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

ERROR MESSAGE: Running with the -et NO_ET or -et STDOUT option requires a GATK Key file
by Carlos Borroto 27 Apr '12

27 Apr '12

It seems like GATK authors at Broad really really want you to phone home every time you use their software. I'm getting this error while running the lastest version: "ERROR MESSAGE: Running with the -et NO_ET or -et STDOUT option requires a GATK Key file. Please see http://www.broadinstitute.org/gsa/wiki/index.php/Phone_home for more information and instructions on how to obtain a key." >From the Phone_home wiki page: "How to Obtain a GATK Key To obtain a GATK key, email gsahelp(a)broadinstitute.org with the subject line GATK Key Request. In your email, please provide us with the reason(s) you need to run the GATK with the phone-home feature disabled. Please be as explicit as possible about why you cannot participate in the phone home feature. Note that the key you will be issued is linked to the email address you used to contact us." In general I don't have an issue with phone home features from software providers I trust, and I do completely trust The Broad Institute. Although, this does sound a little draconian how is being imposed. Nevertheless, I would like to ask for an easier way to deactivate the use of "-et NO_ET" on Galaxy GATK's wrappers. Right now I'm manually commenting the relevant line, but I think this means my mercurial repository won't get any update from upstream, or that I will have to deal with merging. Regards, Carlos

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Increasing EBS storage above 1TB for use with Galaxy cloudman.
by Mohammad Heydarian 26 Apr '12

26 Apr '12

Hello, I am performing NGS data analysis using Galaxy cloudman. I am working with very large Fastq files that add up and approach the 1TB limit of the EBS volume when I perform my analysis. Is there a way to use multiple EBS volumes with one EC2 instance of Galaxy cloudman. For example, could I direct which EBS volume holds certain files to prevent reaching the 1 TB limit while still allowing my EC2 instance to access and perform jobs on all files? Many thank in advance! Cheers, Mo Heydarian

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What macs version support in Galaxy
by Waldron, Michael H 26 Apr '12

26 Apr '12

On our local installation of Galaxy, we get the following error when running Macs: Usage: macs <-t tfile> [-n name] [-g genomesize] [options] Example: macs -t ChIP.bam -c Control.bam -f BAM -g h -n test -w --call-subpeaks macs: error: no such option: --lambdaset What is the latest version of macs supported by Galaxy? We are running 1.4.1. Mike Waldron

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Re: [galaxy-dev] 503 Error when adding a tool from local toolshed
by Greg Von Kuster 26 Apr '12

26 Apr '12

Hi Ira, I'm not quite sure what's causing this, as the 503 error is usually stating that the web server is not available. Setting up your servers behind a proxy is probably not necessary as it just adds another level of complexity - I was just wondering if that's what you had already. It's better that you have the simpler setup while we try to figure this out. When you get back from your trip, send me a message and we'll work on it. As I said in my previous response, your repository installs just fine in my environment, so we'll focus on tracking down what is different in yours. Thanks! Greg Von Kuster On Apr 26, 2012, at 2:27 PM, Ira Cooke wrote: > Hi Greg, > > I seem to run into the problem regardless of the revision of Galaxy I use ... it was happening infrequently until recently ... but now it happens every single time I try to install my tools (with the latest galaxy-dist). Yesterday ... I tested with the latest galaxy-central in order to create my bug report. > > Unfortunately I'm on a trip until saturday ... so I can't get at the paster log for the VM I did my testing on. I looked at the paster log though and I can remember that the request shown is the same as the request shown in the error. It's this; > >>> http://127.0.0.1:8080/admin_toolshed/install_repository?tool_shed_url=http:… > > All my settings are default except very tiny modifications to add myself as an admin. When I get back from my trip I'll try setting up things behind a proxy and see if that fixes the issue. > > Will let you know how I go > > Ira > > > On 26/04/2012, at 11:40 PM, Greg Von Kuster wrote: > >> Hello Ira, >> >> Sorry you bumped into this problem. I've cloned your protk-toolshed repository and made a bz2 compressed archive as you did. I was able to upload it to a local tool shed, and was successful installing from there to my local Galaxy instance, where my environment is running Galaxy change set revision 7116:0cffe389e1b3. This tells me that the problem is most likely due to your running an older version of Galaxy. >> >> Are you tracking our galaxy-central repository in your environment? Since the galaxy-dist repository is generally 4-8 weeks older than the galaxy-central repository, many of the features enabling the Galaxy <-> tool shed communication are not functional in galaxy-dist. >> >> If this is not the problem, can you send me the snippet of your paster log from your tool shed that shows the request that produced the 503 error? This should help get things figured out. By the way, from your description, I assume you are not running an Apache front-end on either your Galaxy instance or your tool shed - is this correct? >> >> Thanks! >> >> Greg Von Kuster >> >> >> On Apr 26, 2012, at 3:41 AM, Ira Cooke wrote: >> >>> Dear List, >>> >>> I'm trying to check my toolshed tools by installing first on a local toolshed, but running into an error every time I try to add my tools. >>> >>> In order to rule out possible idiosyncracies of my system I've reproduced the error on an Ubuntu VM ... the system was not completely clean ... a few packages required by galaxy and some dependencies of my tools have been installed, but I performed the following steps after creating a fresh "galaxy" user. >>> >>> # Create new user "galaxy" >>> # Create galaxy_env via virtualenv.py >>> # Add entry to .bashrc to ensure python in galaxy_env is the default python for the galaxy user >>> # Fresh checkout of galaxy-central >>> # sh run.sh --reload >>> # Add admin user to galaxy by configuring universe_wsgi.ini >>> # Configure tool_sheds_conf.xml as follows; >>> <?xml version="1.0"?> >>> <tool_sheds> >>> <tool_shed name="Local" url="http://127.0.0.1:9009/"/> >>> <tool_shed name="Galaxy main tool shed" url="http://toolshed.g2.bx.psu.edu/"/> >>> <tool_shed name="Galaxy test tool shed" url="http://testtoolshed.g2.bx.psu.edu/"/> >>> </tool_sheds> >>> >>> # Restart galaxy >>> # Register myself as a user of galaxy >>> >>> # Add database_connection line to community_wsgi.ini >>> - database_connection=sqlite:///./database/community.sqlite?isolation_level=IMMEDIATE >>> >>> # Add admin user to community_wsgi.ini (same as for galaxy admin user) >>> # run sh run_community.sh >>> # Register myself as a user of the local toolshed >>> # Checked out my tools >>> hg clone https://bitbucket.org/iracooke/protk-toolshed >>> >>> # Made a bz2 file of all my tools >>> cd protk-toolshed >>> ./make_package_data.sh >>> >>> # Created a new category on the local toolshed ("Proteomics") >>> # Added a tool called "protk" to the Proteomics category >>> # Uploaded a bz2 file with my tools to the local toolshed. >>> Looking at the tool after upload everything seems fine >>> >>> # Back on galaxy I attempted to load my tools. >>> After clicking the install button in galaxy I get the following traceback (as text) >>> >>> URL: http://127.0.0.1:8080/admin_toolshed/install_repository?tool_shed_url=http:… >>> File '/home/galaxy/central/galaxy-central/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/galaxy/central/galaxy-central/eggs/Paste-1.6-py2.7.egg/paste/debug/prints.py', line 98 in __call__ >>> environ, self.app) >>> File '/home/galaxy/central/galaxy-central/eggs/Paste-1.6-py2.7.egg/paste/wsgilib.py', line 539 in intercept_output >>> app_iter = application(environ, replacement_start_response) >>> File '/home/galaxy/central/galaxy-central/eggs/Paste-1.6-py2.7.egg/paste/recursive.py', line 80 in __call__ >>> return self.application(environ, start_response) >>> File '/home/galaxy/central/galaxy-central/eggs/Paste-1.6-py2.7.egg/paste/httpexceptions.py', line 632 in __call__ >>> return self.application(environ, start_response) >>> File '/home/galaxy/central/galaxy-central/lib/galaxy/web/framework/base.py', line 160 in __call__ >>> body = method( trans, **kwargs ) >>> File '/home/galaxy/central/galaxy-central/lib/galaxy/web/framework/__init__.py', line 184 in decorator >>> return func( self, trans, *args, **kwargs ) >>> File '/home/galaxy/central/galaxy-central/lib/galaxy/web/controllers/admin_toolshed.py', line 371 in install_repository >>> response = urllib2.urlopen( url ) >>> File '/usr/lib/python2.7/urllib2.py', line 126 in urlopen >>> return _opener.open(url, data, timeout) >>> File '/usr/lib/python2.7/urllib2.py', line 400 in open >>> response = meth(req, response) >>> File '/usr/lib/python2.7/urllib2.py', line 513 in http_response >>> 'http', request, response, code, msg, hdrs) >>> File '/usr/lib/python2.7/urllib2.py', line 438 in error >>> return self._call_chain(*args) >>> File '/usr/lib/python2.7/urllib2.py', line 372 in _call_chain >>> result = func(*args) >>> File '/usr/lib/python2.7/urllib2.py', line 521 in http_error_default >>> raise HTTPError(req.get_full_url(), code, msg, hdrs, fp) >>> HTTPError: HTTP Error 503: Service Unavailable >>> >>> >>> I've since tried to figure out where this error actually occurs ... and (according to my crude debugging methods) the actual error originates at line 371 in admin_toolshed.py .. which looks like this .. >>> >>> owner = get_repository_owner( clean_repository_clone_url( repository_clone_url ) ) >>> url = '%s/repository/get_readme?name=%s&owner=%s&changeset_revision=%s&webapp=galaxy' % ( tool_shed_url, name, owner, changeset_revision ) >>> response = urllib2.urlopen( url ) >>> >>> ... so galaxy attempts to fetch a url for the tool readme file ... and that is failing. I've tried adding a readme.txt and that didn't solve the issue. >>> >>> Hopefully this is enough for you to be able to reproduce the error ... I'm mainly just keen to get a workable setup for testing my tools, so a workaround would be much appreciated ... if there is anything obviously wrong with how I've set things up above can you let me know. >>> >>> Thanks >>> Ira >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> ___________________________________________________________ >>> Please keep all replies on the list by using "reply all" >>> in your mail client. To manage your subscriptions to this >>> and other Galaxy lists, please use the interface at: >>> >>> http://lists.bx.psu.edu/ >> >

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New Tool - Can provide a template file to user
by Unknown 26 Apr '12

26 Apr '12

Hi all, I am trying to add a tool to galaxy. I want to collect some data from the user. The data may contain hundreds of records each has 7 or 8 fields. Either user can upload a spreadsheet for that or I shall provide a template file to fill up the data. When I checked there is no provision for uploading a speadsheet in my galaxy instance. What about the second method? Is it possible to provide a template file for the user? Deepthi

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library_import_dir -- How is it supposed to work?
by Michael Moore 26 Apr '12

26 Apr '12

I set library_import_dir to a path and tried uploading a directory of bam files. After fixing the situation so galaxy could find samtools in that subshell, I was able to upload links to the history. But moving things to one directory did not appear to be terribly useful, so I tested what happened if I had subdirectories existing in library import directory. Test 1 I used folders u1 and u2, each with data, and some data in the root library_import_directory. After clearing the samtools eror I was presented with a drop-down list with choices 'None', 'u1' and 'u2'. Selecting 'None' did not result in seeking data but a sharp reminder that I had to pick a directory. Selecting those directories led to uploads, with the Non-Copy correctly sized and even downloadable from the data library, but NOT usable in the history, because upload.py decided the file did not exist (probably the 'path' variable in os.path.exists() line 99). It also became apparent that the upload would look one level down from the root directory and no further (tested by adding u3 with data and a subdirectory of u3 called v3, also with data. So the current state of affairs is that it is a single directory to which one must move files in order to upload links to a galaxy library or folders thereof.. OR, alternatively, make a directory of links called directory A, and then another directory of links to the links in directory A at the library_import_dir and then ask Galaxy to copy the data. (Not fully tested yet). But it is apparent from the UI that more utility was intended. If I have time, I will help with that. Michael Moore

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Composite datatypes and peek and main display
by Peter Cock 26 Apr '12

26 Apr '12

Hello all, I'm looking at 'basic' composite datatypes in Galaxy, based on how Edward did BLAST databases in his BLAST+ fork on the toolshed. I've extended his work to handle both protein and nucleotide databases, and have got this working for tools to create a database (i.e. wrapped makeblastdb) and use a database from the history (e.g. blastp tool). That side of things seems to be working OK. What I am not quite understanding is how to modify the behaviour of these datatypes in the galaxy GUI. Thinks like the peek contents and what happens when clicking on the "eye" icon are not explained here: http://wiki.g2.bx.psu.edu/Admin/Datatypes/Composite%20Datatypes What I have in mind is to show a simple text summary as the peek or 'eye' display view giving the database name and size (perhaps captured when the database is created, or on the fly via the blastdbcmd command). It seems one option would be to use an 'auto_primary_file' composite instead of 'basic'? Then I can use the generate_primary_file method to show some text? Have I overlooked some documentation? Thanks, Peter

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A job is stuck in queue
by cwardman.umass 26 Apr '12

26 Apr '12

Hello, I am working with galaxy for a bioinfomatics class at Umass Amherst. I have tried doing the http://manuals.bioinformatics.ucr.edu/home/gui-ngs-analysis tutorial. I am currently on the quality control section trying to use the illumina human data set and the NGS mapping bowtie for illumina program. I enter all of the parameters and hit execute and the job sit in the history/job queue waiting to for the job to run and never runs. What can i do to fix this?? Thanks for your help ~Colin

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503 Error when adding a tool from local toolshed
by Ira Cooke 26 Apr '12

26 Apr '12

Dear List, I'm trying to check my toolshed tools by installing first on a local toolshed, but running into an error every time I try to add my tools. In order to rule out possible idiosyncracies of my system I've reproduced the error on an Ubuntu VM ... the system was not completely clean ... a few packages required by galaxy and some dependencies of my tools have been installed, but I performed the following steps after creating a fresh "galaxy" user. # Create new user "galaxy" # Create galaxy_env via virtualenv.py # Add entry to .bashrc to ensure python in galaxy_env is the default python for the galaxy user # Fresh checkout of galaxy-central # sh run.sh --reload # Add admin user to galaxy by configuring universe_wsgi.ini # Configure tool_sheds_conf.xml as follows; <?xml version="1.0"?> <tool_sheds> <tool_shed name="Local" url="http://127.0.0.1:9009/"/> <tool_shed name="Galaxy main tool shed" url="http://toolshed.g2.bx.psu.edu/"/> <tool_shed name="Galaxy test tool shed" url="http://testtoolshed.g2.bx.psu.edu/"/> </tool_sheds> # Restart galaxy # Register myself as a user of galaxy # Add database_connection line to community_wsgi.ini - database_connection=sqlite:///./database/community.sqlite?isolation_level=IMMEDIATE # Add admin user to community_wsgi.ini (same as for galaxy admin user) # run sh run_community.sh # Register myself as a user of the local toolshed # Checked out my tools hg clone https://bitbucket.org/iracooke/protk-toolshed # Made a bz2 file of all my tools cd protk-toolshed ./make_package_data.sh # Created a new category on the local toolshed ("Proteomics") # Added a tool called "protk" to the Proteomics category # Uploaded a bz2 file with my tools to the local toolshed. Looking at the tool after upload everything seems fine # Back on galaxy I attempted to load my tools. After clicking the install button in galaxy I get the following traceback (as text) URL: http://127.0.0.1:8080/admin_toolshed/install_repository?tool_shed_url=http:… File '/home/galaxy/central/galaxy-central/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/galaxy/central/galaxy-central/eggs/Paste-1.6-py2.7.egg/paste/debug/prints.py', line 98 in __call__ environ, self.app) File '/home/galaxy/central/galaxy-central/eggs/Paste-1.6-py2.7.egg/paste/wsgilib.py', line 539 in intercept_output app_iter = application(environ, replacement_start_response) File '/home/galaxy/central/galaxy-central/eggs/Paste-1.6-py2.7.egg/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response) File '/home/galaxy/central/galaxy-central/eggs/Paste-1.6-py2.7.egg/paste/httpexceptions.py', line 632 in __call__ return self.application(environ, start_response) File '/home/galaxy/central/galaxy-central/lib/galaxy/web/framework/base.py', line 160 in __call__ body = method( trans, **kwargs ) File '/home/galaxy/central/galaxy-central/lib/galaxy/web/framework/__init__.py', line 184 in decorator return func( self, trans, *args, **kwargs ) File '/home/galaxy/central/galaxy-central/lib/galaxy/web/controllers/admin_toolshed.py', line 371 in install_repository response = urllib2.urlopen( url ) File '/usr/lib/python2.7/urllib2.py', line 126 in urlopen return _opener.open(url, data, timeout) File '/usr/lib/python2.7/urllib2.py', line 400 in open response = meth(req, response) File '/usr/lib/python2.7/urllib2.py', line 513 in http_response 'http', request, response, code, msg, hdrs) File '/usr/lib/python2.7/urllib2.py', line 438 in error return self._call_chain(*args) File '/usr/lib/python2.7/urllib2.py', line 372 in _call_chain result = func(*args) File '/usr/lib/python2.7/urllib2.py', line 521 in http_error_default raise HTTPError(req.get_full_url(), code, msg, hdrs, fp) HTTPError: HTTP Error 503: Service Unavailable I've since tried to figure out where this error actually occurs ... and (according to my crude debugging methods) the actual error originates at line 371 in admin_toolshed.py .. which looks like this .. owner = get_repository_owner( clean_repository_clone_url( repository_clone_url ) ) url = '%s/repository/get_readme?name=%s&owner=%s&changeset_revision=%s&webapp=galaxy' % ( tool_shed_url, name, owner, changeset_revision ) response = urllib2.urlopen( url ) ... so galaxy attempts to fetch a url for the tool readme file ... and that is failing. I've tried adding a readme.txt and that didn't solve the issue. Hopefully this is enough for you to be able to reproduce the error ... I'm mainly just keen to get a workable setup for testing my tools, so a workaround would be much appreciated ... if there is anything obviously wrong with how I've set things up above can you let me know. Thanks Ira

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ERROR on History export
by Todd Oakley 26 Apr '12

26 Apr '12

Hello, I'd am trying to export histories to upload to another galaxy instance. For some histories, it works fine. However, for others, I get an error. When I turn on debug, I get the error pasted below. Any thoughts on what is the cause of "object has no attribute 'hid'"? Thanks! Todd Server Error Module paste.exceptions.errormiddleware:*143* in |__call__| |>> <http://knot.cnsi.ucsb.edu:8080/history/export_archive#>app_iter *=* self*.*application*(*environ*,* start_response*)*| Module paste.debug.prints:*98* in |__call__| |>> <http://knot.cnsi.ucsb.edu:8080/history/export_archive#>environ*,* self*.*app*)*| Module paste.wsgilib:*539* in |intercept_output| |>> <http://knot.cnsi.ucsb.edu:8080/history/export_archive#>app_iter *=* application*(*environ*,* replacement_start_response*)*| Module paste.recursive:*80* in |__call__| |>> <http://knot.cnsi.ucsb.edu:8080/history/export_archive#>*return* self*.*application*(*environ*,* start_response*)*| Module paste.httpexceptions:*632* in |__call__| |>> <http://knot.cnsi.ucsb.edu:8080/history/export_archive#>*return* self*.*application*(*environ*,* start_response*)*| Module galaxy.web.framework.base:*145* in |__call__| |>> <http://knot.cnsi.ucsb.edu:8080/history/export_archive#>body *=* method*(* trans*,* ****kwargs *)*| Module galaxy.web.controllers.history:*591* in |export_archive| |>> <http://knot.cnsi.ucsb.edu:8080/history/export_archive#>history_exp_tool*.*execute*(* trans*,* incoming *=* params*,* set_output_hid *=* True *)*| Module galaxy.tools:*1276* in |execute| |>> <http://knot.cnsi.ucsb.edu:8080/history/export_archive#>*return* self*.*tool_action*.*execute*(* self*,* trans*,* incoming*=*incoming*,* set_output_hid*=*set_output_hid*,* history*=*history*,* ****kwargs *)*| Module galaxy.tools.actions.history_imp_exp:*103* in |execute| |>> <http://knot.cnsi.ucsb.edu:8080/history/export_archive#>include_deleted*=*incoming*[* 'include_deleted' *]* *)*| Module galaxy.tools.imp_exp:*419* in |setup_job| |>> <http://knot.cnsi.ucsb.edu:8080/history/export_archive#>input_datasets *=* *[* assoc*.*dataset*.*hid *for* assoc *in* job*.*input_datasets *]*| *AttributeError: 'NoneType' object has no attribute 'hid'* -- *************************************** Todd Oakley, Professor Ecology Evolution and Marine Biology University of California, Santa Barbara Santa Barbara, CA 93106 USA ***************************************

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