January 2012 - galaxy-dev - lists.galaxyproject.org

Re: [galaxy-dev] (no subject)
by Vidya .H.K 24 Jan '12

24 Jan '12

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/ >>>>

3 4

CloudMan Autoscaling Question
by Jesse Erdmann 24 Jan '12

24 Jan '12

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

2 1

unit tests failures
by Anne Pajon 24 Jan '12

24 Jan '12

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 NOTICE AND DISCLAIMER This e-mail (including any attachments) is intended for the above-named person(s). If you are not the intended recipient, notify the sender immediately, delete this email from your system and do not disclose or use for any purpose. We may monitor all incoming and outgoing emails in line with current legislation. We have taken steps to ensure that this email and attachments are free from any virus, but it remains your responsibility to ensure that viruses do not adversely affect you. Cancer Research UK Registered in England and Wales Company Registered Number: 4325234. Registered Charity Number: 1089464 and Scotland SC041666 Registered Office Address: Angel Building, 407 St John Street, London EC1V 4AD.

2 2

(no subject)
by Vidya .H.K 23 Jan '12

23 Jan '12

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

1 0

Galaxy installation with mysql database
by Alex R Bigelow 23 Jan '12

23 Jan '12

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

3 5

Documentation for Galaxy's tool dependency environment system
by Nate Coraor 23 Jan '12

23 Jan '12

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

1 0

"allow administrators to impersonate other users"
by Hans-Rudolf Hotz 23 Jan '12

23 Jan '12

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"

2 1

Galaxy Hang after DrmCommunicationException
by Ann Black 23 Jan '12

23 Jan '12

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

3 6

Re: [galaxy-dev] (no subject)
by Hans-Rudolf Hotz 22 Jan '12

22 Jan '12

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 >>> >> > > > >

1 0

samtools version detection issue
by Matt Shirley 20 Jan '12

20 Jan '12

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

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