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

Purge datasets without purging the associated history?
by Luobin Yang 08 Nov '12

08 Nov '12

Hi, guys, Is it possible to purge some datasets in a history without purging the whole history? Thanks, Luobin

2 1

can't use bowtie mapper
by Shuqing Xu 07 Nov '12

07 Nov '12

Dear Galaxy developers, I am using a locally installed galaxy system. I have tested many different function, it works pretty well. But now i am having a problem with NGS tools. I have installed bowtie2 and tophat2 etc locally, but when i run bowtie to align the short reads to reference genome (selected from history), it does not work, just shows waiting for running. I then checked the files from bowtie2_wrapper.py with my own files as following under command line: python2.7 bowtie2_wrapper.py --num-threads=4 --output=test.out --own-file=Nagenome.fasta --input1=control_R1.fq --input2=control_R2.fq However, it didn't run well, it shows following error message: Settings: Output files: "/tmp/tmplBdrjc/Nagenome.*.bt2" Line rate: 6 (line is 64 bytes) Lines per side: 1 (side is 64 bytes) Offset rate: 4 (one in 16) FTable chars: 10 Strings: unpacked Max bucket size: default Max bucket size, sqrt multiplier: default Max bucket size, len divisor: 4 Difference-cover sample period: 1024 Endianness: little Actual local endianness: little Sanity checking: disabled Assertions: disabled Random seed: 0 Sizeofs: void*:8, int:4, long:8, size_t:8 Input files DNA, FASTA: Nagenome.fasta Total time for call to driver() for forward index: 00:00:00 Error indexing reference sequence Error: could not open Nagenome.fasta Error: Encountered internal Bowtie 2 exception (#1) Command: bowtie2-build -f Nagenome.fasta /tmp/tmplBdrjc/Nagenome I also tested with pre-build reference genome index, it worked well. So, i guess there is something wrong with building index. However, i couldn't figure out what could be the reason. The genome size is pretty small, only 2000 sequences. I am looking forward to hearing your feedback and helps. best wishes, Shuqing -- ################################################# Department of Molecular Ecology Max Planck Institute for Chemical Ecology Hans-Knöll-Straße 8 D-07745 Jena Germany E-mail: sxu(a)ice.mpg.de Phone:+49 (0)3641 57 1129 #################################################

2 1

Dataset upload fail
by Vladimir Yamshchikov 07 Nov '12

07 Nov '12

Local install of Galaxy on SciLinux55. Fails to upload 5.2 GB fastq file from local HD, while normally loading smaller fastq and fasta datasets (less than 1 GB). Chunks of 1.2 GB size remain in */database/tmp, which all represent beginning of the file that fails to upload. Several attempts to upload made and several chunks of the same size are present. Can I just copy the file dataset to database directory instead of uploading through web interface? This shows up when clicking the button "Run this job again" ⇝ Exception: Failed to get job information for dataset hid 5 clear this clear this URL: http://127.0.0.1:8080/tool_runner/rerun?id=8 Module weberror.evalexception.middleware:364 in respond view << try: __traceback_supplement__ = errormiddleware.Supplement, self, environ app_iter = self.application(environ, detect_start_response) try: return_iter = list(app_iter)>> app_iter = self.application(environ, detect_start_response) Module paste.debug.prints:98 in __call__ view << try: status, headers, body = wsgilib.intercept_output( environ, self.app) if status is None: # Some error occurred>> environ, self.app) Module paste.wsgilib:539 in intercept_output view << data.append(headers) return output.write app_iter = application(environ, replacement_start_response) if data[0] is None: return (None, None, app_iter)>> app_iter = application(environ, replacement_start_response) Module paste.recursive:80 in __call__ view << environ['paste.recursive.script_name'] = my_script_name try: return self.application(environ, start_response) except ForwardRequestException, e: middleware = CheckForRecursionMiddleware(>> return self.application(environ, start_response) Module paste.httpexceptions:632 in __call__ view << []).append(HTTPException) try: return self.application(environ, start_response) except HTTPException, exc: return exc(environ, start_response)>> return self.application(environ, start_response) Module galaxy.web.framework.base:160 in __call__ view << kwargs.pop( '_', None ) try: body = method( trans, **kwargs ) except Exception, e: body = self.handle_controller_exception( e, trans, **kwargs )>> body = method( trans, **kwargs ) Module galaxy.webapps.galaxy.controllers.tool_runner:129 in rerun view << job = data.creating_job if not job: raise Exception("Failed to get job information for dataset hid %d" % data.hid) # Get the tool object tool_id = job.tool_id>> raise Exception("Failed to get job information for dataset hid %d" % data.hid) Exception: Failed to get job information for dataset hid 5 URL: http://127.0.0.1:8080/tool_runner/rerun?id=8 File '/home/yaximik/galaxy-dist/eggs/WebError-0.8a-py2.7.egg/weberror/evalexception/middleware.py', line 364 in respond app_iter = self.application(environ, detect_start_response) File '/home/yaximik/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/debug/prints.py', line 98 in __call__ environ, self.app) File '/home/yaximik/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/wsgilib.py', line 539 in intercept_output app_iter = application(environ, replacement_start_response) File '/home/yaximik/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response) File '/home/yaximik/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/httpexceptions.py', line 632 in __call__ return self.application(environ, start_response) File '/home/yaximik/galaxy-dist/lib/galaxy/web/framework/base.py', line 160 in __call__ body = method( trans, **kwargs ) File '/home/yaximik/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/tool_runner.py', line 129 in rerun raise Exception("Failed to get job information for dataset hid %d" % data.hid) Exception: Failed to get job information for dataset hid 5 <?xml version="1.0" ?> <traceback> <sysinfo> <language version="2.7"> Python </language> </sysinfo> <stack> <frame> <module> weberror.evalexception.middleware </module> <filename> /home/yaximik/galaxy-dist/eggs/WebError-0.8a-py2.7.egg/weberror/evalexception/middleware.py </filename> <line> 364 </line> <function> respond </function> <operation> app_iter = self.application(environ, detect_start_response) </operation> <operation_context> try: __traceback_supplement__ = errormiddleware.Supplement, self, environ app_iter = self.application(environ, detect_start_response) try: return_iter = list(app_iter) </operation_context> </frame> <frame> <module> paste.debug.prints </module> <filename> /home/yaximik/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/debug/prints.py </filename> <line> 98 </line> <function> __call__ </function> <operation> environ, self.app) </operation> <operation_context> try: status, headers, body = wsgilib.intercept_output( environ, self.app) if status is None: # Some error occurred </operation_context> </frame> <frame> <module> paste.wsgilib </module> <filename> /home/yaximik/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/wsgilib.py </filename> <line> 539 </line> <function> intercept_output </function> <operation> app_iter = application(environ, replacement_start_response) </operation> <operation_context> data.append(headers) return output.write app_iter = application(environ, replacement_start_response) if data[0] is None: return (None, None, app_iter) </operation_context> </frame> <frame> <module> paste.recursive </module> <filename> /home/yaximik/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/recursive.py </filename> <line> 80 </line> <function> __call__ </function> <operation> return self.application(environ, start_response) </operation> <operation_context> environ['paste.recursive.script_name'] = my_script_name try: return self.application(environ, start_response) except ForwardRequestException, e: middleware = CheckForRecursionMiddleware( </operation_context> </frame> <frame> <module> paste.httpexceptions </module> <filename> /home/yaximik/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/httpexceptions.py </filename> <line> 632 </line> <function> __call__ </function> <operation> return self.application(environ, start_response) </operation> <operation_context> []).append(HTTPException) try: return self.application(environ, start_response) except HTTPException, exc: return exc(environ, start_response) </operation_context> </frame> <frame> <module> galaxy.web.framework.base </module> <filename> /home/yaximik/galaxy-dist/lib/galaxy/web/framework/base.py </filename> <line> 160 </line> <function> __call__ </function> <operation> body = method( trans, **kwargs ) </operation> <operation_context> kwargs.pop( '_', None ) try: body = method( trans, **kwargs ) except Exception, e: body = self.handle_controller_exception( e, trans, **kwargs ) </operation_context> </frame> <frame> <module> galaxy.webapps.galaxy.controllers.tool_runner </module> <filename> /home/yaximik/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/tool_runner.py </filename> <line> 129 </line> <function> rerun </function> <operation> raise Exception("Failed to get job information for dataset hid %d" % data.hid) </operation> <operation_context> job = data.creating_job if not job: raise Exception("Failed to get job information for dataset hid %d" % data.hid) # Get the tool object tool_id = job.tool_id </operation_context> </frame> </stack> <exception> <type> Exception </type> <value> Failed to get job information for dataset hid 5 </value> </exception> </traceback> <?xml version="1.0" ?> <traceback> <sysinfo> <language version="2.7"> Python </language> </sysinfo> <stack> <frame> <module> weberror.evalexception.middleware </module> <filename> /home/yaximik/galaxy-dist/eggs/WebError-0.8a-py2.7.egg/weberror/evalexception/middleware.py </filename> <line> 364 </line> <function> respond </function> <operation> app_iter = self.application(environ, detect_start_response) </operation> <operation_context> try: __traceback_supplement__ = errormiddleware.Supplement, self, environ app_iter = self.application(environ, detect_start_response) try: return_iter = list(app_iter) </operation_context> </frame> <frame> <module> paste.debug.prints </module> <filename> /home/yaximik/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/debug/prints.py </filename> <line> 98 </line> <function> __call__ </function> <operation> environ, self.app) </operation> <operation_context> try: status, headers, body = wsgilib.intercept_output( environ, self.app) if status is None: # Some error occurred </operation_context> </frame> <frame> <module> paste.wsgilib </module> <filename> /home/yaximik/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/wsgilib.py </filename> <line> 539 </line> <function> intercept_output </function> <operation> app_iter = application(environ, replacement_start_response) </operation> <operation_context> data.append(headers) return output.write app_iter = application(environ, replacement_start_response) if data[0] is None: return (None, None, app_iter) </operation_context> </frame> <frame> <module> paste.recursive </module> <filename> /home/yaximik/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/recursive.py </filename> <line> 80 </line> <function> __call__ </function> <operation> return self.application(environ, start_response) </operation> <operation_context> environ['paste.recursive.script_name'] = my_script_name try: return self.application(environ, start_response) except ForwardRequestException, e: middleware = CheckForRecursionMiddleware( </operation_context> </frame> <frame> <module> paste.httpexceptions </module> <filename> /home/yaximik/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/httpexceptions.py </filename> <line> 632 </line> <function> __call__ </function> <operation> return self.application(environ, start_response) </operation> <operation_context> []).append(HTTPException) try: return self.application(environ, start_response) except HTTPException, exc: return exc(environ, start_response) </operation_context> </frame> <frame> <module> galaxy.web.framework.base </module> <filename> /home/yaximik/galaxy-dist/lib/galaxy/web/framework/base.py </filename> <line> 160 </line> <function> __call__ </function> <operation> body = method( trans, **kwargs ) </operation> <operation_context> kwargs.pop( '_', None ) try: body = method( trans, **kwargs ) except Exception, e: body = self.handle_controller_exception( e, trans, **kwargs ) </operation_context> </frame> <frame> <module> galaxy.webapps.galaxy.controllers.tool_runner </module> <filename> /home/yaximik/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/tool_runner.py </filename> <line> 129 </line> <function> rerun </function> <operation> raise Exception("Failed to get job information for dataset hid %d" % data.hid) </operation> <operation_context> job = data.creating_job if not job: raise Exception("Failed to get job information for dataset hid %d" % data.hid) # Get the tool object tool_id = job.tool_id </operation_context> </frame> </stack> <exception> <type> Exception </type> <value> Failed to get job information for dataset hid 5 </value> </exception> </traceback> -- Vladimir Yamshchikov <yaximik(a)gmail.com>

3 3

Think I found a bug
by Juan González-Vallinas 07 Nov '12

07 Nov '12

Hi galaxy devs, We are in the final stages of deploying a new Galaxy instance. We downloaded the galaxy-dist version a month ago aprox. We realized that, when launching a job and deleting it in the middle of the execution (hitting the Delete button in the history bar) will output the following error in the logger: galaxy.jobs.handler DEBUG 2012-11-05 15:56:33,537 Stopping job 45: galaxy.jobs.handler DEBUG 2012-11-05 15:56:33,537 stopping job 45 in local runner galaxy.jobs.handler ERROR 2012-11-05 15:56:33,538 Exception in monitor_step Traceback (most recent call last): File "/usr/local/www/galaxy-dist/lib/galaxy/jobs/handler.py", line 298, in monitor self.monitor_step() File "/usr/local/www/galaxy-dist/lib/galaxy/jobs/handler.py", line 341, in monitor_step self.dispatcher.stop( job ) File "/usr/local/www/galaxy-dist/lib/galaxy/jobs/handler.py", line 438, in stop self.job_runners[runner_name].stop_job( job ) File "/usr/local/www/galaxy-dist/lib/galaxy/jobs/runners/local.py", line 180, in stop_job if job.get_external_output_metadata(): AttributeError: 'Job' object has no attribute 'get_external_output_metadata' By copying the definition of get_external_output_data from the Task class into the Job class, we fixed the problem and now the jobs are terminated successfully. This is the code I added: class Job( object ): ... def get_external_output_metadata( self ): return None ... In this file: https://bitbucket.org/galaxy/galaxy-central/src/9d6a61f060d359a0289b3163990… Do you think this fix is correct, or is it a potential problem? Also, sorry I sent you through this channel, I couldn't find the way of reporting this on BitBucket. Regards, -- Juan González-Vallinas PhD Student Regulatory Genomics Group Research Unit in Biomedical Informatics (GRIB) Universitat Pompeu Fabra (UPF) Barcelona Spain (Currently @ UPenn)

3 4

Syntax error (!) in latest pull?!
by Anthonius deBoer 07 Nov '12

07 Nov '12

Got this in the latest pull of galaxy central... Ideas? Traceback (most recent call last): File "./scripts/set_metadata.py", line 24, in ? import galaxy.model.mapping #need to load this before we unpickle, in order to setup properties assigned by the mappers File "/mnt/ngs/analysis/svcgalaxy/galaxy-central/lib/galaxy/model/__init__.py", line 13, in ? import galaxy.datatypes.registry File "/mnt/ngs/analysis/svcgalaxy/galaxy-central/lib/galaxy/datatypes/registry.py", line 145 finally: ^ SyntaxError: invalid syntax

5 5

missing BWA tools on AWS AMI
by Quang Trinh 07 Nov '12

07 Nov '12

Hi dev, I launched an instance of Galaxy on Amazon ( AMI ami-da58aab3 ) this morning and noticed bwa is no longer available. Is this temporary or if we want to use bwa, we have to add the bwa ourselves? Thanks, Q

2 1

Workflow extraction breaks on a bwa step
by Oleksandr Moskalenko 07 Nov '12

07 Nov '12

Hi, I wonder if it's a known problem. I had a quick look through the mailing list, but didn't see any relevant messages: An extraction of a workflow from a history breaks on the bwa step: Error - <type 'exceptions.ValueError'>: invalid literal for int() with base 10: 'False' URL: http://galaxy.hpc.ufl.edu/workflow/build_from_current_history File '/galaxy/run/prod/eggs/Paste-1.6-py2.6.egg/paste/exceptions/errormiddleware.py', line 143 in __call__ app_iter = self.application(environ, start_response) File '/galaxy/run/prod/eggs/Paste-1.6-py2.6.egg/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response) File '/galaxy/run/prod/lib/galaxy/web/framework/middleware/remoteuser.py', line 91 in __call__ return self.app( environ, start_response ) File '/galaxy/run/prod/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py', line 632 in __call__ return self.application(environ, start_response) File '/galaxy/run/prod/lib/galaxy/web/framework/base.py', line 160 in __call__ body = method( trans, **kwargs ) File '/galaxy/run/prod/lib/galaxy/web/controllers/workflow.py', line 1253 in build_from_current_history param_values = job.get_param_values( trans.app ) File '/galaxy/run/prod/lib/galaxy/model/__init__.py', line 263 in get_param_values param_dict = tool.params_from_strings( param_dict, app, ignore_errors=ignore_errors ) File '/galaxy/run/prod/lib/galaxy/tools/__init__.py', line 2041 in params_from_strings return params_from_strings( self.inputs, params, app, ignore_errors ) File '/galaxy/run/prod/lib/galaxy/tools/parameters/__init__.py', line 94 in params_from_strings value = params[key].value_from_basic( value, app, ignore_errors ) File '/galaxy/run/prod/lib/galaxy/tools/parameters/grouping.py', line 462 in value_from_basic rval[ input.name ] = input.value_from_basic( value[ input.name ], app, ignore_errors ) File '/galaxy/run/prod/lib/galaxy/tools/parameters/basic.py', line 136 in value_from_basic return self.to_python( value, app ) File '/galaxy/run/prod/lib/galaxy/tools/parameters/basic.py', line 267 in to_python raise err ValueError: invalid literal for int() with base 10: 'False'

2 2

Network directories
by Bram Slabbinck 07 Nov '12

07 Nov '12

Hi We have several network directories that we want to link to Galaxy within the data libraries framework. The current functionality of letting users symlink files to a data library is a bit limited and a hassle, both from user as administrator perspective. It would be very handy if we could map and symlink our network directories and its contents to data libraries so that when users click on the data library they can immediately see and use the current contents of the directory. Or thus, the library should behave like a mirror of the network folder. We have already linked our LDAP to Galaxy so that the existing users and groups can easily be linked to the data libraries. In this way, only users that do have access to these folder(s) will also have access to its contents through Galaxy. Library creation and linking it to a particular role (group) is not the problem, establishing the mirror however is. I can see this implementation comes with different questions and issues: 1. Even though an administrator can 'create' a library, the user Galaxy does not necessarily have the right permissions to these network folders in order to fill the library with the associated network files. 2. The updating of the folder could however be set as a responsibility of the users having access to these data. 2.1 Could something like the run-job-as-real-user implementation work, so that the libraries are updated by real users? 2.2 Would updating the data library on access be a good solution? Or what about providing an 'update' button next to the already fetched files? 3. Galaxy works with library data set versions on each new import/upload. Logically, this would become redundant in a mirrorring setup. Is this setup possible/feasible? Did anybody already implemented this kind of feature? Or is the galaxy-team developing this kind of implementation? We started already digging into the objectstore code but can someone get us on the right track to tackle this problem? Any ideas/hints are most welcome! thx Bram

1 0

Jobs are slow to start on my galaxy instance. Used to be much faster
by Anthonius deBoer 07 Nov '12

07 Nov '12

Hi, Jobs that I start on my in-house Galaxy instance now take up to 3-4 min to go from queued to Running, even though there is nothing much going on on the galaxy server... I have been running this instance since June and use a relatively new version of Galaxy-central (Last update, 22-Aug changeset: 7535:bf6517b2b336) I have noticed that my jobs table in the galaxy Postgres database contains about 60,000 jobs... Could that be the culprit? Does it slow to the complete database to see if there are any jobs that need to run? Could I purge the jobs and related tables to speed up the submissions? Thanks, Thon

4 6

Cannot run Galaxy : socket.gaierror: [Errno -2] Name or service not known
by Marcelo Timmerman 07 Nov '12

07 Nov '12

Hello all, I'm trying to install Galaxy in a production server using CentOS 6.3, with python 2.6.6 (default CentOS) and PostgreSQL 9.2. I've followed instructions in http://wiki.g2.bx.psu.edu/Events/GCC2012/TrainingDay/WS5 After typing galaxy@myhost$ sh run.sh --reload the script produces the following output, resulting in a Python exception. Do you have any solution or hint for solving this issue? Maybe a service is missing? /home/galaxy/galaxy-dist/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: /home/galaxy/galaxy-dist/eggs/numpy-1.6.0-py2.6-linux-x86_64-ucs4.egg, /home/galaxy/galaxy-dist/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.6-linux-x86_64-ucs4.egg, /home/galaxy/galaxy-dist/eggs/boto-2.5.2-py2.6.egg, /home/galaxy/galaxy-dist/eggs/mercurial-2.2.3-py2.6-linux-x86_64-ucs4.egg, /home/galaxy/galaxy-dist/eggs/Fabric-1.4.2-py2.6.egg, /home/galaxy/galaxy-dist/eggs/ssh-1.7.14-py2.6.egg, /home/galaxy/galaxy-dist/eggs/Whoosh-0.3.18-py2.6.egg, /home/galaxy/galaxy-dist/eggs/pycrypto-2.5-py2.6-linux-x86_64-ucs4.egg, /home/galaxy/galaxy-dist/eggs/python_lzo-1.08_2.03_static-py2.6-linux-x86_64-ucs4.egg, /home/galaxy/galaxy-dist/eggs/bx_python-0.7.1_7b95ff194725-py2.6-linux-x86_64-ucs4.egg, /home/galaxy/galaxy-dist/eggs/amqplib-0.6.1-py2.6.egg, /home/galaxy/galaxy-dist/eggs/pexpect-2.4-py2.6.egg, /home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg, /home/galaxy/galaxy-dist/eggs/Babel-0.9.4-py2.6.egg, /home/galaxy/galaxy-dist/eggs/MarkupSafe-0.12-py2.6-linux-x86_64-ucs4.egg, /home/galaxy/galaxy-dist/eggs/Mako-0.4.1-py2.6.egg, /home/galaxy/galaxy-dist/eggs/WebHelpers-0.2-py2.6.egg, /home/galaxy/galaxy-dist/eggs/simplejson-2.1.1-py2.6-linux-x86_64-ucs4.egg, /home/galaxy/galaxy-dist/eggs/wchartype-0.1-py2.6.egg, /home/galaxy/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.6.egg, /home/galaxy/galaxy-dist/eggs/docutils-0.7-py2.6.egg, /home/galaxy/galaxy-dist/eggs/WebOb-0.8.5-py2.6.egg, /home/galaxy/galaxy-dist/eggs/Routes-1.12.3-py2.6.egg, /home/galaxy/galaxy-dist/eggs/Cheetah-2.2.2-py2.6-linux-x86_64-ucs4.egg, /home/galaxy/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.6.egg, /home/galaxy/galaxy-dist/eggs/PasteScript-1.7.3-py2.6.egg, /home/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg, /home/galaxy/galaxy-dist/lib, /home/galaxy/galaxy_env/lib/python2.6/site-packages/setuptools-0.6c11-py2.6.egg, /home/galaxy/galaxy_env/lib/python2.6/site-packages/pip-1.2.1-py2.6.egg, /home/galaxy/galaxy_env/lib64/python26.zip, /home/galaxy/galaxy_env/lib64/python2.6, /home/galaxy/galaxy_env/lib64/python2.6/plat-linux2, /home/galaxy/galaxy_env/lib64/python2.6/lib-tk, /home/galaxy/galaxy_env/lib64/python2.6/lib-old, /home/galaxy/galaxy_env/lib64/python2.6/lib-dynload, /usr/lib/python2.6, /usr/lib64/python2.6, /home/galaxy/galaxy_env/lib/python2.6/site-packages galaxy.tool_shed.tool_shed_registry DEBUG 2012-11-01 10:35:47,749 Loading references to tool sheds from tool_sheds_conf.xml galaxy.tool_shed.tool_shed_registry DEBUG 2012-11-01 10:35:47,749 Loaded reference to tool shed: Galaxy main tool shed galaxy.tool_shed.tool_shed_registry DEBUG 2012-11-01 10:35:47,749 Loaded reference to tool shed: Galaxy test tool shed galaxy.model.migrate.check DEBUG 2012-11-01 10:35:47,857 psycopg2 egg successfully loaded for postgres dialect galaxy.model.migrate.check INFO 2012-11-01 10:35:48,010 At database version 107 galaxy.tool_shed.migrate.check DEBUG 2012-11-01 10:35:48,025 psycopg2 egg successfully loaded for postgres dialect galaxy.tool_shed.migrate.check INFO 2012-11-01 10:35:48,054 At migrate_tools version 5 galaxy.model.custom_types DEBUG 2012-11-01 10:35:48,060 psycopg2 egg successfully loaded for postgres dialect galaxy.datatypes.registry DEBUG 2012-11-01 10:35:48,341 Loading datatypes from datatypes_conf.xml galaxy.datatypes.registry DEBUG 2012-11-01 10:35:48,353 Loaded sniffer for datatype 'galaxy.datatypes.tabular:Vcf' galaxy.datatypes.registry DEBUG 2012-11-01 10:35:48,353 Loaded sniffer for datatype 'galaxy.datatypes.binary:TwoBit' galaxy.datatypes.registry DEBUG 2012-11-01 10:35:48,353 Loaded sniffer for datatype 'galaxy.datatypes.binary:Bam' galaxy.datatypes.registry DEBUG 2012-11-01 10:35:48,353 Loaded sniffer for datatype 'galaxy.datatypes.binary:Sff' galaxy.datatypes.registry DEBUG 2012-11-01 10:35:48,354 Loaded sniffer for datatype 'galaxy.datatypes.xml:Phyloxml' galaxy.datatypes.registry DEBUG 2012-11-01 10:35:48,354 Loaded sniffer for datatype 'galaxy.datatypes.xml:GenericXml' galaxy.datatypes.registry DEBUG 2012-11-01 10:35:48,354 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Maf' galaxy.datatypes.registry DEBUG 2012-11-01 10:35:48,354 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Lav' galaxy.datatypes.registry DEBUG 2012-11-01 10:35:48,354 Loaded sniffer for datatype 'galaxy.datatypes.sequence:csFasta' galaxy.datatypes.registry DEBUG 2012-11-01 10:35:48,354 Loaded sniffer for datatype 'galaxy.datatypes.qualityscore:QualityScoreSOLiD' galaxy.datatypes.registry DEBUG 2012-11-01 10:35:48,355 Loaded sniffer for datatype 'galaxy.datatypes.qualityscore:QualityScore454' galaxy.datatypes.registry DEBUG 2012-11-01 10:35:48,355 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Fasta' galaxy.datatypes.registry DEBUG 2012-11-01 10:35:48,355 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Fastq' galaxy.datatypes.registry DEBUG 2012-11-01 10:35:48,355 Loaded sniffer for datatype 'galaxy.datatypes.interval:Wiggle' galaxy.datatypes.registry DEBUG 2012-11-01 10:35:48,355 Loaded sniffer for datatype 'galaxy.datatypes.images:Html' galaxy.datatypes.registry DEBUG 2012-11-01 10:35:48,355 Loaded sniffer for datatype 'galaxy.datatypes.images:Pdf' galaxy.datatypes.registry DEBUG 2012-11-01 10:35:48,355 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Axt' galaxy.datatypes.registry DEBUG 2012-11-01 10:35:48,356 Loaded sniffer for datatype 'galaxy.datatypes.interval:Bed' galaxy.datatypes.registry DEBUG 2012-11-01 10:35:48,356 Loaded sniffer for datatype 'galaxy.datatypes.interval:CustomTrack' galaxy.datatypes.registry DEBUG 2012-11-01 10:35:48,356 Loaded sniffer for datatype 'galaxy.datatypes.interval:Gtf' galaxy.datatypes.registry DEBUG 2012-11-01 10:35:48,356 Loaded sniffer for datatype 'galaxy.datatypes.interval:Gff' galaxy.datatypes.registry DEBUG 2012-11-01 10:35:48,356 Loaded sniffer for datatype 'galaxy.datatypes.interval:Gff3' galaxy.datatypes.registry DEBUG 2012-11-01 10:35:48,356 Loaded sniffer for datatype 'galaxy.datatypes.tabular:Pileup' galaxy.datatypes.registry DEBUG 2012-11-01 10:35:48,357 Loaded sniffer for datatype 'galaxy.datatypes.interval:Interval' galaxy.datatypes.registry DEBUG 2012-11-01 10:35:48,357 Loaded sniffer for datatype 'galaxy.datatypes.tabular:Sam' galaxy.datatypes.registry DEBUG 2012-11-01 10:35:48,357 Loaded sniffer for datatype 'galaxy.datatypes.data:Newick' galaxy.datatypes.registry DEBUG 2012-11-01 10:35:48,357 Loaded sniffer for datatype 'galaxy.datatypes.data:Nexus' galaxy.datatypes.registry DEBUG 2012-11-01 10:35:48,357 Loaded sniffer for datatype 'galaxy.datatypes.images:Jpg' galaxy.datatypes.registry DEBUG 2012-11-01 10:35:48,357 Loaded sniffer for datatype 'galaxy.datatypes.images:Png' galaxy.datatypes.registry DEBUG 2012-11-01 10:35:48,358 Loaded sniffer for datatype 'galaxy.datatypes.images:Tiff' galaxy.datatypes.registry DEBUG 2012-11-01 10:35:48,358 Loaded sniffer for datatype 'galaxy.datatypes.images:Bmp' galaxy.datatypes.registry DEBUG 2012-11-01 10:35:48,358 Loaded sniffer for datatype 'galaxy.datatypes.images:Gif' galaxy.datatypes.registry DEBUG 2012-11-01 10:35:48,358 Loaded sniffer for datatype 'galaxy.datatypes.images:Im' galaxy.datatypes.registry DEBUG 2012-11-01 10:35:48,358 Loaded sniffer for datatype 'galaxy.datatypes.images:Pcd' galaxy.datatypes.registry DEBUG 2012-11-01 10:35:48,358 Loaded sniffer for datatype 'galaxy.datatypes.images:Pcx' galaxy.datatypes.registry DEBUG 2012-11-01 10:35:48,359 Loaded sniffer for datatype 'galaxy.datatypes.images:Ppm' galaxy.datatypes.registry DEBUG 2012-11-01 10:35:48,359 Loaded sniffer for datatype 'galaxy.datatypes.images:Psd' galaxy.datatypes.registry DEBUG 2012-11-01 10:35:48,359 Loaded sniffer for datatype 'galaxy.datatypes.images:Xbm' galaxy.datatypes.registry DEBUG 2012-11-01 10:35:48,359 Loaded sniffer for datatype 'galaxy.datatypes.images:Rgb' galaxy.datatypes.registry DEBUG 2012-11-01 10:35:48,359 Loaded sniffer for datatype 'galaxy.datatypes.images:Pbm' galaxy.datatypes.registry DEBUG 2012-11-01 10:35:48,359 Loaded sniffer for datatype 'galaxy.datatypes.images:Pgm' galaxy.datatypes.registry DEBUG 2012-11-01 10:35:48,360 Loaded sniffer for datatype 'galaxy.datatypes.images:Xpm' galaxy.datatypes.registry DEBUG 2012-11-01 10:35:48,360 Loaded sniffer for datatype 'galaxy.datatypes.images:Eps' galaxy.datatypes.registry DEBUG 2012-11-01 10:35:48,360 Loaded sniffer for datatype 'galaxy.datatypes.images:Rast' galaxy.tools.data DEBUG 2012-11-01 10:35:48,378 Loaded tool data table 'all_fasta' galaxy.tools.data DEBUG 2012-11-01 10:35:48,378 Loaded tool data table 'bfast_indexes' galaxy.tools.data DEBUG 2012-11-01 10:35:48,378 Loaded tool data table 'blastdb' galaxy.tools.data DEBUG 2012-11-01 10:35:48,379 Loaded tool data table 'blastdb_p' galaxy.tools.data DEBUG 2012-11-01 10:35:48,379 Loaded tool data table 'bowtie_indexes' galaxy.tools.data DEBUG 2012-11-01 10:35:48,379 Loaded tool data table 'bowtie2_indexes' galaxy.tools.data DEBUG 2012-11-01 10:35:48,379 Loaded tool data table 'bowtie_indexes_color' galaxy.tools.data WARNING 2012-11-01 10:35:48,380 Cannot find index file 'tool-data/bwa_index.loc' for tool data table 'bwa_indexes' galaxy.tools.data DEBUG 2012-11-01 10:35:48,380 Loaded tool data table 'bwa_indexes' galaxy.tools.data WARNING 2012-11-01 10:35:48,380 Cannot find index file 'tool-data/bwa_index_color.loc' for tool data table 'bwa_indexes_color' galaxy.tools.data DEBUG 2012-11-01 10:35:48,380 Loaded tool data table 'bwa_indexes_color' galaxy.tools.data DEBUG 2012-11-01 10:35:48,380 Loaded tool data table 'indexed_maf_files' galaxy.tools.data DEBUG 2012-11-01 10:35:48,380 Loaded tool data table 'ngs_sim_fasta' galaxy.tools.data DEBUG 2012-11-01 10:35:48,381 Loaded tool data table 'lastz_seqs' galaxy.tools.data DEBUG 2012-11-01 10:35:48,381 Loaded tool data table 'perm_base_indexes' galaxy.tools.data DEBUG 2012-11-01 10:35:48,381 Loaded tool data table 'perm_color_indexes' galaxy.tools.data DEBUG 2012-11-01 10:35:48,381 Loaded tool data table 'sam_fa_indexes' galaxy.tools.data DEBUG 2012-11-01 10:35:48,382 Loaded tool data table 'picard_indexes' galaxy.tools.data DEBUG 2012-11-01 10:35:48,382 Loaded tool data table 'gatk_picard_indexes' galaxy.tools.data DEBUG 2012-11-01 10:35:48,382 Loaded tool data table 'gatk_annotations' galaxy.tools.data DEBUG 2012-11-01 10:35:48,382 Loaded tool data table 'srma_indexes' galaxy.tools.data DEBUG 2012-11-01 10:35:48,382 Loaded tool data table 'tophat_indexes' galaxy.tools.data DEBUG 2012-11-01 10:35:48,383 Loaded tool data table 'tophat_indexes_color' galaxy.tools.data DEBUG 2012-11-01 10:35:48,383 Loaded tool data table 'tophat2_indexes' galaxy.tools.data DEBUG 2012-11-01 10:35:48,383 Loaded tool data table 'ccat_configurations' galaxy.tools.data DEBUG 2012-11-01 10:35:48,383 Loaded tool data table 'mosaik_indexes' galaxy.tools INFO 2012-11-01 10:35:48,398 Parsing the tool configuration ./tool_conf.xml galaxy.tools WARNING 2012-11-01 10:35:51,637 A when tag has not been defined for 'master_variable_type (master_variable_type_selector) --> allPairs', assuming empty inputs. galaxy.tools WARNING 2012-11-01 10:35:53,858 A when tag has been defined for 'manipulation (manipulation_selector) --> modify_each_score', but does not appear to be selectable. galaxy.tools.test DEBUG 2012-11-01 10:35:55,561 Error in add_param for report_discordant_pairs: Unable to determine parameter type of test input 'report_discordant_pairs'. Ensure that the parameter exists and that any container groups are defined first. docutils WARNING 2012-11-01 10:35:55,606 <string>:50: (WARNING/2) Literal block expected; none found. galaxy.tools.test DEBUG 2012-11-01 10:35:55,621 Error in add_param for min_coverage_intron: Unable to determine parameter type of test input 'min_coverage_intron'. Ensure that the parameter exists and that any container groups are defined first. galaxy.tools.test DEBUG 2012-11-01 10:35:55,622 Error in add_param for max_coverage_intron: Unable to determine parameter type of test input 'max_coverage_intron'. Ensure that the parameter exists and that any container groups are defined first. galaxy.tools.test DEBUG 2012-11-01 10:35:57,402 Error in add_param for force: Unable to determine parameter type of test input 'force'. Ensure that the parameter exists and that any container groups are defined first. galaxy.tools INFO 2012-11-01 10:35:58,305 Parsing the tool configuration ./migrated_tools_conf.xml galaxy.tools DEBUG 2012-11-01 10:35:58,305 Loading section: Get Data galaxy.tools DEBUG 2012-11-01 10:35:58,306 Loaded tool id: upload1, version: 1.1.3 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,306 Loaded tool id: ucsc_table_direct1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,306 Loaded tool id: ucsc_table_direct_test1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,306 Loaded tool id: ucsc_table_direct_archaea1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,306 Loaded tool id: bx_browser, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,306 Loaded tool id: ebi_sra_main, version: 1.0.1 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,306 Loaded tool id: microbial_import1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,307 Loaded tool id: biomart, version: 1.0.1 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,307 Loaded tool id: biomart_test, version: 1.0.1 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,307 Loaded tool id: cbi_rice_mart, version: 1.0.1 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,307 Loaded tool id: gramenemart, version: 1.0.1 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,307 Loaded tool id: modENCODEfly, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,307 Loaded tool id: flymine, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,307 Loaded tool id: flymine_test, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,307 Loaded tool id: modmine, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,308 Loaded tool id: ratmine, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,308 Loaded tool id: yeastmine, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,308 Loaded tool id: metabolicmine, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,308 Loaded tool id: modENCODEworm, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,308 Loaded tool id: wormbase, version: 1.0.1 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,308 Loaded tool id: wormbase_test, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,308 Loaded tool id: eupathdb, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,308 Loaded tool id: encode_db1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,309 Loaded tool id: epigraph_import, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,309 Loaded tool id: epigraph_import_test, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,309 Loaded tool id: hbvar, version: 2.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,309 Loaded tool id: genomespace_file_browser_prod, version: 0.0.1 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,309 Loaded tool id: genomespace_importer, version: 0.0.1 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,309 Loaded tool id: fix_errors, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,309 Loading section: Send Data galaxy.tools DEBUG 2012-11-01 10:35:58,309 Loaded tool id: epigraph_export, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,310 Loaded tool id: epigraph_test_export, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,310 Loaded tool id: genomespace_exporter, version: 0.0.1 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,310 Loading section: ENCODE Tools galaxy.tools DEBUG 2012-11-01 10:35:58,310 Loaded tool id: gencode_partition1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,310 Loaded tool id: random_intervals1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,310 Loading section: Lift-Over galaxy.tools DEBUG 2012-11-01 10:35:58,310 Loaded tool id: liftOver1, version: 1.0.3 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,310 Loading section: Text Manipulation galaxy.tools DEBUG 2012-11-01 10:35:58,311 Loaded tool id: addValue, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,311 Loaded tool id: Add_a_column1, version: 1.1.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,311 Loaded tool id: cat1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,311 Loaded tool id: Cut1, version: 1.0.1 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,311 Loaded tool id: mergeCols1, version: 1.0.1 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,311 Loaded tool id: Convert characters1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,311 Loaded tool id: createInterval, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,311 Loaded tool id: ChangeCase, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,312 Loaded tool id: Paste1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,312 Loaded tool id: Remove beginning1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,312 Loaded tool id: random_lines1, version: 2.0.1 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,312 Loaded tool id: Show beginning1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,312 Loaded tool id: Show tail1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,312 Loaded tool id: trimmer, version: 0.0.1 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,312 Loaded tool id: wc_gnu, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,312 Loaded tool id: secure_hash_message_digest, version: 0.0.1 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,313 Loaded tool id: dna_filter, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,313 Loaded tool id: tables_arithmetic_operations, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,313 Loading section: Filter and Sort galaxy.tools DEBUG 2012-11-01 10:35:58,313 Loaded tool id: Filter1, version: 1.1.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,313 Loaded tool id: sort1, version: 1.0.1 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,313 Loaded tool id: Grep1, version: 1.0.1 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,313 Loaded label: GFF galaxy.tools DEBUG 2012-11-01 10:35:58,313 Loaded tool id: Extract_features1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,314 Loaded tool id: gff_filter_by_attribute, version: 0.1 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,314 Loaded tool id: gff_filter_by_feature_count, version: 0.1 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,314 Loaded tool id: gtf_filter_by_attribute_values_list, version: 0.1 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,314 Loading section: Join, Subtract and Group galaxy.tools DEBUG 2012-11-01 10:35:58,314 Loaded tool id: join1, version: 2.0.2 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,314 Loaded tool id: comp1, version: 1.0.2 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,314 Loaded tool id: subtract_query1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,314 Loaded tool id: Grouping1, version: 2.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,315 Loaded tool id: column_join, version: 1.1.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,315 Loading section: Convert Formats galaxy.tools DEBUG 2012-11-01 10:35:58,315 Loaded tool id: axt_to_concat_fasta, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,315 Loaded tool id: axt_to_fasta, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,315 Loaded tool id: axt_to_lav_1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,315 Loaded tool id: bed2gff1, version: 2.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,315 Loaded tool id: fasta2tab, version: 1.1.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,315 Loaded tool id: gff2bed1, version: 1.0.1 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,316 Loaded tool id: lav_to_bed1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,316 Loaded tool id: MAF_To_BED1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,316 Loaded tool id: MAF_To_Interval1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,316 Loaded tool id: MAF_To_Fasta1, version: 1.0.1 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,316 Loaded tool id: tab2fasta, version: 1.1.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,316 Loaded tool id: fastq_to_fasta_python, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,316 Loaded tool id: wiggle2simple1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,316 Loaded tool id: Sff_extractor, version: 1.0.1 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,317 Loaded tool id: gtf2bedgraph, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,317 Loaded tool id: wig_to_bigWig, version: 1.1.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,317 Loaded tool id: bed_to_bigBed, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,317 Loading section: Extract Features galaxy.tools DEBUG 2012-11-01 10:35:58,317 Loaded tool id: gene2exon1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,317 Loading section: Fetch Sequences galaxy.tools DEBUG 2012-11-01 10:35:58,317 Loaded tool id: Extract genomic DNA 1, version: 2.2.2 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,317 Loading section: Fetch Alignments galaxy.tools DEBUG 2012-11-01 10:35:58,318 Loaded tool id: Interval2Maf_pairwise1, version: 1.0.1 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,318 Loaded tool id: Interval2Maf1, version: 1.0.1 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,318 Loaded tool id: MAF_split_blocks_by_species1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,318 Loaded tool id: Interval_Maf_Merged_Fasta2, version: 1.0.1 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,318 Loaded tool id: GeneBed_Maf_Fasta2, version: 1.0.1 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,318 Loaded tool id: maf_stats1, version: 1.0.1 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,318 Loaded tool id: MAF_Thread_For_Species1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,318 Loaded tool id: MAF_Limit_To_Species1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,319 Loaded tool id: maf_limit_size1, version: 1.0.1 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,319 Loaded tool id: maf_by_block_number1, version: 1.0.1 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,319 Loaded tool id: MAF_Reverse_Complement_1, version: 1.0.1 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,319 Loaded tool id: MAF_filter, version: 1.0.1 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,319 Loading section: Get Genomic Scores galaxy.tools DEBUG 2012-11-01 10:35:58,319 Loaded tool id: wiggle2simple1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,319 Loaded tool id: aggregate_scores_in_intervals2, version: 1.1.3 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,319 Loaded tool id: phastOdds_for_intervals, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,320 Loading section: Operate on Genomic Intervals galaxy.tools DEBUG 2012-11-01 10:35:58,320 Loaded tool id: gops_intersect_1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,320 Loaded tool id: gops_subtract_1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,320 Loaded tool id: gops_merge_1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,320 Loaded tool id: gops_concat_1, version: 1.0.1 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,320 Loaded tool id: gops_basecoverage_1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,320 Loaded tool id: gops_coverage_1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,320 Loaded tool id: gops_complement_1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,321 Loaded tool id: gops_cluster_1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,321 Loaded tool id: gops_join_1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,321 Loaded tool id: get_flanks1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,321 Loaded tool id: flanking_features_1, version: 4.0.1 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,321 Loaded tool id: Annotation_Profiler_0, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,321 Loading section: Statistics galaxy.tools DEBUG 2012-11-01 10:35:58,321 Loaded tool id: Summary_Statistics1, version: 1.1.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,321 Loaded tool id: Count1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,322 Loaded tool id: cor2, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,322 Loaded tool id: generate_matrix_for_pca_and_lda1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,322 Loaded tool id: lda_analy1, version: 1.0.1 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,322 Loaded tool id: plot_for_lda_output1, version: 1.0.1 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,322 Loaded tool id: t_test_two_samples, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,322 Loaded tool id: compute_q_values, version: 1.0.1 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,322 Loaded tool id: maximal_information_based_nonparametric_exploration, version: 0.0.1 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,322 Loaded label: GFF galaxy.tools DEBUG 2012-11-01 10:35:58,323 Loaded tool id: count_gff_features, version: 0.1 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,323 Loading section: Wavelet Analysis galaxy.tools DEBUG 2012-11-01 10:35:58,323 Loaded tool id: dwt_var1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,323 Loading section: Graph/Display Data galaxy.tools DEBUG 2012-11-01 10:35:58,323 Loaded tool id: histogram_rpy, version: 1.0.3 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,323 Loaded tool id: scatterplot_rpy, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,323 Loaded tool id: barchart_gnuplot, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,323 Loaded tool id: XY_Plot_1, version: 1.0.1 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,324 Loaded tool id: qual_stats_boxplot, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,324 Loaded tool id: gmaj_1, version: 2.0.1 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,324 Loaded tool id: laj_1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,324 Loaded tool id: build_ucsc_custom_track_1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,324 Loaded tool id: vcf_to_maf_customtrack1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,324 Loaded tool id: mutation_visualize, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,324 Loading section: Regional Variation galaxy.tools DEBUG 2012-11-01 10:35:58,324 Loaded tool id: winSplitter, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,325 Loaded tool id: featureCoverage1, version: 2.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,325 Loaded tool id: wtavg, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,325 Loaded tool id: qualityFilter, version: 1.0.1 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,325 Loaded tool id: cpgFilter, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,325 Loaded tool id: getIndels_2way, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,325 Loaded tool id: indels_3way, version: 1.0.3 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,325 Loaded tool id: indelRates_3way, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,325 Loaded tool id: substitutions1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,326 Loaded tool id: subRate1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,326 Loaded tool id: microsats_align1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,326 Loaded tool id: microsats_mutability1, version: 1.1.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,326 Loaded tool id: delete_overlapping_indels, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,326 Loaded tool id: compute_motifs_frequency, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,326 Loaded tool id: compute_motif_frequencies_for_all_motifs, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,326 Loaded tool id: categorize_elements_satisfying_criteria, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,326 Loaded tool id: draw_stacked_barplots, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,327 Loading section: Multiple regression galaxy.tools DEBUG 2012-11-01 10:35:58,327 Loaded tool id: LinearRegression1, version: 1.0.1 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,327 Loaded tool id: LogisticRegression, version: 1.0.1 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,327 Loaded tool id: BestSubsetsRegression1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,327 Loaded tool id: rcve1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,327 Loaded tool id: partialRsq, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,327 Loading section: Multivariate Analysis galaxy.tools DEBUG 2012-11-01 10:35:58,327 Loaded tool id: pca1, version: 1.0.2 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,328 Loaded tool id: cca1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,328 Loaded tool id: kpca1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,328 Loaded tool id: kcca1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,328 Loading section: Evolution galaxy.tools DEBUG 2012-11-01 10:35:58,328 Loaded tool id: hyphy_branch_lengths_wrapper1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,328 Loaded tool id: hyphy_nj_tree_wrapper1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,328 Loaded tool id: hyphy_dnds_wrapper1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,328 Loaded tool id: mutate_snp_codon_1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,329 Loaded tool id: hgv_codingSnps, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,329 Loaded tool id: hgv_add_scores, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,329 Loading section: Motif Tools galaxy.tools DEBUG 2012-11-01 10:35:58,329 Loaded tool id: meme_meme, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,329 Loaded tool id: meme_fimo, version: 0.0.1 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,329 Loaded tool id: rgweblogo3, version: 0.4 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,329 Loading section: Multiple Alignments galaxy.tools DEBUG 2012-11-01 10:35:58,329 Loaded tool id: clustalw, version: 0.1 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,330 Loading section: Metagenomic analyses galaxy.tools DEBUG 2012-11-01 10:35:58,330 Loaded tool id: Fetch Taxonomic Ranks, version: 1.1.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,330 Loaded tool id: t2t_report, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,330 Loaded tool id: Draw_phylogram, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,330 Loaded tool id: find_diag_hits, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,330 Loaded tool id: lca1, version: 1.0.1 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,330 Loaded tool id: poisson2test, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,330 Loading section: FASTA manipulation galaxy.tools DEBUG 2012-11-01 10:35:58,331 Loaded tool id: fasta_compute_length, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,331 Loaded tool id: fasta_filter_by_length, version: 1.1 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,331 Loaded tool id: fasta_concatenate0, version: 0.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,331 Loaded tool id: fasta2tab, version: 1.1.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,331 Loaded tool id: tab2fasta, version: 1.1.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,331 Loaded tool id: cshl_fasta_formatter, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,331 Loaded tool id: cshl_fasta_nucleotides_changer, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,331 Loaded tool id: cshl_fastx_collapser, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,332 Loading section: NGS: QC and manipulation galaxy.tools DEBUG 2012-11-01 10:35:58,332 Loaded label: FastQC: fastq/sam/bam galaxy.tools DEBUG 2012-11-01 10:35:58,332 Loaded tool id: fastqc, version: 0.51 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,332 Loaded label: Illumina fastq galaxy.tools DEBUG 2012-11-01 10:35:58,332 Loaded tool id: fastq_groomer, version: 1.0.4 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,332 Loaded tool id: fastq_paired_end_splitter, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,332 Loaded tool id: fastq_paired_end_joiner, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,332 Loaded tool id: fastq_stats, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,333 Loaded label: Roche-454 data galaxy.tools DEBUG 2012-11-01 10:35:58,333 Loaded tool id: quality_score_distribution, version: 1.0.2 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,333 Loaded tool id: trim_reads, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,333 Loaded tool id: fastq_combiner, version: 1.0.1 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,333 Loaded label: AB-SOLiD data galaxy.tools DEBUG 2012-11-01 10:35:58,333 Loaded tool id: solid2fastq, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,333 Loaded tool id: solid_qual_stats, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,333 Loaded tool id: solid_qual_boxplot, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,334 Loaded label: Generic FASTQ manipulation galaxy.tools DEBUG 2012-11-01 10:35:58,334 Loaded tool id: fastq_filter, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,334 Loaded tool id: fastq_trimmer, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,334 Loaded tool id: fastq_quality_trimmer, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,334 Loaded tool id: fastq_masker_by_quality, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,334 Loaded tool id: fastq_paired_end_interlacer, version: 1.1 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,334 Loaded tool id: fastq_paired_end_deinterlacer, version: 1.1 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,334 Loaded tool id: fastq_manipulation, version: 1.0.1 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,335 Loaded tool id: fastq_to_fasta_python, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,335 Loaded tool id: fastq_to_tabular, version: 1.1.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,335 Loaded tool id: tabular_to_fastq, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,335 Loaded label: FASTX-Toolkit for FASTQ data galaxy.tools DEBUG 2012-11-01 10:35:58,335 Loaded tool id: cshl_fastq_quality_converter, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,335 Loaded tool id: cshl_fastx_quality_statistics, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,335 Loaded tool id: cshl_fastq_quality_boxplot, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,335 Loaded tool id: cshl_fastx_nucleotides_distribution, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,335 Loaded tool id: cshl_fastq_to_fasta, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,336 Loaded tool id: cshl_fastq_quality_filter, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,336 Loaded tool id: cshl_fastx_artifacts_filter, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,336 Loaded tool id: cshl_fastx_barcode_splitter, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,336 Loaded tool id: cshl_fastx_clipper, version: 1.0.1 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,336 Loaded tool id: cshl_fastx_collapser, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,336 Loaded tool id: cshl_fastx_renamer, version: 0.0.11 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,336 Loaded tool id: cshl_fastx_reverse_complement, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,336 Loaded tool id: cshl_fastx_trimmer, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,337 Loading section: NGS: Picard (beta) galaxy.tools DEBUG 2012-11-01 10:35:58,337 Loaded label: Conversion galaxy.tools DEBUG 2012-11-01 10:35:58,337 Loaded tool id: picard_FastqToSam, version: 1.56.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,337 Loaded tool id: picard_SamToFastq, version: 1.56.1 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,337 Loaded label: QC/Metrics for sam/bam galaxy.tools DEBUG 2012-11-01 10:35:58,337 Loaded tool id: picard_BamIndexStats, version: 1.56.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,337 Loaded tool id: PicardASMetrics, version: 1.56.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,337 Loaded tool id: PicardGCBiasMetrics, version: 1.56.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,338 Loaded tool id: rgEstLibComp, version: 1.56.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,338 Loaded tool id: PicardInsertSize, version: 1.56.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,338 Loaded tool id: PicardHsMetrics, version: 1.56.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,338 Loaded label: bam/sam Cleaning galaxy.tools DEBUG 2012-11-01 10:35:58,338 Loaded tool id: picard_ARRG, version: 1.56.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,338 Loaded tool id: picard_ReorderSam, version: 1.56.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,338 Loaded tool id: picard_ReplaceSamHeader, version: 1.56.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,338 Loaded tool id: rgPicFixMate, version: 1.56.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,339 Loaded tool id: rgPicardMarkDups, version: 1.56.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,339 Loading section: NGS: Mapping galaxy.tools DEBUG 2012-11-01 10:35:58,339 Loaded tool id: lastz_wrapper_2, version: 1.2.2 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,339 Loaded tool id: lastz_paired_reads_wrapper, version: 1.1.1 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,339 Loaded tool id: bowtie_wrapper, version: 1.1.2 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,339 Loaded tool id: bowtie2, version: 0.1 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,339 Loaded tool id: bowtie_color_wrapper, version: 1.1.2 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,339 Loaded tool id: bfast_wrapper, version: 0.1.3 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,340 Loaded tool id: megablast_wrapper, version: 1.2.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,340 Loaded tool id: megablast_xml_parser, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,340 Loaded tool id: PerM, version: 1.1.2 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,340 Loaded tool id: srma_wrapper, version: 0.2.5 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,340 Loaded tool id: mosaik_wrapper, version: 1.1.1 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,340 Loading section: NGS: Indel Analysis galaxy.tools DEBUG 2012-11-01 10:35:58,340 Loaded tool id: sam_indel_filter, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,340 Loaded tool id: indel_sam2interval, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,341 Loaded tool id: indel_table, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,341 Loaded tool id: indel_analysis, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,341 Loading section: NGS: RNA Analysis galaxy.tools DEBUG 2012-11-01 10:35:58,341 Loaded label: RNA-seq galaxy.tools DEBUG 2012-11-01 10:35:58,341 Loaded tool id: tophat, version: 1.5.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,341 Loaded tool id: tophat2, version: 0.5 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,341 Loaded tool id: tophat_color, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,341 Loaded tool id: cufflinks, version: 0.0.5 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,342 Loaded tool id: cuffcompare, version: 0.0.5 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,342 Loaded tool id: express, version: 1.1.1 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,342 Loaded tool id: cuffmerge, version: 0.0.5 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,342 Loaded tool id: cuffdiff, version: 0.0.5 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,342 Loaded label: Filtering galaxy.tools DEBUG 2012-11-01 10:35:58,342 Loaded tool id: filter_combined_via_tracking, version: 0.1 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,342 Loading section: NGS: SAM Tools galaxy.tools DEBUG 2012-11-01 10:35:58,342 Loaded tool id: sam_bw_filter, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,343 Loaded tool id: sam2interval, version: 1.0.1 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,343 Loaded tool id: sam_to_bam, version: 1.1.2 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,343 Loaded tool id: bam_to_sam, version: 1.0.3 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,343 Loaded tool id: sam_merge2, version: 1.1.2 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,343 Loaded tool id: samtools_mpileup, version: 0.0.1 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,343 Loaded tool id: sam_pileup, version: 1.1.1 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,343 Loaded tool id: pileup_parser, version: 1.0.2 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,343 Loaded tool id: pileup_interval, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,344 Loaded tool id: samtools_flagstat, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,344 Loaded tool id: samtools_rmdup, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,344 Loaded tool id: samtools_slice_bam, version: 0.0.1 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,344 Loading section: NGS: GATK Tools (beta) galaxy.tools DEBUG 2012-11-01 10:35:58,344 Loaded label: Alignment Utilities galaxy.tools DEBUG 2012-11-01 10:35:58,344 Loaded tool id: gatk_depth_of_coverage, version: 0.0.2 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,344 Loaded tool id: gatk_print_reads, version: 0.0.1 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,344 Loaded label: Realignment galaxy.tools DEBUG 2012-11-01 10:35:58,345 Loaded tool id: gatk_realigner_target_creator, version: 0.0.4 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,345 Loaded tool id: gatk_indel_realigner, version: 0.0.6 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,345 Loaded label: Base Recalibration galaxy.tools DEBUG 2012-11-01 10:35:58,345 Loaded tool id: gatk_count_covariates, version: 0.0.5 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,345 Loaded tool id: gatk_table_recalibration, version: 0.0.5 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,345 Loaded tool id: gatk_analyze_covariates, version: 0.0.5 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,345 Loaded label: Genotyping galaxy.tools DEBUG 2012-11-01 10:35:58,345 Loaded tool id: gatk_unified_genotyper, version: 0.0.6 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,346 Loaded label: Annotation galaxy.tools DEBUG 2012-11-01 10:35:58,346 Loaded tool id: gatk_variant_annotator, version: 0.0.5 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,346 Loaded label: Filtration galaxy.tools DEBUG 2012-11-01 10:35:58,346 Loaded tool id: gatk_variant_filtration, version: 0.0.5 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,346 Loaded tool id: gatk_variant_select, version: 0.0.2 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,346 Loaded label: Variant Quality Score Recalibration galaxy.tools DEBUG 2012-11-01 10:35:58,346 Loaded tool id: gatk_variant_recalibrator, version: 0.0.4 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,346 Loaded tool id: gatk_variant_apply_recalibration, version: 0.0.4 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,346 Loaded label: Variant Utilities galaxy.tools DEBUG 2012-11-01 10:35:58,347 Loaded tool id: gatk_validate_variants, version: 0.0.4 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,347 Loaded tool id: gatk_variant_eval, version: 0.0.8 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,347 Loaded tool id: gatk_variant_combine, version: 0.0.4 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,347 Loading section: NGS: Peak Calling galaxy.tools DEBUG 2012-11-01 10:35:58,347 Loaded tool id: peakcalling_macs, version: 1.0.1 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,347 Loaded tool id: peakcalling_sicer, version: 0.0.1 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,347 Loaded tool id: peakcalling_ccat, version: 0.0.1 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,347 Loaded tool id: bed2genetrack, version: 1.0.1 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,348 Loaded tool id: predict2genetrack, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,348 Loading section: NGS: Simulation galaxy.tools DEBUG 2012-11-01 10:35:58,348 Loaded tool id: ngs_simulation, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,348 Loading section: SNP/WGA: Data; Filters galaxy.tools DEBUG 2012-11-01 10:35:58,348 Loaded label: Data: Import and upload galaxy.tools DEBUG 2012-11-01 10:35:58,348 Loaded tool id: upload1, version: 1.1.3 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,348 Loaded tool id: library_access1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,348 Loaded label: Data: Filter and Clean galaxy.tools DEBUG 2012-11-01 10:35:58,349 Loaded tool id: rgClean1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,349 Loaded tool id: rgPedSub1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,349 Loaded tool id: rgLDIndep1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,349 Loaded label: Simulate galaxy.tools DEBUG 2012-11-01 10:35:58,349 Loaded tool id: fakePhe1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,349 Loaded tool id: rgfakePed1, version: 0.02 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,349 Loading section: SNP/WGA: QC; LD; Plots galaxy.tools DEBUG 2012-11-01 10:35:58,349 Loaded label: QC; Eigenstrat galaxy.tools DEBUG 2012-11-01 10:35:58,350 Loaded tool id: rgQC1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,350 Loaded tool id: rgEigPCA1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,350 Loaded label: LD; Manhattan/QQ; GRR galaxy.tools DEBUG 2012-11-01 10:35:58,350 Loaded tool id: rgHaploView1, version: 0.3 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,350 Loaded tool id: rgManQQ1, version: 1.0.3 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,350 Loaded tool id: rgGRR1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,350 Loading section: SNP/WGA: Statistical Models galaxy.tools DEBUG 2012-11-01 10:35:58,350 Loaded tool id: rgCaCo1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,351 Loaded tool id: rgTDT1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,351 Loaded tool id: rgGLM1, version: 0.2 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,351 Loaded tool id: rgManQQ1, version: 1.0.3 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,351 Loading section: Phenotype Association galaxy.tools DEBUG 2012-11-01 10:35:58,351 Loaded tool id: hgv_codingSnps, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,351 Loaded tool id: hgv_add_scores, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,351 Loaded tool id: hgv_sift, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,351 Loaded tool id: hgv_linkToGProfile, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,352 Loaded tool id: hgv_david, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,352 Loaded tool id: ctdBatch_1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,352 Loaded tool id: hgv_funDo, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,352 Loaded tool id: hgv_snpFreq, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,352 Loaded tool id: hgv_ldtools, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,352 Loaded tool id: hgv_pass, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,352 Loaded tool id: hgv_gpass, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,352 Loaded tool id: hgv_beam, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,353 Loaded tool id: hgv_lps, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,353 Loaded tool id: hgv_hilbertvis, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,353 Loaded tool id: freebayes_wrapper, version: 0.5.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,353 Loaded tool id: hgv_master2pgSnp, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,353 Loaded tool id: vcf2pgSnp, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,353 Loaded tool id: dividePgSnp, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,353 Loading section: VCF Tools galaxy.tools DEBUG 2012-11-01 10:35:58,353 Loaded tool id: vcf_intersect, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,354 Loaded tool id: vcf_annotate, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,354 Loaded tool id: vcf_filter, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,354 Loaded tool id: vcf_extract, version: 1.0.0 into tool panel. galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,498 Loaded display application 'ucsc_bam' for datatype 'bam', inherit=False. galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,501 Loaded display application 'ensembl_bam' for datatype 'bam', inherit=False. galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,503 Loaded display application 'igv_bam' for datatype 'bam', inherit=False. galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,504 Loaded display application 'igb_bam' for datatype 'bam', inherit=False. galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,505 Loaded display application 'genetrack_interval' for datatype 'bed', inherit=False. galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,506 Loaded display application 'igb_bed' for datatype 'bed', inherit=False. galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,509 Loaded display application 'ucsc_bigbed' for datatype 'bigbed', inherit=False. galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,510 Loaded display application 'igb_bb' for datatype 'bigbed', inherit=False. galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,514 Loaded display application 'ucsc_bigwig' for datatype 'bigwig', inherit=False. galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,515 Loaded display application 'igb_bigwig' for datatype 'bigwig', inherit=False. galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,521 Loaded display application 'ensembl_gff' for datatype 'gff', inherit=True. galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,522 Loaded display application 'genetrack_interval' for datatype 'interval', inherit=True. galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,531 Loaded display application 'ensembl_interval' for datatype 'interval', inherit=True. galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,540 Loaded display application 'gbrowse_interval_as_bed' for datatype 'interval', inherit=True. galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,541 Loaded display application 'rviewer_interval' for datatype 'interval', inherit=True. galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,544 Loaded display application 'ucsc_maf_customtrack' for datatype 'mafcustomtrack', inherit=False. galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,548 Loaded display application 'ucsc_vcf' for datatype 'vcf', inherit=False. galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,550 Loaded display application 'igv_vcf' for datatype 'vcf', inherit=False. galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,551 Loaded display application 'rviewer_vcf' for datatype 'vcf', inherit=True. galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,553 Loaded display application 'igb_wig' for datatype 'wig', inherit=False. galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,555 Loaded display application 'igv_vcf' for datatype 'vcf_bgzip', inherit=False. galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,555 Adding inherited display application 'ensembl_gff' to datatype 'gtf' galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,555 Adding inherited display application 'genetrack_interval' to datatype 'bedstrict' galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,556 Adding inherited display application 'ensembl_interval' to datatype 'bedstrict' galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,556 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bedstrict' galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,556 Adding inherited display application 'rviewer_interval' to datatype 'bedstrict' galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,556 Adding inherited display application 'genetrack_interval' to datatype 'bedgraph' galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,556 Adding inherited display application 'ensembl_interval' to datatype 'bedgraph' galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,556 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bedgraph' galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,557 Adding inherited display application 'rviewer_interval' to datatype 'bedgraph' galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,557 Adding inherited display application 'genetrack_interval' to datatype 'bed12' galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,557 Adding inherited display application 'ensembl_interval' to datatype 'bed12' galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,557 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bed12' galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,557 Adding inherited display application 'rviewer_interval' to datatype 'bed12' galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,558 Adding inherited display application 'ensembl_interval' to datatype 'bed' galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,558 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bed' galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,558 Adding inherited display application 'rviewer_interval' to datatype 'bed' galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,558 Adding inherited display application 'ensembl_gff' to datatype 'gff3' galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,559 Adding inherited display application 'genetrack_interval' to datatype 'bed6' galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,559 Adding inherited display application 'ensembl_interval' to datatype 'bed6' galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,559 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bed6' galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,559 Adding inherited display application 'rviewer_interval' to datatype 'bed6' galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,559 Adding inherited display application 'genetrack_interval' to datatype 'encodepeak' galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,559 Adding inherited display application 'ensembl_interval' to datatype 'encodepeak' galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,560 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'encodepeak' galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,560 Adding inherited display application 'rviewer_interval' to datatype 'encodepeak' galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,567 Loaded converter: CONVERTER_Bam_Bai_0 galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,574 Loaded converter: CONVERTER_bam_to_summary_tree_0 galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,581 Loaded converter: CONVERTER_bed_to_gff_0 galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,588 Loaded converter: CONVERTER_interval_to_coverage_0 galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,595 Loaded converter: CONVERTER_bed_to_bgzip_0 galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,602 Loaded converter: CONVERTER_bed_to_tabix_0 galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,609 Loaded converter: CONVERTER_bed_to_summary_tree_0 galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,616 Loaded converter: CONVERTER_bed_to_fli_0 galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,623 Loaded converter: CONVERTER_bedgraph_to_bigwig galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,632 Loaded converter: CONVERTER_bed_to_genetrack_0 galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,639 Loaded converter: CONVERTER_len_to_linecount galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,646 Loaded converter: CONVERTER_fasta_to_tabular galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,653 Loaded converter: CONVERTER_fasta_to_bowtie_base_index galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,660 Loaded converter: CONVERTER_fasta_to_bowtie_color_index galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,667 Loaded converter: CONVERTER_fasta_to_2bit galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,674 Loaded converter: CONVERTER_fasta_to_len galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,681 Loaded converter: CONVERTER_fastq_to_fqtoc0 galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,688 Loaded converter: CONVERTER_fastq_to_fqtoc0 galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,695 Loaded converter: CONVERTER_fastq_to_fqtoc0 galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,702 Loaded converter: CONVERTER_fastq_to_fqtoc0 galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,712 Loaded converter: CONVERTER_fastq_to_fqtoc0 galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,718 Loaded converter: CONVERTER_gff_to_bed_0 galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,725 Loaded converter: CONVERTER_gff_to_interval_index_0 galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,732 Loaded converter: CONVERTER_gff_to_summary_tree_0 galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,739 Loaded converter: CONVERTER_gff_to_fli_0 galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,746 Loaded converter: CONVERTER_gff_to_interval_index_0 galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,753 Loaded converter: CONVERTER_gff_to_summary_tree_0 galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,760 Loaded converter: CONVERTER_interval_to_bed_0 galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,767 Loaded converter: CONVERTER_interval_to_bedstrict_0 galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,774 Loaded converter: CONVERTER_interval_to_bed6_0 galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,781 Loaded converter: CONVERTER_interval_to_bed12_0 galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,788 Loaded converter: CONVERTER_interval_to_bgzip_0 galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,798 Loaded converter: CONVERTER_interval_to_tabix_0 galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,805 Loaded converter: CONVERTER_interval_to_summary_tree_0 galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,812 Loaded converter: CONVERTER_picard_interval_list_to_bed6 galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,819 Loaded converter: CONVERTER_maf_to_fasta_0 galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,826 Loaded converter: CONVERTER_maf_to_interval_0 galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,833 Loaded converter: CONVERTER_encodepeak_to_tabix_0 galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,840 Loaded converter: CONVERTER_encodepeak_to_bgzip_0 galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,847 Loaded converter: CONVERTER_encodepeak_to_summary_tree_0 galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,854 Loaded converter: CONVERTER_sam_to_bam galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,861 Loaded converter: CONVERTER_sam_to_summary_tree_0 galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,868 Loaded converter: CONVERTER_vcf_to_bgzip_0 galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,875 Loaded converter: CONVERTER_vcf_to_vcf_bgzip_0 galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,885 Loaded converter: CONVERTER_vcf_to_tabix_0 galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,892 Loaded converter: CONVERTER_vcf_to_summary_tree_0 galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,899 Loaded converter: CONVERTER_wig_to_bigwig galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,900 Loaded converter: CONVERTER_wiggle_to_interval_0 galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,907 Loaded converter: CONVERTER_vcf_bgzip_to_tabix_0 galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,914 Loaded converter: lped2fpedconvert galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,921 Loaded converter: lped2pbedconvert galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,928 Loaded converter: pbed2lpedconvert galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,935 Loaded converter: pbed2ldindepconvert galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,936 Loaded external metadata tool: __SET_METADATA__ galaxy.tools.imp_exp DEBUG 2012-11-01 10:35:58,938 Loaded history export tool: __EXPORT_HISTORY__ galaxy.tools.imp_exp DEBUG 2012-11-01 10:35:58,939 Loaded history import tool: __IMPORT_HISTORY__ galaxy.tools.genome_index DEBUG 2012-11-01 10:35:58,940 Loaded genome index tool: __GENOME_INDEX__ galaxy.jobs.runners.local INFO 2012-11-01 10:35:58,942 starting workers galaxy.jobs.runners.local DEBUG 2012-11-01 10:35:58,943 5 workers ready galaxy.jobs.handler DEBUG 2012-11-01 10:35:58,943 Loaded job runner: galaxy.jobs.runners.local:LocalJobRunner galaxy.jobs.runners.lwr INFO 2012-11-01 10:35:58,944 starting workers galaxy.jobs.runners.lwr DEBUG 2012-11-01 10:35:58,949 5 workers ready galaxy.jobs.handler DEBUG 2012-11-01 10:35:58,950 Loaded job runner: galaxy.jobs.runners.lwr:LwrJobRunner galaxy.jobs.handler DEBUG 2012-11-01 10:35:58,950 Job runners: local:lwr galaxy.jobs.handler INFO 2012-11-01 10:35:58,950 job handler stop queue started galaxy.jobs.manager INFO 2012-11-01 10:35:58,957 job manager queue started galaxy.jobs.manager INFO 2012-11-01 10:35:58,958 job manager stop queue started galaxy.jobs.handler INFO 2012-11-01 10:35:58,963 job handler queue started galaxy.sample_tracking.external_service_types DEBUG 2012-11-01 10:35:58,966 Loaded external_service_type: Simple unknown sequencer 1.0.0 galaxy.sample_tracking.external_service_types DEBUG 2012-11-01 10:35:58,970 Loaded external_service_type: Applied Biosystems SOLiD 1.0.0 >>> /home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/controllers ['/home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/controllers'] galaxy.webapps.galaxy.controllers root galaxy.webapps.galaxy.controllers.root galaxy.web.framework.base DEBUG 2012-11-01 10:35:58,978 Enabling 'root' controller, class: RootController galaxy.webapps.galaxy.controllers mobile galaxy.webapps.galaxy.controllers.mobile galaxy.web.framework.base DEBUG 2012-11-01 10:35:58,979 Enabling 'mobile' controller, class: Mobile galaxy.webapps.galaxy.controllers user galaxy.webapps.galaxy.controllers.user galaxy.web.framework.base DEBUG 2012-11-01 10:35:58,981 Enabling 'user' controller, class: User galaxy.webapps.galaxy.controllers requests galaxy.webapps.galaxy.controllers.requests galaxy.web.framework.base DEBUG 2012-11-01 10:35:58,984 Enabling 'requests' controller, class: Requests galaxy.webapps.galaxy.controllers admin_toolshed galaxy.webapps.galaxy.controllers.admin_toolshed galaxy.web.framework.base DEBUG 2012-11-01 10:35:58,996 Enabling 'admin_toolshed' controller, class: AdminGalaxy galaxy.web.framework.base DEBUG 2012-11-01 10:35:58,996 Enabling 'admin_toolshed' controller, class: AdminToolshed galaxy.webapps.galaxy.controllers external_services galaxy.webapps.galaxy.controllers.external_services galaxy.web.framework.base DEBUG 2012-11-01 10:35:58,998 Enabling 'external_services' controller, class: ExternalServiceController galaxy.webapps.galaxy.controllers library_admin galaxy.webapps.galaxy.controllers.library_admin galaxy.web.framework.base DEBUG 2012-11-01 10:35:59,009 Enabling 'library_admin' controller, class: LibraryAdmin galaxy.webapps.galaxy.controllers data_admin galaxy.webapps.galaxy.controllers.data_admin galaxy.web.framework.base DEBUG 2012-11-01 10:35:59,016 Enabling 'data_admin' controller, class: DataAdmin galaxy.webapps.galaxy.controllers workflow galaxy.webapps.galaxy.controllers.workflow galaxy.web.framework.base DEBUG 2012-11-01 10:35:59,067 Enabling 'workflow' controller, class: WorkflowController galaxy.webapps.galaxy.controllers forms galaxy.webapps.galaxy.controllers.forms galaxy.web.framework.base DEBUG 2012-11-01 10:35:59,069 Enabling 'forms' controller, class: Forms galaxy.webapps.galaxy.controllers cloudlaunch galaxy.webapps.galaxy.controllers.cloudlaunch galaxy.web.framework.base DEBUG 2012-11-01 10:35:59,083 Enabling 'cloudlaunch' controller, class: CloudController galaxy.webapps.galaxy.controllers tag galaxy.webapps.galaxy.controllers.tag galaxy.web.framework.base DEBUG 2012-11-01 10:35:59,084 Enabling 'tag' controller, class: TagsController galaxy.webapps.galaxy.controllers history galaxy.webapps.galaxy.controllers.history galaxy.web.framework.base DEBUG 2012-11-01 10:35:59,086 Enabling 'history' controller, class: HistoryController galaxy.webapps.galaxy.controllers requests_common galaxy.webapps.galaxy.controllers.requests_common galaxy.web.framework.base DEBUG 2012-11-01 10:35:59,087 Enabling 'requests_common' controller, class: RequestsCommon galaxy.webapps.galaxy.controllers async galaxy.webapps.galaxy.controllers.async galaxy.web.framework.base DEBUG 2012-11-01 10:35:59,088 Enabling 'async' controller, class: ASync galaxy.webapps.galaxy.controllers dataset galaxy.webapps.galaxy.controllers.dataset galaxy.web.framework.base DEBUG 2012-11-01 10:35:59,096 Enabling 'dataset' controller, class: DatasetInterface galaxy.webapps.galaxy.controllers request_type galaxy.webapps.galaxy.controllers.request_type galaxy.web.framework.base DEBUG 2012-11-01 10:35:59,098 Enabling 'request_type' controller, class: RequestType galaxy.webapps.galaxy.controllers tool_runner galaxy.webapps.galaxy.controllers.tool_runner galaxy.web.framework.base DEBUG 2012-11-01 10:35:59,100 Enabling 'tool_runner' controller, class: ToolRunner galaxy.webapps.galaxy.controllers requests_admin galaxy.webapps.galaxy.controllers.requests_admin galaxy.web.framework.base DEBUG 2012-11-01 10:35:59,119 Enabling 'requests_admin' controller, class: RequestsAdmin galaxy.webapps.galaxy.controllers page galaxy.webapps.galaxy.controllers.page galaxy.web.framework.base DEBUG 2012-11-01 10:35:59,121 Enabling 'page' controller, class: PageController galaxy.webapps.galaxy.controllers visualization galaxy.webapps.galaxy.controllers.visualization galaxy.web.framework.base DEBUG 2012-11-01 10:35:59,124 Enabling 'visualization' controller, class: VisualizationController galaxy.webapps.galaxy.controllers ucsc_proxy galaxy.webapps.galaxy.controllers.ucsc_proxy galaxy.web.framework.base DEBUG 2012-11-01 10:35:59,125 Enabling 'ucsc_proxy' controller, class: UCSCProxy galaxy.webapps.galaxy.controllers external_service galaxy.webapps.galaxy.controllers.external_service galaxy.web.framework.base DEBUG 2012-11-01 10:35:59,126 Enabling 'external_service' controller, class: ExternalService galaxy.webapps.galaxy.controllers library_common galaxy.webapps.galaxy.controllers.library_common galaxy.web.framework.base DEBUG 2012-11-01 10:35:59,127 Enabling 'library_common' controller, class: LibraryCommon galaxy.webapps.galaxy.controllers admin galaxy.webapps.galaxy.controllers.admin galaxy.web.framework.base DEBUG 2012-11-01 10:35:59,128 Enabling 'admin' controller, class: AdminGalaxy galaxy.webapps.galaxy.controllers library galaxy.webapps.galaxy.controllers.library galaxy.web.framework.base DEBUG 2012-11-01 10:35:59,129 Enabling 'library' controller, class: Library galaxy.webapps.galaxy.controllers error galaxy.webapps.galaxy.controllers.error galaxy.web.framework.base DEBUG 2012-11-01 10:35:59,130 Enabling 'error' controller, class: Error galaxy.web.framework.base DEBUG 2012-11-01 10:35:59,132 Enabling 'visualizations' API controller, class: VisualizationsController galaxy.web.framework.base DEBUG 2012-11-01 10:35:59,133 Enabling 'tools' API controller, class: ToolsController galaxy.web.framework.base DEBUG 2012-11-01 10:35:59,134 Enabling 'roles' API controller, class: RoleAPIController galaxy.web.framework.base DEBUG 2012-11-01 10:35:59,135 Enabling 'requests' API controller, class: RequestsAPIController galaxy.web.framework.base DEBUG 2012-11-01 10:35:59,136 Enabling 'permissions' API controller, class: PermissionsController galaxy.web.framework.base DEBUG 2012-11-01 10:35:59,137 Enabling 'workflows' API controller, class: WorkflowsAPIController galaxy.web.framework.base DEBUG 2012-11-01 10:35:59,137 Enabling 'group_users' API controller, class: GroupUsersAPIController galaxy.web.framework.base DEBUG 2012-11-01 10:35:59,144 Enabling 'history_contents' API controller, class: HistoryContentsController galaxy.web.framework.base DEBUG 2012-11-01 10:35:59,144 Enabling 'request_types' API controller, class: RequestTypeAPIController galaxy.web.framework.base DEBUG 2012-11-01 10:35:59,145 Enabling 'datasets' API controller, class: DatasetsController galaxy.web.framework.base DEBUG 2012-11-01 10:35:59,147 Enabling 'folders' API controller, class: FoldersController galaxy.web.framework.base DEBUG 2012-11-01 10:35:59,148 Enabling 'quotas' API controller, class: QuotaAPIController galaxy.web.framework.base DEBUG 2012-11-01 10:35:59,148 Enabling 'forms' API controller, class: FormDefinitionAPIController galaxy.web.framework.base DEBUG 2012-11-01 10:35:59,149 Enabling 'group_roles' API controller, class: GroupRolesAPIController galaxy.web.framework.base DEBUG 2012-11-01 10:35:59,149 Enabling 'folder_contents' API controller, class: FolderContentsController galaxy.web.framework.base DEBUG 2012-11-01 10:35:59,151 Enabling 'library_contents' API controller, class: LibraryContentsController galaxy.web.framework.base DEBUG 2012-11-01 10:35:59,152 Enabling 'users' API controller, class: UserAPIController galaxy.web.framework.base DEBUG 2012-11-01 10:35:59,152 Enabling 'histories' API controller, class: HistoriesController galaxy.web.framework.base DEBUG 2012-11-01 10:35:59,153 Enabling 'groups' API controller, class: GroupAPIController galaxy.web.framework.base DEBUG 2012-11-01 10:35:59,154 Enabling 'libraries' API controller, class: LibrariesController galaxy.web.framework.base DEBUG 2012-11-01 10:35:59,155 Enabling 'samples' API controller, class: SamplesAPIController galaxy.web.framework.base DEBUG 2012-11-01 10:35:59,156 Enabling 'genomes' API controller, class: GenomesController galaxy.webapps.galaxy.buildapp DEBUG 2012-11-01 10:35:59,156 app.config.api_folders: False galaxy.webapps.galaxy.buildapp DEBUG 2012-11-01 10:35:59,498 Enabling 'httpexceptions' middleware galaxy.webapps.galaxy.buildapp DEBUG 2012-11-01 10:35:59,499 Enabling 'recursive' middleware galaxy.webapps.galaxy.buildapp DEBUG 2012-11-01 10:35:59,500 Enabling 'print debug' middleware galaxy.webapps.galaxy.buildapp DEBUG 2012-11-01 10:35:59,506 Enabling 'error' middleware galaxy.webapps.galaxy.buildapp DEBUG 2012-11-01 10:35:59,507 Enabling 'trans logger' middleware galaxy.webapps.galaxy.buildapp DEBUG 2012-11-01 10:35:59,507 Enabling 'config' middleware galaxy.webapps.galaxy.buildapp DEBUG 2012-11-01 10:35:59,507 Enabling 'x-forwarded-host' middleware Starting server in PID 20622. Traceback (most recent call last): File "./scripts/paster.py", line 34, in <module> command.run() File "/home/galaxy/galaxy-dist/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/command.py", line 84, in run invoke(command, command_name, options, args[1:]) File "/home/galaxy/galaxy-dist/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/command.py", line 123, in invoke exit_code = runner.run(args) File "/home/galaxy/galaxy-dist/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/command.py", line 218, in run result = self.command() File "/home/galaxy/galaxy-dist/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/serve.py", line 303, in command serve() File "/home/galaxy/galaxy-dist/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/serve.py", line 287, in serve server(app) File "/home/galaxy/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py", line 151, in server_wrapper **context.local_conf) File "/home/galaxy/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/util/fixtypeerror.py", line 57, in fix_call val = callable(*args, **kw) File "/home/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpserver.py", line 1314, in server_runner serve(wsgi_app, **kwargs) File "/home/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpserver.py", line 1264, in serve threadpool_options=threadpool_options) File "/home/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpserver.py", line 1114, in __init__ RequestHandlerClass, ssl_context) File "/home/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpserver.py", line 1094, in __init__ RequestHandlerClass, ssl_context) File "/home/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpserver.py", line 328, in __init__ HTTPServer.__init__(self, server_address, RequestHandlerClass) File "/usr/lib64/python2.6/SocketServer.py", line 402, in __init__ self.server_bind() File "/usr/lib64/python2.6/BaseHTTPServer.py", line 108, in server_bind SocketServer.TCPServer.server_bind(self) File "/usr/lib64/python2.6/SocketServer.py", line 413, in server_bind self.socket.bind(self.server_address) File "<string>", line 1, in bind socket.gaierror: [Errno -2] Name or service not known

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