Re: [galaxy-dev] galaxy cuffdiff running too long
Hello, When I install from binary files the boost problem doesn't go away and I get one extra error message in the beginning. Error running cuffdiff. cuffdiff: /usr/lib64/libz.so.1: no version information available (required by cuffdiff) [14:51:54] Loading reference annotation. Warning: No conditions are replicated, switching to 'blind' dispersion method [14:52:05] Inspecting maps and determining fragment length distributions. terminate called after throwing an instance of 'boost::exception_detail::clone_implboost::exception_detail::error_info_injectorboost::thread_resource_error ' what(): boost::thread_resource_error When I inspect the file libz.so.1 I get a symbolic link to another file, libz.so.1.2.3 which appears in the same directory. [@]# file /usr/lib/libz.so.1 /usr/lib/libz.so.1: symbolic link to `libz.so.1.2.3' [@]# file /usr/lib/libz.so.1.2.3 /usr/lib/libz.so.1.2.3: ELF 32-bit LSB shared object, Intel 80386, version 1 (SYSV), stripped -Rob On Mon, Jun 24, 2013 at 8:15 PM, Jeremy Goecks jeremy.goe...@emory.eduwrote: Error running cuffdiff. [12:48:21] Loading reference annotation. Warning: No conditions are replicated, switching to 'blind' dispersion method [12:48:33] Inspecting maps and determining fragment length distributions. terminate called after throwing an instance of 'boost::exception_detail::clone_implboost::exception_detail::error_info_injectorboost::thread_resource_error' what(): boost::thread_resource_error: Resource temporarily unavailable This is a linkage error with the Boost library; you might need to modify the Boost path and then recompile Cufflinks. That said, I don't recommend compiling from source unless needed; the Cufflinks suite is provided precompiled for many platforms. Getting the Cufflinks suite working and getting it working with Galaxy are two different things. I recommend: (a) getting Cufflinks working from the command line first using the tutorial: http://cufflinks.cbcb.umd.edu/tutorial.html (b) doing the tutorial in Galaxy; (c) using your own data with Cufflinks in Galaxy. Cufflinks can run very slow, especially if using a limited number of threads, so long running time is not necessarily an indication of error. Good luck, J. ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] Toolshed bwa wrapper mistake
Hello, I found two mistakes in the code of the bwa wrapper . The first one comes from the following error message: --- File /galaxy-dist/tools/bwa_wrappers/bwa_wrapper.py, line 79 parser.add_option( '-y', '--ion', dest='ion', action=store_true, help='Ion Torrent data mode using bwasw' ) ^ SyntaxError: EOL while scanning string literal --- in the bwa_wrapper.py file line 79: -there is a missing double quote character after sur store_true in the bwasw_wrapper.xml file line 9: -there --ion option must not have a value Till, with those corrections, the mapping with bwa for Ion Torrent does not seem to work properly. My ouput sam file had only the header in it. Best regards Yec'han Dr. Yec'han LAIZET Ingenieur Bioinformatique Tel: +33 (0)5 57 12 27 75 _ Plateforme Genome Transcriptome INRA-UMR BIOGECO 1202 Equipe Genetique 69 route d'Arcachon 33612 CESTAS ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Missing test results on (Test) Tool Shed
On Tue, Jun 25, 2013 at 9:43 PM, Dave Bouvier d...@bx.psu.edu wrote: Peter, It turns out that the automated functional testing framework was not actually running. I suggest having a look in the morning, and if there are still any missing test results, I'll get them resolved then. --Dave B. Thanks Dave, That has made a difference but there are still a couple of issues here - at least in my current browser (Safari): Here is the current list of my failing repositories from the Test Tool Shed, http://testtoolshed.g2.bx.psu.edu/view/peterjc/blast2go/f3a61c2cf309 - can see test failure, good. No change, good. http://testtoolshed.g2.bx.psu.edu/view/peterjc/effectivet3/392279f2e120 - shows one passing test (which is odd, where is the failure?) Improved, says there are test failures, but the arrow section fails to expand with any details. Could this just be a slow connection issue? http://testtoolshed.g2.bx.psu.edu/view/peterjc/get_orfs_or_cdss/26ce6e046040 - no test results visible Tests have passed now :) http://testtoolshed.g2.bx.psu.edu/view/peterjc/mira_assembler/da604cc07658 - can see test failure, good. No change, good. http://testtoolshed.g2.bx.psu.edu/view/peterjc/nlstradamus/2be36fa7565e - some test results visible, but no failures No change, bad. As above, the arrow/section for the failing test does not expand. http://testtoolshed.g2.bx.psu.edu/view/peterjc/seq_rename/44b2e489e26f - no test results visible Can see test failures, good. http://testtoolshed.g2.bx.psu.edu/view/peterjc/tmhmm_and_signalp/4cd848c5590b - no test results visible (strange, should be skipping the tests, so why is this listed as failing?) No change, bad. http://testtoolshed.g2.bx.psu.edu/view/peterjc/venn_list/51fe47a5a803 - can see test failure, good. No change, good. Regards, Peter ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] unable to enter the Admin pages
Hi guys, we are currently establishing our own local Galaxy instance. However, after we tried to install the mothur toolsuite we could not enter the admin pages anymore. Every time we try we we obtain the following error: Internal Server Error Galaxy was unable to successfully complete your request An error occurred. This may be an intermittent problem due to load or other unpredictable factors, reloading the page may address the problem. The error has been logged to our team. Here is what the paster.log says: 172.31.30.58 - - [26/Jun/2013:11:02:14 +0200] GET /history/get_display_application_links HTTP/1.0 200 - http://galaxy.jki.bund.de/history; Mozilla/5.0 (Windows NT 6.1; rv:21.0) Gecko/20100101 Firefox/21.0 172.31.30.58 - - [26/Jun/2013:11:02:33 +0200] GET /admin HTTP/1.0 500 - http://galaxy.jki.bund.de/; Mozilla/5.0 (Windows NT 6.1; rv:21.0) Gecko/20100101 Firefox/21.0 Error - class 'simplejson.decoder.JSONDecodeError': Expecting object: line 1 column 65534 (char 65534) URL: http://galaxy.jki.bund.de/admin File '/opt/galaxy/galaxy-dist/lib/galaxy/web/framework/middleware/error.py', line 149 in __call__ app_iter = self.application(environ, sr_checker) File '/opt/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.6.egg/paste/recursive.py', line 84 in __call__ return self.application(environ, start_response) File '/opt/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpexceptions.py', line 633 in __call__ return self.application(environ, start_response) File '/opt/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 132 in __call__ return self.handle_request( environ, start_response ) File '/opt/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 190 in handle_request body = method( trans, **kwargs ) File '/opt/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 221 in decorator return func( self, trans, *args, **kwargs ) File '/opt/galaxy/galaxy-dist/lib/galaxy/web/base/controllers/admin.py', line 31 in index installing_repository_ids = get_ids_of_tool_shed_repositories_being_installed( trans, as_string=True ) File '/opt/galaxy/galaxy-dist/lib/galaxy/web/base/controllers/admin.py', line 1080 in get_ids_of_tool_shed_repositories_being_installed trans.model.ToolShedRepository.status == loading_datatypes_status ) ): File '/opt/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/query.py', line 2348 in instances File '/opt/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/mapper.py', line 2120 in _instance File '/opt/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/mapper.py', line 1974 in populate_state File '/opt/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/strategies.py', line 150 in fetch_col File '/opt/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/types.py', line 658 in process File '/opt/galaxy/galaxy-dist/lib/galaxy/model/custom_types.py', line 52 in process_result_value return json_decoder.decode( str( _sniffnfix_pg9_hex(value) ) ) File '/opt/galaxy/galaxy-dist/eggs/simplejson-2.1.1-py2.6-linux-x86_64-ucs4.egg/simplejson/decoder.py', line 402 in decode File '/opt/galaxy/galaxy-dist/eggs/simplejson-2.1.1-py2.6-linux-x86_64-ucs4.egg/simplejson/decoder.py', line 418 in raw_decode JSONDecodeError: Expecting object: line 1 column 65534 (char 65534) CGI Variables - CONTENT_LENGTH: '0' HTTP_ACCEPT: 'text/html,application/xhtml+xml,application/xml;q=0.9,*/*;q=0.8' HTTP_ACCEPT_ENCODING: 'gzip, deflate' HTTP_ACCEPT_LANGUAGE: 'de-de,de;q=0.8,en-us;q=0.5,en;q=0.3' HTTP_CACHE_CONTROL: 'max-age=0' HTTP_CONNECTION: 'keep-alive' HTTP_COOKIE: 'galaxysession=c6ca0ddb55be603a29d379ce3a444c9b5d260e535a8d6224324fc4d09af0e63592f8cd6e92ad7996' HTTP_HOST: 'galaxy.jki.bund.de' HTTP_REFERER: 'http://galaxy.jki.bund.de/' HTTP_USER_AGENT: 'Mozilla/5.0 (Windows NT 6.1; rv:21.0) Gecko/20100101 Firefox/21.0' HTTP_VIA: '1.1 proxy.jki.bund.de:8000 (squid/2.7.STABLE9)' HTTP_X_FORWARDED_FOR: '172.31.30.58' ORGINAL_REMOTE_ADDR: '172.16.20.52' PATH_INFO: '/admin' REMOTE_ADDR: '172.31.30.58' REQUEST_METHOD: 'GET' SERVER_NAME: '0.0.0.0' SERVER_PORT: '8080' SERVER_PROTOCOL: 'HTTP/1.0' WSGI Variables -- application: paste.recursive.RecursiveMiddleware object at 0x98fb190 is_api_request: False paste.cookies: (SimpleCookie: galaxysession='c6ca0ddb55be603a29d379ce3a444c9b5d260e535a8d6224324fc4d09af0e63592f8cd6e92ad7996', 'galaxysession=c6ca0ddb55be603a29d379ce3a444c9b5d260e535a8d6224324fc4d09af0e63592f8cd6e92ad7996') paste.expected_exceptions: [class 'paste.httpexceptions.HTTPException'] paste.httpexceptions: paste.httpexceptions.HTTPExceptionHandler object at 0x9d5ad90 paste.httpserver.thread_pool: paste.httpserver.ThreadPool object at 0xa33d990 paste.recursive.forward: paste.recursive.Forwarder from /
[galaxy-dev] Dataset appears as running job in history when changing datatype
Dear all, We are running a local Galaxy instance up-to-date against galaxy/galaxy-dist. When we edit attributes of a dataset in current history and request a datatype change (Datatype tab), the selected dataset appears as a running job (yellow box with spinning icon) for ever. The type has been changed and if we refresh the history manually, the dataset appears in green again. Is anyone experiencing the same issue ? Regards, Julien -- Julien Seiler IGBMC Directeur des systèmes d'information Email : julien.sei...@igbmc.fr Tel : 03 88 65 33 63 ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Bowtie2 Specifying -k value (Alignment Search)
I was looking at galaxy/dist/tools/sr_mapping/bowtie2_wrapper.* and it does not seem to challenging to add another field where a user could specify some integer value that we simply pass to the the command tag in the xml file. Would this be the correct way to go about this? Yes, this is correct; the -X or -I option are good examples of using integer parameters. The Bowtie2 wrapper has never been fleshed out; if you do decided to add options, please consider submitting a pull request so that others can benefit from your work as well. Best, J. ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] June update breaks saved histories
I've tried updating a couple of times to the latest stable release and each time I find that I can no longer see my saved histories. Roll back my machine to an earlier snapshot and it is fine. The thing that may be different about our system is that we're using Apache authentication rather than using the built in accounts. Nothing about the apache install has changed, just do the update to the June release, start it, run the manage_db.sh upgrade and restart (database is on postgres by the way) and then saved histories is empty and creating new histories never populates the list either. I would like to upgrade since the previous release had issues with sending BAM files to UCSC which this update has fixed. Maybe it's related to the upgraded SQLAlchemy? Shane -- For urgent cases, contact supp...@biomatters.com Dr Shane Sturrock shane.sturr...@biomatters.com Senior Scientist Tel: +64 (0) 9 379 5064 76 Anzac Ave Auckland New Zealand ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] Fwd: GATK fasta file not found ERROR
Dear Developers, I am using GATK for first time. I am doing Targeted reseq Analysis. while i am running Unified Genotyper in Galaxy interface. it gives error message as mentioned below.. ERROR MESSAGE: The fasta file you specified (/tmp/tmp-gatk-WBrGTf) does not exist. But i places the Fasta file path in .loc file(gatk_sorted_picard_index.loc). Also could anyone tell what are the preprocessing steps before using Bam file for Unified Genotyper?? Your answers are very much Appericiated. Thanks Sridhar ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Fwd: How to Clean up Old Data
Hello, Regards your comment about keeping history but deleting data, I suggest you convert your history into a Workflow. You could then delete the history and therefore all files attached to it but keep a copy of the protocol for future use. Hope it helps Best Jean-François Also is there a way a user can keep her history around as a record of what was done and be able to rerun it later, but still delete the actual data? I don't think that is possible at the moment. Cheers, Bjoern -- # Jean-François Taly Bioinformatician Bioinformatics Core Facility http://biocore.crg.cat CRG - Centre de Regulació Genòmica (Room 439) Parc de Recerca Biomèdica de Barcelona (PRBB) Doctor Aiguader, 88 08003 Barcelona Spain email: jean-francois.t...@crg.eu phone: +34 93 316 0202 fax: +34 93 316 0099 # ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Missing test results on (Test) Tool Shed
Peter, It looks like the failed tests container is being populated, but there is some odd behavior with displaying it. As soon as we've tracked down the issue, I'll update you. --Dave B. On 6/26/13 02:00:30.000, Peter Cock wrote: On Tue, Jun 25, 2013 at 9:43 PM, Dave Bouvier d...@bx.psu.edu wrote: Peter, It turns out that the automated functional testing framework was not actually running. I suggest having a look in the morning, and if there are still any missing test results, I'll get them resolved then. --Dave B. Thanks Dave, That has made a difference but there are still a couple of issues here - at least in my current browser (Safari): Here is the current list of my failing repositories from the Test Tool Shed, http://testtoolshed.g2.bx.psu.edu/view/peterjc/blast2go/f3a61c2cf309 - can see test failure, good. No change, good. http://testtoolshed.g2.bx.psu.edu/view/peterjc/effectivet3/392279f2e120 - shows one passing test (which is odd, where is the failure?) Improved, says there are test failures, but the arrow section fails to expand with any details. Could this just be a slow connection issue? http://testtoolshed.g2.bx.psu.edu/view/peterjc/get_orfs_or_cdss/26ce6e046040 - no test results visible Tests have passed now :) http://testtoolshed.g2.bx.psu.edu/view/peterjc/mira_assembler/da604cc07658 - can see test failure, good. No change, good. http://testtoolshed.g2.bx.psu.edu/view/peterjc/nlstradamus/2be36fa7565e - some test results visible, but no failures No change, bad. As above, the arrow/section for the failing test does not expand. http://testtoolshed.g2.bx.psu.edu/view/peterjc/seq_rename/44b2e489e26f - no test results visible Can see test failures, good. http://testtoolshed.g2.bx.psu.edu/view/peterjc/tmhmm_and_signalp/4cd848c5590b - no test results visible (strange, should be skipping the tests, so why is this listed as failing?) No change, bad. http://testtoolshed.g2.bx.psu.edu/view/peterjc/venn_list/51fe47a5a803 - can see test failure, good. No change, good. Regards, Peter ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Styling the Galaxy tool config xml
Graham, this is not supported. The goal with the tool config is not to specify any particular user interface format so that we are not locked into a particular UI technology in the future. It is an abstract description from which we can generate HTML, but also potentially other interfaces. -- James Taylor, Assistant Professor, Biology/CS, Emory University On Fri, Jun 21, 2013 at 11:11 AM, graham etherington (TSL) graham.ethering...@sainsbury-laboratory.ac.uk wrote: Hi, I'm trying to see if I can style Galaxy tools, so instead of all the input fields being a long list one after the other, I can align a few of the fields side-by-side. Has anyone any suggestions on how I might accomplish this? Best wishes, Graham Dr. Graham Etherington Bioinformatics Support Officer, The Sainsbury Laboratory, Norwich Research Park, Norwich NR4 7UH. UK Tel: +44 (0)1603 450601 ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] DRMAA Runner URL Specify TORQUE host
Is it possible to specify the torque host as part of a DRMAA runner URL? I haven't been able to find a *native_options *parameter to allow for this. I'm using the old style cluster configuration. *drmaa://[native_options]/* * * Also, I haven't been able to find a list of native_options anywhere. Does anyone have a link to a comprehensive list? - Bart ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] DRMAA Runner URL Specify TORQUE host
Is it possible to specify the torque host as part of a DRMAA runner URL? I haven't been able to find a *native_options *parameter to allow for this. I'm using the old style cluster configuration. *drmaa://[native_options]/* * * Also, I haven't been able to find a list of native_options anywhere. Does such a list exist? If so, where? ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Missing test results on (Test) Tool Shed
Peter, The empty failed tests folder issue has been resolved in 10171:eaa5112fefcd, and the test tool shed has been updated to that revision. --Dave B. On 6/26/13 11:34:38.000, Dave Bouvier wrote: Peter, It looks like the failed tests container is being populated, but there is some odd behavior with displaying it. As soon as we've tracked down the issue, I'll update you. --Dave B. On 6/26/13 02:00:30.000, Peter Cock wrote: On Tue, Jun 25, 2013 at 9:43 PM, Dave Bouvier d...@bx.psu.edu wrote: Peter, It turns out that the automated functional testing framework was not actually running. I suggest having a look in the morning, and if there are still any missing test results, I'll get them resolved then. --Dave B. Thanks Dave, That has made a difference but there are still a couple of issues here - at least in my current browser (Safari): Here is the current list of my failing repositories from the Test Tool Shed, http://testtoolshed.g2.bx.psu.edu/view/peterjc/blast2go/f3a61c2cf309 - can see test failure, good. No change, good. http://testtoolshed.g2.bx.psu.edu/view/peterjc/effectivet3/392279f2e120 - shows one passing test (which is odd, where is the failure?) Improved, says there are test failures, but the arrow section fails to expand with any details. Could this just be a slow connection issue? http://testtoolshed.g2.bx.psu.edu/view/peterjc/get_orfs_or_cdss/26ce6e046040 - no test results visible Tests have passed now :) http://testtoolshed.g2.bx.psu.edu/view/peterjc/mira_assembler/da604cc07658 - can see test failure, good. No change, good. http://testtoolshed.g2.bx.psu.edu/view/peterjc/nlstradamus/2be36fa7565e - some test results visible, but no failures No change, bad. As above, the arrow/section for the failing test does not expand. http://testtoolshed.g2.bx.psu.edu/view/peterjc/seq_rename/44b2e489e26f - no test results visible Can see test failures, good. http://testtoolshed.g2.bx.psu.edu/view/peterjc/tmhmm_and_signalp/4cd848c5590b - no test results visible (strange, should be skipping the tests, so why is this listed as failing?) No change, bad. http://testtoolshed.g2.bx.psu.edu/view/peterjc/venn_list/51fe47a5a803 - can see test failure, good. No change, good. Regards, Peter ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] DRMAA Runner URL Specify TORQUE host
Bart, I believe drmaa://-q somehost@queue-name will work. However I could be very wrong. It has been a while since I messed with the actual drmaa runners. -- Adam Brenner Computer Science, Undergraduate Student Donald Bren School of Information and Computer Sciences Research Computing Support Office of Information Technology http://www.oit.uci.edu/rcs/ University of California, Irvine www.ics.uci.edu/~aebrenne/ aebre...@uci.edu On Wed, Jun 26, 2013 at 1:28 PM, Bart Gottschalk bgott...@umn.edu wrote: Is it possible to specify the torque host as part of a DRMAA runner URL? I haven't been able to find a native_options parameter to allow for this. I'm using the old style cluster configuration. drmaa://[native_options]/ Also, I haven't been able to find a list of native_options anywhere. Does such a list exist? If so, where? ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Path to the bedtools for getting trackster working properly
To have Trackster visualization working properly in Galaxy, one needs bedtools. Yet in our instance (running under Ubuntu OS), installing bedtools in the galaxy home directory and setting the environmental variable PATH in the .profile file so that it includes the path to ~/bin/bedtools does not work. Yet the PATH variable is indeed including the appropriate information as the owner of the galaxy home directory can run the bedtools in command lines. I have also to precise that we use a lot of third party tools (bowtie, cufflinks, etc...) including wigToBigWig which is also required for trackster, and that we have no path problem with these tools. Indeed the only way to get galaxy accessing properly to the bedtools currently is to put the bedtools in the /usr/local/bin directory. Here it works ! I suspect it is a problem of shell specification when the bedtools are used for trackster, but I could not figure out further the issue. It's difficult to speculate about what's going on. Trackster uses the same infrastructure (PATH, submission script, etc.) for running bedtools that other Galaxy tools use, so there's reason to think that Trackster requires something special in any way. I also have multiple instances where bedtools is installed alongside bowtie/cufflinks/tophat/wigToBigWig/etc. in a single bin directory that is in the Galaxy user's path, and that works for me. You could certainly modify the conversion tools that Trackster uses to echo and inspect the PATH. Let us know if you find anything interesting. Best, J. ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] Problem updating galaxy (No such file or directory: './shed_tool_data_table_conf.xml')
I've started up an instance using cloudman, and it seemed to be running fine. When I tried to install a tool from the toolshed I got an error, and in trying to resolve the error I used the admin console to update galaxy. Now when Galaxy tries to start I get the following error: galaxy.datatypes.registry DEBUG 2013-06-26 22:20:49,969 Loaded sniffer for datatype 'galaxy.datatypes.images:Pbm' galaxy.datatypes.registry DEBUG 2013-06-26 22:20:49,969 Loaded sniffer for datatype 'galaxy.datatypes.images:Pgm' galaxy.datatypes.registry DEBUG 2013-06-26 22:20:49,969 Loaded sniffer for datatype 'galaxy.datatypes.images:Xpm' galaxy.datatypes.registry DEBUG 2013-06-26 22:20:49,970 Loaded sniffer for datatype 'galaxy.datatypes.images:Eps' galaxy.datatypes.registry DEBUG 2013-06-26 22:20:49,970 Loaded sniffer for datatype 'galaxy.datatypes.images:Rast' galaxy.tools.data DEBUG 2013-06-26 22:20:49,988 Loaded tool data table 'all_fasta' galaxy.tools.data DEBUG 2013-06-26 22:20:49,988 Loaded tool data table 'blastdb' galaxy.tools.data DEBUG 2013-06-26 22:20:49,989 Loaded tool data table 'bowtie_indexes' galaxy.tools.data DEBUG 2013-06-26 22:20:49,989 Loaded tool data table 'bowtie_indexes_color' galaxy.tools.data DEBUG 2013-06-26 22:20:49,990 Loaded tool data table 'bwa_indexes' galaxy.tools.data DEBUG 2013-06-26 22:20:49,990 Loaded tool data table 'lastz_seqs' galaxy.tools.data DEBUG 2013-06-26 22:20:49,990 Loaded tool data table 'perm_base_indexes' galaxy.tools.data DEBUG 2013-06-26 22:20:49,996 Loaded tool data table 'perm_color_indexes' galaxy.tools.data DEBUG 2013-06-26 22:20:49,996 Loaded tool data table 'sam_fa_indexes' galaxy.tools.data DEBUG 2013-06-26 22:20:49,997 Loaded tool data table 'picard_indexes' galaxy.tools.data DEBUG 2013-06-26 22:20:49,997 Loaded tool data table 'srma_indexes' galaxy.tools.data DEBUG 2013-06-26 22:20:49,997 Loaded tool data table 'tophat_indexes' galaxy.tools.data DEBUG 2013-06-26 22:20:49,998 Loaded tool data table 'mosaik_indexes' galaxy.tools.data DEBUG 2013-06-26 22:20:49,998 Loaded tool data table 'sam_indexes' galaxy.tools.data DEBUG 2013-06-26 22:20:49,998 Loaded tool data table 'twobit' galaxy.tools.data DEBUG 2013-06-26 22:20:49,999 Loaded tool data table 'lift_over' Traceback (most recent call last): File /mnt/galaxyTools/galaxy-central/lib/galaxy/webapps/galaxy/buildapp.py, line 35, in app_factory app = UniverseApplication( global_conf = global_conf, **kwargs ) File /mnt/galaxyTools/galaxy-central/lib/galaxy/app.py, line 95, in __init__ from_shed_config=False ) File /mnt/galaxyTools/galaxy-central/lib/galaxy/tools/data/__init__.py, line 56, in load_from_config_file tree = util.parse_xml( config_filename ) File /mnt/galaxyTools/galaxy-central/lib/galaxy/util/__init__.py, line 132, in parse_xml tree = ElementTree.parse(fname) File /mnt/galaxyTools/galaxy-central/eggs/elementtree-1.2.6_20050316-py2.6.egg/elementtree/ElementTree.py, line 859, in parse tree.parse(source, parser) File /mnt/galaxyTools/galaxy-central/eggs/elementtree-1.2.6_20050316-py2.6.egg/elementtree/ElementTree.py, line 576, in parse source = open(source, rb) IOError: [Errno 2] No such file or directory: './shed_tool_data_table_conf.xml' Removing PID file paster.pid How do I resolve the no such file or directory error? I found an email conversation on this that said to restart galaxy, and I've done this multiple times but the problem is persisting. Thanks, -Brad ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] Problem installing tools on cloud instance
I've started up an instance using cloudman, and it seemed to be running fine. When I tried to install a tool from the toolshed I got an error, and in trying to resolve the error I used the admin console to update galaxy. Now when Galaxy tries to start I get the following error: galaxy.datatypes.registry DEBUG 2013-06-26 22:20:49,969 Loaded sniffer for datatype 'galaxy.datatypes.images:Pbm' galaxy.datatypes.registry DEBUG 2013-06-26 22:20:49,969 Loaded sniffer for datatype 'galaxy.datatypes.images:Pgm' galaxy.datatypes.registry DEBUG 2013-06-26 22:20:49,969 Loaded sniffer for datatype 'galaxy.datatypes.images:Xpm' galaxy.datatypes.registry DEBUG 2013-06-26 22:20:49,970 Loaded sniffer for datatype 'galaxy.datatypes.images:Eps' galaxy.datatypes.registry DEBUG 2013-06-26 22:20:49,970 Loaded sniffer for datatype 'galaxy.datatypes.images:Rast' galaxy.tools.data DEBUG 2013-06-26 22:20:49,988 Loaded tool data table 'all_fasta' galaxy.tools.data DEBUG 2013-06-26 22:20:49,988 Loaded tool data table 'blastdb' galaxy.tools.data DEBUG 2013-06-26 22:20:49,989 Loaded tool data table 'bowtie_indexes' galaxy.tools.data DEBUG 2013-06-26 22:20:49,989 Loaded tool data table 'bowtie_indexes_color' galaxy.tools.data DEBUG 2013-06-26 22:20:49,990 Loaded tool data table 'bwa_indexes' galaxy.tools.data DEBUG 2013-06-26 22:20:49,990 Loaded tool data table 'lastz_seqs' galaxy.tools.data DEBUG 2013-06-26 22:20:49,990 Loaded tool data table 'perm_base_indexes' galaxy.tools.data DEBUG 2013-06-26 22:20:49,996 Loaded tool data table 'perm_color_indexes' galaxy.tools.data DEBUG 2013-06-26 22:20:49,996 Loaded tool data table 'sam_fa_indexes' galaxy.tools.data DEBUG 2013-06-26 22:20:49,997 Loaded tool data table 'picard_indexes' galaxy.tools.data DEBUG 2013-06-26 22:20:49,997 Loaded tool data table 'srma_indexes' galaxy.tools.data DEBUG 2013-06-26 22:20:49,997 Loaded tool data table 'tophat_indexes' galaxy.tools.data DEBUG 2013-06-26 22:20:49,998 Loaded tool data table 'mosaik_indexes' galaxy.tools.data DEBUG 2013-06-26 22:20:49,998 Loaded tool data table 'sam_indexes' galaxy.tools.data DEBUG 2013-06-26 22:20:49,998 Loaded tool data table 'twobit' galaxy.tools.data DEBUG 2013-06-26 22:20:49,999 Loaded tool data table 'lift_over' Traceback (most recent call last): File /mnt/galaxyTools/galaxy-central/lib/galaxy/webapps/galaxy/buildapp.py, line 35, in app_factory app = UniverseApplication( global_conf = global_conf, **kwargs ) File /mnt/galaxyTools/galaxy-central/lib/galaxy/app.py, line 95, in __init__ from_shed_config=False ) File /mnt/galaxyTools/galaxy-central/lib/galaxy/tools/data/__init__.py, line 56, in load_from_config_file tree = util.parse_xml( config_filename ) File /mnt/galaxyTools/galaxy-central/lib/galaxy/util/__init__.py, line 132, in parse_xml tree = ElementTree.parse(fname) File /mnt/galaxyTools/galaxy-central/eggs/elementtree-1.2.6_20050316-py2.6.egg/elementtree/ElementTree.py, line 859, in parse tree.parse(source, parser) File /mnt/galaxyTools/galaxy-central/eggs/elementtree-1.2.6_20050316-py2.6.egg/elementtree/ElementTree.py, line 576, in parse source = open(source, rb) IOError: [Errno 2] No such file or directory: './shed_tool_data_table_conf.xml' Removing PID file paster.pid How do I resolve the no such file or directory error? I found an email conversation on this that said to restart galaxy, and I've done this multiple times but the problem is persisting. Thanks, -Brad ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Problem installing tools on cloud instance
Hi Brad, In your Galaxy installation directory, try copying shed_tool_data_table_conf.xml.sample to shed_tool_data_table_conf.xml. Hopefully that will resolve the problem. Greg Von Kuster On Jun 26, 2013, at 6:22 PM, Brad Zeitner bzeit...@benaroyaresearch.org wrote: I've started up an instance using cloudman, and it seemed to be running fine. When I tried to install a tool from the toolshed I got an error, and in trying to resolve the error I used the admin console to update galaxy. Now when Galaxy tries to start I get the following error: galaxy.datatypes.registry DEBUG 2013-06-26 22:20:49,969 Loaded sniffer for datatype 'galaxy.datatypes.images:Pbm' galaxy.datatypes.registry DEBUG 2013-06-26 22:20:49,969 Loaded sniffer for datatype 'galaxy.datatypes.images:Pgm' galaxy.datatypes.registry DEBUG 2013-06-26 22:20:49,969 Loaded sniffer for datatype 'galaxy.datatypes.images:Xpm' galaxy.datatypes.registry DEBUG 2013-06-26 22:20:49,970 Loaded sniffer for datatype 'galaxy.datatypes.images:Eps' galaxy.datatypes.registry DEBUG 2013-06-26 22:20:49,970 Loaded sniffer for datatype 'galaxy.datatypes.images:Rast' galaxy.tools.data DEBUG 2013-06-26 22:20:49,988 Loaded tool data table 'all_fasta' galaxy.tools.data DEBUG 2013-06-26 22:20:49,988 Loaded tool data table 'blastdb' galaxy.tools.data DEBUG 2013-06-26 22:20:49,989 Loaded tool data table 'bowtie_indexes' galaxy.tools.data DEBUG 2013-06-26 22:20:49,989 Loaded tool data table 'bowtie_indexes_color' galaxy.tools.data DEBUG 2013-06-26 22:20:49,990 Loaded tool data table 'bwa_indexes' galaxy.tools.data DEBUG 2013-06-26 22:20:49,990 Loaded tool data table 'lastz_seqs' galaxy.tools.data DEBUG 2013-06-26 22:20:49,990 Loaded tool data table 'perm_base_indexes' galaxy.tools.data DEBUG 2013-06-26 22:20:49,996 Loaded tool data table 'perm_color_indexes' galaxy.tools.data DEBUG 2013-06-26 22:20:49,996 Loaded tool data table 'sam_fa_indexes' galaxy.tools.data DEBUG 2013-06-26 22:20:49,997 Loaded tool data table 'picard_indexes' galaxy.tools.data DEBUG 2013-06-26 22:20:49,997 Loaded tool data table 'srma_indexes' galaxy.tools.data DEBUG 2013-06-26 22:20:49,997 Loaded tool data table 'tophat_indexes' galaxy.tools.data DEBUG 2013-06-26 22:20:49,998 Loaded tool data table 'mosaik_indexes' galaxy.tools.data DEBUG 2013-06-26 22:20:49,998 Loaded tool data table 'sam_indexes' galaxy.tools.data DEBUG 2013-06-26 22:20:49,998 Loaded tool data table 'twobit' galaxy.tools.data DEBUG 2013-06-26 22:20:49,999 Loaded tool data table 'lift_over' Traceback (most recent call last): File /mnt/galaxyTools/galaxy-central/lib/galaxy/webapps/galaxy/buildapp.py, line 35, in app_factory app = UniverseApplication( global_conf = global_conf, **kwargs ) File /mnt/galaxyTools/galaxy-central/lib/galaxy/app.py, line 95, in __init__ from_shed_config=False ) File /mnt/galaxyTools/galaxy-central/lib/galaxy/tools/data/__init__.py, line 56, in load_from_config_file tree = util.parse_xml( config_filename ) File /mnt/galaxyTools/galaxy-central/lib/galaxy/util/__init__.py, line 132, in parse_xml tree = ElementTree.parse(fname) File /mnt/galaxyTools/galaxy-central/eggs/elementtree-1.2.6_20050316-py2.6.egg/elementtree/ElementTree.py, line 859, in parse tree.parse(source, parser) File /mnt/galaxyTools/galaxy-central/eggs/elementtree-1.2.6_20050316-py2.6.egg/elementtree/ElementTree.py, line 576, in parse source = open(source, rb) IOError: [Errno 2] No such file or directory: './shed_tool_data_table_conf.xml' Removing PID file paster.pid How do I resolve the no such file or directory error? I found an email conversation on this that said to restart galaxy, and I've done this multiple times but the problem is persisting. Thanks, -Brad ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Missing test results on (Test) Tool Shed
On Wed, Jun 26, 2013 at 10:01 PM, Dave Bouvier d...@bx.psu.edu wrote: Peter, The empty failed tests folder issue has been resolved in 10171:eaa5112fefcd, and the test tool shed has been updated to that revision. --Dave B. Great - currently all the missing test failures have been resolved :) The bad news is there seems to be a new sniffer bug. http://testtoolshed.g2.bx.psu.edu/view/peterjc/blast2go/f3a61c2cf309 Can see test failures (tool configuration problem). http://testtoolshed.g2.bx.psu.edu/view/peterjc/effectivet3/392279f2e120 One test pass, on test failure. The failure is a bit odd and is likely a new sniffer related bug. http://testtoolshed.g2.bx.psu.edu/view/peterjc/get_orfs_or_cdss/26ce6e046040 Tests pass. http://testtoolshed.g2.bx.psu.edu/view/peterjc/mira_assembler/da604cc07658 Can see test failure, good. http://testtoolshed.g2.bx.psu.edu/view/peterjc/nlstradamus/2be36fa7565e One pass, one failure - same new failure as effectiveT3 above. http://testtoolshed.g2.bx.psu.edu/view/peterjc/seq_rename/44b2e489e26f Can see a failure, also seems to be sniffer related (but using a different datatype). http://testtoolshed.g2.bx.psu.edu/view/peterjc/tmhmm_and_signalp/4cd848c5590b As before, no test results as there are marked as skip - yet this is still listed under Latest revision: failing tool tests. The filter for this needs to exclude repositories marked as skip testing. http://testtoolshed.g2.bx.psu.edu/view/peterjc/venn_list/51fe47a5a803 Can see test failure, good (missing undeclared dependency) Thanks, Peter ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
