters.validation)
Doctest: galaxy.tools.parameters.validation.RegexValidator ... ok
Params (galaxy.util)
Doctest: galaxy.util.Params ... ok
file_iter (galaxy.util)
Doctest: galaxy.util.file_iter ... ok
nice_size (galaxy.util)
Doctest: galaxy.util.nice_size ... ok
unique_id (galaxy.util)
Doctest: galaxy.util.unique_id ... ok
CheckboxField (galaxy.web.form_builder)
Doctest: galaxy.web.form_builder.CheckboxField ... ok
DrillDownField (galaxy.web.form_builder)
Doctest: galaxy.web.form_builder.DrillDownField ... ok
FileField (galaxy.web.form_builder)
Doctest: galaxy.web.form_builder.FileField ... ok
HiddenField (galaxy.web.form_builder)
Doctest: galaxy.web.form_builder.HiddenField ... ok
PasswordField (galaxy.web.form_builder)
Doctest: galaxy.web.form_builder.PasswordField ... ok
SelectField (galaxy.web.form_builder)
Doctest: galaxy.web.form_builder.SelectField ... ok
TextArea (galaxy.web.form_builder)
Doctest: galaxy.web.form_builder.TextArea ... ok
TextField (galaxy.web.form_builder)
Doctest: galaxy.web.form_builder.TextField ... ok
======================================================================
FAIL: DiskObjectStore (galaxy.objectstore)
Doctest: galaxy.objectstore.DiskObjectStore
----------------------------------------------------------------------
Traceback (most recent call last):
File "/opt/local/home/webapp/galaxy/python/lib/python2.7/doctest.py", line 2166, in runTest
raise self.failureException(self.format_failure(new.getvalue()))
AssertionError: Failed doctest test for galaxy.objectstore.DiskObjectStore
File "/opt/local/home/webapp/galaxy/galaxy-dist/lib/galaxy/objectstore/__init__.py", line 190, in DiskObjectStore
----------------------------------------------------------------------
File "/opt/local/home/webapp/galaxy/galaxy-dist/lib/galaxy/objectstore/__init__.py", line 198, in galaxy.objectstore.DiskObjectStore
Failed example:
s = DiskObjectStore(Bunch(umask=077), file_path=file_path)
Exception raised:
Traceback (most recent call last):
File "/opt/local/home/webapp/galaxy/python/lib/python2.7/doctest.py", line 1254, in __run
compileflags, 1) in test.globs
File "<doctest galaxy.objectstore.DiskObjectStore[3]>", line 1, in <module>
s = DiskObjectStore(Bunch(umask=077), file_path=file_path)
File "/opt/local/home/webapp/galaxy/galaxy-dist/lib/galaxy/objectstore/__init__.py", line 208, in __init__
self.extra_dirs['job_work'] = config.job_working_directory
AttributeError: 'Bunch' object has no attribute 'job_working_directory'
----------------------------------------------------------------------
File "/opt/local/home/webapp/galaxy/galaxy-dist/lib/galaxy/objectstore/__init__.py", line 199, in galaxy.objectstore.DiskObjectStore
Failed example:
s.create(1)
Exception raised:
Traceback (most recent call last):
File "/opt/local/home/webapp/galaxy/python/lib/python2.7/doctest.py", line 1254, in __run
compileflags, 1) in test.globs
File "<doctest galaxy.objectstore.DiskObjectStore[4]>", line 1, in <module>
s.create(1)
NameError: name 's' is not defined
----------------------------------------------------------------------
File "/opt/local/home/webapp/galaxy/galaxy-dist/lib/galaxy/objectstore/__init__.py", line 200, in galaxy.objectstore.DiskObjectStore
Failed example:
s.exists(1)
Exception raised:
Traceback (most recent call last):
File "/opt/local/home/webapp/galaxy/python/lib/python2.7/doctest.py", line 1254, in __run
compileflags, 1) in test.globs
File "<doctest galaxy.objectstore.DiskObjectStore[5]>", line 1, in <module>
s.exists(1)
NameError: name 's' is not defined
----------------------------------------------------------------------
File "/opt/local/home/webapp/galaxy/galaxy-dist/lib/galaxy/objectstore/__init__.py", line 202, in galaxy.objectstore.DiskObjectStore
Failed example:
assert s.get_filename(1) == file_path + '/000/dataset_1.dat'
Exception raised:
Traceback (most recent call last):
File "/opt/local/home/webapp/galaxy/python/lib/python2.7/doctest.py", line 1254, in __run
compileflags, 1) in test.globs
File "<doctest galaxy.objectstore.DiskObjectStore[6]>", line 1, in <module>
assert s.get_filename(1) == file_path + '/000/dataset_1.dat'
NameError: name 's' is not defined
----------------------------------------------------------------------
Ran 60 tests in 3.651s
FAILED (failures=1)
Thanks in advance for your help.
Anne.
--
Anne Pajon, Ph.D.
Cancer Research UK - Cambridge Research Institute
Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE
anne.pajon(a)cancer.org.uk | +44 (0)7958 511 353
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10 years, 4 months
(no subject)
by Vidya .H.K
Hi,
I have locally installed galaxy on a linux(ubuntu) machine. I have not
installed all the tools on the local galaxy server. I am not able to
integrate MACS peak calling tool with galaxy. I have followed all the
instructions for installation of MACS and it is running fine on the
commandline(standalone is fine).But with galaxy it is giving the following
error:
"An error occurred running this job: /bin/sh: macs: not found"
I have tried executing the macs_wrapper.py in the commandline and I have
got the following error:
"Traceback (most recent call last):
File "macs_wrapper.py", line 135, in <module>
if __name__ == "__main__": main()
File "macs_wrapper.py", line 45, in main
options = simplejson.load( open( sys.argv[1] ) )
IndexError: list index out of range"
I have set the PYTHONPATH(i.e PYTHONPATH=~/galaxy-dist/lib) and I have
macs in PATH. I am not a technical/computer expert as well, hence I would
appreciate if any one could help me resolve this problem & tell me where I
am going wrong
Thanks in advance
Regards
10 years, 4 months
Galaxy installation with mysql database
by Alex R Bigelow
Hi,
I am trying to install a local instance of Galaxy with an infobright mysql server; I created a database called "galaxy" (the user is also "galaxy," and it has all the privileges it should need), and the database_connection line is as follows:
database_connection = mysql://galaxy:***********@localhost/galaxy?unix_socket=/tmp/mysql-ib.sock
When I do this, I get the following error:
Traceback (most recent call last):
File "/gen21/alex/Apps/galaxy-dist/lib/galaxy/web/buildapp.py", line 82, in app_factory
app = UniverseApplication( global_conf = global_conf, **kwargs )
File "/gen21/alex/Apps/galaxy-dist/lib/galaxy/app.py", line 32, in __init__
create_or_verify_database( db_url, kwargs.get( 'global_conf', {} ).get( '__file__', None ), self.config.database_engine_options )
File "/gen21/alex/Apps/galaxy-dist/lib/galaxy/model/migrate/check.py", line 65, in create_or_verify_database
db_schema = schema.ControlledSchema( engine, migrate_repository )
File "/gen21/alex/Apps/galaxy-dist/eggs/sqlalchemy_migrate-0.5.4-py2.7.egg/migrate/versioning/schema.py", line 24, in __init__
self._load()
File "/gen21/alex/Apps/galaxy-dist/eggs/sqlalchemy_migrate-0.5.4-py2.7.egg/migrate/versioning/schema.py", line 36, in _load
self.table = Table(tname, self.meta, autoload=True)
File "/gen21/alex/Apps/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/schema.py", line 108, in __call__
return type.__call__(self, name, metadata, *args, **kwargs)
File "/gen21/alex/Apps/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/schema.py", line 236, in __init__
_bind_or_error(metadata).reflecttable(self, include_columns=include_columns)
File "/gen21/alex/Apps/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/engine/base.py", line 1265, in reflecttable
self.dialect.reflecttable(conn, table, include_columns)
File "/gen21/alex/Apps/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/databases/mysql.py", line 1664, in reflecttable
sql = self._show_create_table(connection, table, charset)
File "/gen21/alex/Apps/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/databases/mysql.py", line 1835, in _show_create_table
raise exc.NoSuchTableError(full_name)
NoSuchTableError: migrate_version
I found this question in the archives:
http://lists.bx.psu.edu/pipermail/galaxy-dev/2010-March/002216.html
As per both replies, I tried a virtual_env, which didn't work, and I also deleted the "galaxy" database so that it would create a fresh one, but, of course, now it can't connect to the database because it doesn't exist. How do I tell Galaxy to create the database it needs?
Thanks again for all the support,
Alex Bigelow
10 years, 4 months
Documentation for Galaxy's tool dependency environment system
by Nate Coraor
Hi all,
Galaxy has had a tool dependency management system for quite a while now, but it was never documented in the past. I have just written this documentation:
http://wiki.g2.bx.psu.edu/Admin/Config/Tool%20Dependencies
The system does not automatically install anything for you (this is something we plan to work on for the Tool Shed that is not yet under way), but explains how Galaxy expects to find dependencies and how you can do more advanced things than setting $PATH, if doing so would be useful for your environment.
The tool_dependency_dir option is not in the universe_wsgi.ini.sample file in the current stable release. I just added it in the development version (galaxy-central), so it'll be part of the next release. However, the code to handle it is part of the stable release (and has been for over a year), so if you add it to your config file, the system will behave as described.
--nate
10 years, 4 months
"allow administrators to impersonate other users"
by Hans-Rudolf Hotz
Hi
The recently added new function allowing administrators to impersonate
other users is a really useful tool - thank you very much.
It works great on our development server. Unfortunately, it does not
work on our production server which relies on external authentication
via Apache. Is this a common problem? See below for the output in the
logs, when I tried to switch from 'hansrudolf.hotz(a)fmi.ch' to
'Tim.Roloff(a)fmi.ch'.
Has anybody else activated this functionality (with or without success)?
Regards, Hans
172.27.28.201 - - [23/Jan/2012:13:25:11 +0200] "POST /admin/impersonate
HTTP/1.1" 200 - "http://galaxy.fmi.ch/admin/impersonate?webapp=galaxy"
"Mozilla/5.0 (X11; U; Linux i686; en-US) AppleWebKit/533.4 (KHTML, like
Gecko) Chrome/5.0.375.86 Safari/533.4"
galaxy.web.framework WARNING 2012-01-23 13:25:23,526 User logged in as
'hansrudolf.hotz(a)fmi.ch' externally, but has a cookie as
'Tim.Roloff(a)fmi.ch' invalidating session
172.27.28.201 - - [23/Jan/2012:13:25:23 +0200] "GET /root HTTP/1.1" 200
- "http://galaxy.fmi.ch/admin/impersonate" "Mozilla/5.0 (X11; U; Linux
i686; en-US) AppleWebKit/533.4 (KHTML, like Gecko) Chrome/5.0.375.86
Safari/533.4"
10 years, 4 months
Galaxy Hang after DrmCommunicationException
by Ann Black
Good Morning galaxy group!
I was hoping that someone might have some ideas on a problem we have
experienced a handful of times running galaxy on our local cluster.
Occasionally we experience some communication timeouts between out cluster
head node and a compute node which will self heal. However, this in turn
will hang galaxy. Below you will see output from our galaxy log file. When
the ERROR happens (which is not often) it consistently seems to hang galaxy.
We have to kill it off and restart it. We are running galaxy as a single PID
at this time (we are still just testing it out, etc) and it is running on
our head node (which we plan to move off of in the future).
galaxy.jobs.runners.drmaa DEBUG 2012-01-10 19:19:58,800 (1654/698075) state
change: job is running
galaxy.jobs.runners.drmaa ERROR 2012-01-10 20:57:47,021 (1654/698075) Unable
to check job status
Traceback (most recent call last):
File "/data/galaxy-dist/lib/galaxy/jobs/runners/drmaa.py", line 236, in
check_watched_items
state = self.ds.jobStatus( job_id )
File "/data/galaxy-dist/eggs/drmaa-0.4b3-py2.7.egg/drmaa/__init__.py",
line 522, in jobStatus
_h.c(_w.drmaa_job_ps, jobName, _ct.byref(status))
File "/data/galaxy-dist/eggs/drmaa-0.4b3-py2.7.egg/drmaa/helpers.py", line
213, in c
return f(*(args + (error_buffer, sizeof(error_buffer))))
File "/data/galaxy-dist/eggs/drmaa-0.4b3-py2.7.egg/drmaa/errors.py", line
90, in error_check
raise _ERRORS[code-1]("code %s: %s" % (code, error_buffer.value))
DrmCommunicationException: code 2: failed receiving gdi request response for
mid=24442 (got syncron message receive timeout error).
galaxy.jobs.runners.drmaa WARNING 2012-01-10 20:58:05,090 (1654/698075) job
will now be errored
galaxy.jobs.runners.drmaa DEBUG 2012-01-10 20:59:06,396 (1654/698075) User
killed running job, but error encountered removing from DRM queue: code 2:
failed receiving gdi request response for mid=24444 (got syncron message
receive timeout error).
galaxy.datatypes.metadata DEBUG 2012-01-10 20:59:06,896 Cleaning up external
metadata files
galaxy.datatypes.metadata DEBUG 2012-01-10 20:59:06,947 Failed to cleanup
MetadataTempFile temp files from
database/tmp/metadata_out_HistoryDatasetAssociation_2913_ZUTgBy: No JSON
object could be decoded: line 1 column 0 (char 0)
galaxy.datatypes.metadata DEBUG 2012-01-10 20:59:09,640 Cleaning up external
metadata files
galaxy.jobs INFO 2012-01-10 20:59:09,697 job 1656 unable to run: one or more
inputs in error state
galaxy.datatypes.metadata DEBUG 2012-01-10 20:59:10,121 Cleaning up external
metadata files
galaxy.jobs INFO 2012-01-10 20:59:10,159 job 1655 unable to run: one or more
inputs in error state
galaxy.datatypes.metadata DEBUG 2012-01-10 20:59:12,076 Cleaning up external
metadata files
galaxy.jobs INFO 2012-01-10 20:59:12,126 job 1657 unable to run: one or more
inputs in error state
galaxy.datatypes.metadata DEBUG 2012-01-10 20:59:13,601 Cleaning up external
metadata files
galaxy.jobs INFO 2012-01-10 20:59:13,650 job 1658 unable to run: one or more
inputs in error state
Has anyone else experienced this or have some ideas on how we can further
debug to figure out why galaxy hangs?
Thanks much!
Ann Black-Ziegelbein
10 years, 4 months
Re: [galaxy-dev] (no subject)
by Hans-Rudolf Hotz
As I wrote in my previous e-mail: "Please send all follow-up with a cc
to the mailing list ("reply-all")."
In order to debug you situation you need to simulate a complete
commandline, the same Galaxy is doing.
Regards, Hans
On 01/23/2012 05:35 AM, Vidya .H.K wrote:
>
> Hi,
>
> Sorry for delayed reply. When I execute "macs_wrapper.py" on command line,
> I get the following error.
>
> python macs_wrapper.py
> File "<stdin>", line 1
> python macs_wrapper.py
>
> Thanks in advance
>
>
>
>
>>
>> On 01/10/2012 06:31 AM, Vidya .H.K wrote:
>>> Hi,
>>> I think macs is exceutable with galaxy user.
>>>>
>>>>
>>
>> what happens if you execute "macs_wrapper.py" on the command line?
>>
>> Regards, Hans
>>
>>
>> PS: Please send all follow-up with a cc to the mailing list ("reply-all").
>>
>>
>>>> On 01/09/2012 05:04 AM, Vidya .H.K wrote:
>>>>> Hi,
>>>>>
>>>>> I am new user to galaxy. I have installed galaxy on the Linux local
>>>>> server
>>>>> for ChIP-seq analysis. While running MACS, an error is flagged
>>>>> "An error occurred running this job: /bin/sh: macs: not found" .
>>>>> I have set the path for macs in /bin. But still the error persists. It
>>>>> would be great if any one help me resolve this problem.
>>>>>
>>>>
>>>> Hi Vidya
>>>>
>>>> Is macs executable for the galaxy user (ie the user the galaxy server
>>>> is
>>>> running as) ?
>>>>
>>>> Regards, Hans
>>>>
>>>>> Thanks in advance.
>>>>>
>>>>>
>>>>> Regards
>>>>> vidya
>>>>>
>>>>>
>>>>>
>>>>> ___________________________________________________________
>>>>> Please keep all replies on the list by using "reply all"
>>>>> in your mail client. To manage your subscriptions to this
>>>>> and other Galaxy lists, please use the interface at:
>>>>>
>>>>> http://lists.bx.psu.edu/
>>>>
>>>
>>>
>>> Regards
>>> H.K.VIDYA
>>>
>>> -----------------------------------------
>>> Institute of Bioinformatics and Applied Biotechnology, Bangalore
>>>
>>
>
>
>
>
10 years, 4 months
samtools version detection issue
by Matt Shirley
Hi all. I'm sorry if this has been answered before, but I've searched and
cannot find a solution other than "add SAMtools to your PATH", which I
already have done. I can invoke samtools from BASH while logged in as the
"galaxy" user I set up according to the production installation guide. When
I try to add .bam files to a shared data library, I get the following
message:
Traceback (most recent call last):
> File "/home/galaxy/galaxy-dist/tools/data_source/upload.py", line 394, in
> __main__()
> File "/home/galaxy/galaxy-dist/tools/data_source/upload.py", line 386, in
> __main__
> add_file( dataset, registry, json_file, output_path )
> File "/home/galaxy/galaxy-dist/tools/data_source/upload.py", line 327, in
> add_file
> if link_data_only == 'copy_files' and
> datatype.dataset_content_needs_grooming( output_path ):
> File "/home/galaxy/galaxy-dist/lib/galaxy/datatypes/binary.py", line 79,
> in dataset_content_needs_grooming
> version = self._get_samtools_version()
> File "/home/galaxy/galaxy-dist/lib/galaxy/datatypes/binary.py", line 63,
> in _get_samtools_version
> output = subprocess.Popen( [ 'samtools' ], stderr=subprocess.PIPE,
> stdout=subprocess.PIPE ).communicate()[1]
> File "/usr/lib64/python2.6/subprocess.py", line 639, in __init__
> errread, errwrite)
> File "/usr/lib64/python2.6/subprocess.py", line 1220, in _execute_child
> raise child_exception
> OSError: [Errno 2] No such file or directory
I've taken a peek at the "dataset_content_needs_grooming" function and it
looks like there is an OS call that executes "$ samtools" and splits the
resulting string to access the version number of samtools (why couldn't the
developers add a --version flag?). It seems to me like samtools cannot be
executed, but I can't think of any reason why. Invoking samtools as user
"galaxy" (with the user's associated PATH) gives:
Program: samtools (Tools for alignments in the SAM format)
> Version: 0.1.12a (r862)
> Usage: samtools <command> [options]
> Command: view SAM<->BAM conversion
> sort sort alignment file
> pileup generate pileup output
> mpileup multi-way pileup
> faidx index/extract FASTA
> tview text alignment viewer
> index index alignment
> idxstats BAM index stats (r595 or later)
> fixmate fix mate information
> glfview print GLFv3 file
> flagstat simple stats
> calmd recalculate MD/NM tags and '=' bases
> merge merge sorted alignments
> rmdup remove PCR duplicates
> reheader replace BAM header
Does anyone know where I've gone wrong?
--
Matt Shirley
Ph.D Candidate - BCMB
Pevsner Lab <http://pevsnerlab.kennedykrieger.org/>
Johns Hopkins Medicine
10 years, 4 months
