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Tests not being run on toolsheds?
by Peter Briggs 09 Apr '15

09 Apr '15

Hello Apologies as this seems to be quite a frequent question (and I may have missed something) however: are the tool tests being executed on the main or test toolsheds at the moment? The most recent tests results that I can find for any of the tools I've uploaded is the 29th January. I've also looked at a couple of tools from other users and the situation appears to be the same (at least in those cases). Thanks for your help! Best wishes Peter -- Peter Briggs peter.briggs(a)manchester.ac.uk Bioinformatics Core Facility University of Manchester B.1083 Michael Smith Bldg Tel: (0161) 2751482

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Problems after upgrade
by C. Ch. 09 Apr '15

09 Apr '15

Hi all, We had a problem on the NAS where we couldn't write anymore. This problem was solved and I decided that I would profit to upgrade galaxy. Now we have a problem where jobs do not get launched and the handler log shows a lot of error messages. The first error message is copied below. Afterwards it alternates between galaxy.jobs.handler ERROR 2015-04-07 15:58:24,959 Exception in monitor_step galaxy.jobs.runners ERROR 2015-04-07 15:58:23,542 Unhandled exception checking active jobs with, mainly, the same error stack (second error message shown below). Any idea what is going wrong? My first impression is that it is trying to recuperate some job that galaxy believes is still running but the machine has been stopped and rebooted in the mean time. Any help is welcome! Cristian galaxy.jobs.runners ERROR 2015-04-07 15:44:04,809 (27764) Unhandled exception calling queue_jobTraceback (most recent call last): File "/home/galaxy/galaxy-dist/lib/galaxy/jobs/runners/__init__.py", line 97, in run_next method(arg) File "/home/galaxy/galaxy-dist/lib/galaxy/jobs/runners/drmaa.py", line 115, in queue_job if not self.prepare_job( job_wrapper, include_metadata=True ): File "/home/galaxy/galaxy-dist/lib/galaxy/jobs/runners/__init__.py", line 140, in prepare_job job_id = job_wrapper.get_id_tag() File "/home/galaxy/galaxy-dist/lib/galaxy/jobs/__init__.py", line 794, in get_id_tag return self.get_job().get_id_tag() File "/home/galaxy/galaxy-dist/lib/galaxy/jobs/__init__.py", line 790, in get_job return self.sa_session.query( model.Job ).get( self.job_id ) File "/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.9.8-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/query.py", line 840, in get return loading.load_on_ident(self, key) File "/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.9.8-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/loading.py", line 231, in load_on_ident return q.one() File "/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.9.8-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/query.py", line 2395, in one ret = list(self) File "/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.9.8-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/query.py", line 2434, in __iter__ context = self._compile_context() File "/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.9.8-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/query.py", line 2810, in _compile_context entity.setup_context(self, context) File "/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.9.8-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/query.py", line 3194, in setup_context column_collection=context.primary_columns File "/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.9.8-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/interfaces.py", line 466, in setup strat.setup_query(context, entity, path, loader, adapter, **kwargs) File "/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.9.8-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/strategies.py", line 1111, in setup_query column_collection, parentmapper, chained_from_outerjoin File "/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.9.8-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/strategies.py", line 1234, in _generate_row_adapter use_mapper_path=True) File "/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.9.8-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/util.py", line 364, in __init__ else mapper.with_polymorphic_mappers, File "/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.9.8-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/util/langhelpers.py", line 725, in __get__ obj.__dict__[self.__name__] = result = self.fget(obj) File "/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.9.8-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/mapper.py", line 1877, in _with_polymorphic_mappers configure_mappers() File "/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.9.8-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/mapper.py", line 2589, in configure_mappers mapper._post_configure_properties() File "/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.9.8-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/mapper.py", line 1694, in _post_configure_properties prop.init() File "/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.9.8-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/interfaces.py", line 144, in init self.do_init() File "/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.9.8-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/relationships.py", line 1549, in do_init self._process_dependent_arguments() File "/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.9.8-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/relationships.py", line 1605, in _process_dependent_arguments self.target = self.mapper.mapped_table File "/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.9.8-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/util/langhelpers.py", line 725, in __get__ obj.__dict__[self.__name__] = result = self.fget(obj) File "/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.9.8-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/relationships.py", line 1522, in mapper argument = self.argument() File "/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.9.8-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/ext/declarative/clsregistry.py", line 283, in __call__ (self.prop.parent, self.arg, n.args[0], self.cls)InvalidRequestError: When initializing mapper Mapper|Queue|kombu_queue, expression 'Message' failed to locate a name ("name 'Message' is not defined"). If this is a class name, consider adding this relationship() to the <class 'kombu.transport.sqlalchemy.Queue'> class after both dependent classes have been defined. Repeated error messages:galaxy.jobs.runners ERROR 2015-04-07 15:58:23,542 Unhandled exception checking active jobsTraceback (most recent call last): File "/home/galaxy/galaxy-dist/lib/galaxy/jobs/runners/__init__.py", line 501, in monitor self.check_watched_items() File "/home/galaxy/galaxy-dist/lib/galaxy/jobs/runners/drmaa.py", line 238, in check_watched_items galaxy_id_tag = ajs.job_wrapper.get_id_tag() File "/home/galaxy/galaxy-dist/lib/galaxy/jobs/__init__.py", line 794, in get_id_tag return self.get_job().get_id_tag() File "/home/galaxy/galaxy-dist/lib/galaxy/jobs/__init__.py", line 790, in get_job return self.sa_session.query( model.Job ).get( self.job_id ) File "/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.9.8-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/scoping.py", line 150, in do return getattr(self.registry(), name)(*args, **kwargs) File "/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.9.8-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/session.py", line 1165, in query return self._query_cls(entities, self, **kwargs) File "/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.9.8-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/query.py", line 108,in __init__ self._set_entities(entities) File "/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.9.8-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/query.py", line 118,in _set_entities self._set_entity_selectables(self._entities) File "/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.9.8-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/query.py", line 151,in _set_entity_selectables ent.setup_entity(*d[entity]) File "/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.9.8-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/query.py", line 3036, in setup_entity self._with_polymorphic = ext_info.with_polymorphic_mappers File "/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.9.8-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/util/langhelpers.py", line 725, in __get__ obj.__dict__[self.__name__] = result = self.fget(obj) File "/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.9.8-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/mapper.py", line 1877, in _with_polymorphic_mappers configure_mappers() File "/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.9.8-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/mapper.py", line 2586, in configure_mappers raise eInvalidRequestError: One or more mappers failed to initialize - can't proceed with initialization of other mappers. Original exception was: When initializing mapper Mapper|Queue|kombu_queue, expression 'Message' failed to locate a name ("name 'Message' is not defined"). If this is a class name, consider adding this relationship() to the <class 'kombu.transport.sqlalchemy.Queue'> class after both dependent classes have been defined.

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Tool Shed installs: coercing to Unicode: need string or buffer, NoneType found
by Peter Cock 09 Apr '15

09 Apr '15

I just hit a problem installing package_bx_python_0_7 via the Admin GUI. Name: bx-python Version: 0.7.1 Type: package Status: Error Error: Error installing tool dependency bx-python version 0.7.1: coercing to Unicode: need string or buffer, NoneType found Name: galaxy-ops Version: 1.0.0 Type: package Status: Installed Clicked on "Uninstall" for bx-python, told: Uninstall tool dependencies Name: bx-python Version: 0.7.1 Type: package Install directory: This dependency's installation directory does not exist, click <b>Uninstall</b> to reset for installation. Clicked on "Uninstall" again, seemed to work. I went through a series of "repair repositiory" rounds on package_bx_python_0_7 and intersect tool, and it all seems fine now. I'm not sure what the original glitch was, but there are two clear issues here. First, the Unicode error - perhaps previously reported e.g. http://dev.list.galaxyproject.org/How-to-remove-a-broken-toolshed-install-t… http://dev.list.galaxyproject.org/tophat2-install-tc4663736.html Those previous discussions suggest the database and file system were out of sync - but clearly this unexpected None value ought to be better handled. Second, the over-escaped bold in the message, presumably part of: https://trello.com/c/oX6i51Mn/2298-back-off-over-escaping Peter

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Escaped HTML show in import-workflow red message
by Peter Cock 08 Apr '15

08 Apr '15

Hi all, I just imported a workflow and noticed the following glitch with the red message shown to the user about missing tools - the escaped HTML is show to the user (ampersand lt semi-colon etc). Specifically, I imported http://www.myexperiment.org/workflows/4601.html from Bjoern. Using the current v15.03 release, specifically: $ hg log | head changeset: 17050:6395e7035143 tag: tip parent: 17049:708cab19708d parent: 17048:28113eeee212 user: Nate Coraor <nate(a)bx.psu.edu> date: Mon Mar 16 22:50:21 2015 -0400 summary: Merge v15.03.1 to default Peter Red message: Workflow Finding 3 genes close to each other (imported from uploaded file) imported successfully. The workflow requires the following tools that are not available in this Galaxy instance.You can likely install the required tools from one of the Galaxy tool sheds listed below. Tool name Compute, id toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/1.1.0, version 1.1.0 Tool name Intersect, id toolshed.g2.bx.psu.edu/repos/devteam/intersect/gops_intersect_1/0.0.1, version 0.0.1 Tool name Intersect, id toolshed.g2.bx.psu.edu/repos/devteam/intersect/gops_intersect_1/1.0.0, version 1.0.0 <a href="http://toolshed.g2.bx.psu.edu/repository/find_tools?galaxy_url=ht… main tool shed</a> <a href="http://testtoolshed.g2.bx.psu.edu/repository/find_tools?galaxy_ur… test tool shed</a>

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Re: [galaxy-dev] a question on data manager and data table
by Daniel Blankenberg 08 Apr '15

08 Apr '15

Hi Rui, (cc’d back to list) One of the nice things about tool Data Tables is that it allows us to have multiple ‘.loc’ files as the source for the content for a single data table — so we can have many ‘all_fasta.loc’ files, but one ‘all_fasta’ tool data table, with merged contents, and a tool working on ‘all_fasta’ data table doesn’t know or care about the actual .loc files on disk. Then any tool that uses the ‘all_fasta’ table in an input parameter can simply call input.fields.path, to have the actual path to the fasta file passed to the tool. > 1.which file should the downloaded fasta data modify? tool_data_table_conf.xml, or shed_tool_data_table_conf.xml? Tools installed from the toolshed that include data Tables will programmatically modify the shed_ file, the other file can is for manual admin changes. > 2. which loc file is the primary one for tools to reference? the one in $GALAXYHOME/tool-data, or the one in $GALAXYHOME/tool-data//toolshed.g2.bx.psu.edu/repos/devteam/data_manager_fetch_genome_all_fasta/cca219f2b212/? If first one, then should the data manager update that one too(right now it didn't)? Tools shouldn’t be referencing .loc files directly any more, and instead should use the tool data table abstraction. > 3. For now, that tool still uses alignseq.loc, I need to manually update that file, correct? Any tool that makes direct use of a .loc file will need to have that specific file modified. > 4. How to determine if a tool is using data table is to look at the tool xml file to see if it contains reference to a data table, right? And in tool_data_table_conf.xml, it should contain data tables definition for all the possible data, right? a.) Yes, you’ll have to look at the tool.xml, although we could add another section to the ToolShed preview to include this information if it is useful. b.) tool_data_table_conf.xml should contain data tables distributed with the Galaxy distribution and any manually configured data tables. tool_data_table_conf.xml and shed_tool_data_table_conf.xml will be merged into one set of tool data tables — a tool data table does not need to be in tool_data_table_conf.xml if it is in shed_tool_data_table_conf.xml and vis-versa (but can be in both). Thanks for using Galaxy, Dan On Apr 7, 2015, at 12:47 PM, Beginner TI <ruiwang.sz(a)gmail.com> wrote: > Hi Dan, > > Thanks for the reply! > > So, what would be the expected behavior for the tool that uses data table? For example, in my case, the tool_data_table_conf.xml would be modified to reflect the update to all_fasta.loc? > > I'm a little puzzled on how this works. As you could see, after I installed that data manager and downloaded the mm9 fasta data, it modified the file shed_tool_data_table_conf.xml. This should have nothing to do with the tool Extract Genome DNA, am I right? So, my question is, > > 1.which file should the downloaded fasta data modify? tool_data_table_conf.xml, or shed_tool_data_table_conf.xml? > > 2. which loc file is the primary one for tools to reference? the one in $GALAXYHOME/tool-data, or the one in $GALAXYHOME/tool-data//toolshed.g2.bx.psu.edu/repos/devteam/data_manager_fetch_genome_all_fasta/cca219f2b212/? If first one, then should the data manager update that one too(right now it didn't)? > > 3. For now, that tool still uses alignseq.loc, I need to manually update that file, correct? > > 4. How to determine if a tool is using data table is to look at the tool xml file to see if it contains reference to a data table, right? And in tool_data_table_conf.xml, it should contain data tables definition for all the possible data, right? > > If you could please elaborate a bit, I'll really appreciate! > > Thanks, > Rui > > > > > On Tue, Apr 7, 2015 at 7:15 AM, Daniel Blankenberg <dan(a)bx.psu.edu> wrote: > Hi Rui, > > The Extract Genomic DNA Tool has not yet been updated to work with tool Data Tables. > > Additionally, this tool requires TwoBit formatted files when selecting from built-in data — when selecting a FASTA from your history, the fasta file is converted to TwoBit internally in the tool before extracting sequence chunks. > > There is a TwoBit builder Data Manager under development (https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/da…) that hasn’t made it out to the ToolShed just yet, but it won’t be helpful until the the Extract Genomic DNA Tool is updated: https://trello.com/c/8unnSp7H > > > Thanks for using Galaxy, > > Dan > > > On Apr 7, 2015, at 12:16 AM, Beginner TI <ruiwang.sz(a)gmail.com> wrote: > >> Hi All, >> >> I just made a new local instance, installed the fetch_all_fasta data manager, downloaded mm9 fasta. Then I noticed the following: >> >> in tool_data_table_conf.xml, it has: >> >> <table name="all_fasta" comment_char="#"> >> <columns>value, dbkey, name, path</columns> >> <file path="tool-data/all_fasta.loc" /> >> </table> >> >> however in shed_tool_data_table_conf.xml, it has: >> >> <table comment_char="#" name="all_fasta"> >> <columns>value, dbkey, name, path</columns> >> <file path="/auto/rcf-proj/yc1/galaxy-suite/galaxy-dist/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/data_manager_fetch_genome_all_fasta/cca219f2b212/all_fasta.loc" /> >> <tool_shed_repository><tool_shed>toolshed.g2.bx.psu.edu</tool_shed><repository_name>data_manager_fetch_genome_all_fasta</repository_name><repository_owner>devteam</repository_owner><installed_changeset_revision>cca219f2b212</installed_changeset_revision></tool_shed_repository></table> >> >> in tool-data, all_fasta.loc is empty, but in the all_fasta.loc of the shed_tool entry, it shows: >> >> mm9 mm9 Mouse July 2007 (NCBI37/mm9) (mm9) /auto/rcf-proj/yc1/galaxy-suite/galaxy-dist/tool-data/mm9/seq/mm9.fa >> >> So if I try "Extract Genomic DNA function", I could see the parameter passed to the command line is >> >> -g "/auto/rcf-proj/yc1/galaxy-suite/galaxy-dist/tool-data" >> >> which does not host the data. It should be at least >> >> -g "/auto/rcf-proj/yc1/galaxy-suite/galaxy-dist/tool-data/mm9/seq" >> >> I thought that data manager will automatically populate these loc files? Am I missing something obvious? I could manually modify tool_data_table_conf.xml to let it point to >> >> /auto/rcf-proj/yc1/galaxy-suite/galaxy-dist/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/data_manager_fetch_genome_all_fasta/cca219f2b212/all_fasta.loc >> >> This would work, but it is ugly. Could someone please give me a hand to fix this? >> >> Thanks, >> Rui >> ___________________________________________________________ >> 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: >> https://lists.galaxyproject.org/ >> >> To search Galaxy mailing lists use the unified search at: >> http://galaxyproject.org/search/mailinglists/ > >

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DRMAA chmod to world-writable if to user chown fails should not be default?
by David Trudgian 08 Apr '15

08 Apr '15

Hi, Looking through the DRMAA job runner code I noticed that in lib/galaxy/jobs/__init__.py:1582 that if chown to a user in change_ownership_for_run fails then there is chmod 0777 instead. I'm thinking that this probably shouldn't happen by default, or there needs to be a big warning on the wiki? I understand the world-readable security concerns posted there - but world-writable, for whatever reason, on a shared cluster seems like a disaster waiting to happen. Maybe either warn on the wiki, make the chmod 777 a non-default option, or an option to disable it? DT ________________________________ UT Southwestern Medical Center The future of medicine, today.

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Multiple outputs of unknown types
by David Kelly 08 Apr '15

08 Apr '15

Hello, I've looked through the documentation about tools that produce multiple output files, but it seems like you're required to know the data types ahead of time (or make assumptions based on input data). But what about a case where you don't know what the output datatypes will be? Is it just possible to have N output files imported and sniffed? Thanks, Davids

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Re: [galaxy-dev] Galaxy ToolShed Update Problem
by Martin Čech 08 Apr '15

08 Apr '15

Hi Zhaozhen, the --config_file argument needs to point to galaxy.ini config so the script can load the database. Galaxy continues to support Python 2.6 and 2.7, I am sorry that this script required 2.7 (or you could `pip install argparse`) - we will look into improving it. Martin, Galaxy Team On Wed, Apr 8, 2015 at 4:09 AM 孙兆朕 <sunzzn502(a)163.com> wrote: > Hi Martin, > > Thanks for the advise. It helped a lot for me to figure out where the > problem is. However, there were still error messages there. > I tried to run the update_shed_config_path.py script under the /script > folder. At first it says there was no module named argparse, then I found > out it was the python version problem, which required python 2.7+. Then I > updated my python. Then there was another error said there was no module > named galaxy.model.tool_shed_install. Then I tried harder, and found out > that it was the path problem. I figured out the sys path was in the above > folder. Then I copied and pasted the update_shed_config_path.py to the > parent folder and seemed solved the problem. Then I run > the update_shed_config_path.py and the command somehow run for a while, > with the error message No module named _sqlite3. It must be the DB > versions and plug-ins, then I fixed the DB. Then finally there came the > following message: > > usage: update_shed_config_path.py [-h] --config_file CONFIG_FILE --from > BAD_FILENAME --to GOOD_FILENAME [--force] > update_shed_config_path.py: error: argument --config_file is required > > I run the command line in: python2.7 update_shed_config_path.py > I wonder if I need some more input for the command line or something? > By the way, I hope there would be some advise for the new Galaxy > administrtators to know their Python should be 2.7+ and file path issues. > When I started to deploy Galaxy last year, the requirement in the web page > was Python 2.5 or something lower than 2.6 I used. I think that message > need to be updated as well. > Thanks in advance, > > Yours, > > Zhaozhen > > > > > argparse > > > At 2015-04-07 22:43:50, "Martin Čech" <marten(a)bx.psu.edu> wrote: > > Hello Zhaozhen, > > this is a known problem. The shed_tool_conf.xml got moved along with other > configs into /config folder but unfortunately some tools stored the path > absolutely in the DB. You can use the following script (which you should > find in the Galaxy /scripts folder): > > https://github.com/galaxyproject/galaxy/blob/dev/scripts/update_shed_config… > to update your DB to have the correct path to the config. > > Sorry for the inconvenience. > > Martin, Galaxy Team > > > On Tue, Apr 7, 2015 at 10:16 AM 孙兆朕 <sunzzn502(a)163.com> wrote: > >> Hi all, >> >> I want to update some of my tool plug-in and some problem shows, even if >> I updated my Galaxy instance to the latest. I suppose it is not related to >> the version of Galaxy. >> >> The problem occured when I used the administrator's panel and update my >> plug-in using the "Get updates" option. The next page reports that an >> internal Server Error has occured and the update was not successful. All >> the plug-in updates seems had the same problem. >> >> I checked the logs where I get the following message: >> >> CGI Variables >> ------------- >> CONTENT_LENGTH: '0' >> HTTP_ACCEPT: >> 'text/html,application/xhtml+xml,application/xml;q=0.9,image/webp,*/*;q=0.8' >> HTTP_ACCEPT_ENCODING: 'gzip,deflate,sdch' >> HTTP_ACCEPT_LANGUAGE: 'zh-CN,zh;q=0.8' >> HTTP_CONNECTION: 'close' >> HTTP_COOKIE: >> 'galaxysession=c6ca0ddb55be603a23b93349895e875da395c1164de6cfc693d5dd79dc3d9d2edcd8d527c7310424' >> HTTP_HOST: '222.28.163.110' >> HTTP_REFERER: ' >> http://222.28.163.110/admin_toolshed/browse_repositories?status=done&messag… >> .' >> HTTP_USER_AGENT: 'Mozilla/5.0 (Windows NT 5.1) AppleWebKit/537.36 >> (KHTML, like Gecko) Chrome/34.0.1847.116 Safari/537.36' >> HTTP_X_FORWARDED_FOR: '222.28.170.89' >> HTTP_X_FORWARDED_HOST: '222.28.163.110' >> ORGINAL_HTTP_HOST: '127.0.0.1:8080' >> ORGINAL_REMOTE_ADDR: '127.0.0.1' >> PATH_INFO: '/admin_toolshed/update_to_changeset_revision' >> QUERY_STRING: 'tool_shed_url= >> https://toolshed.g2.bx.psu.edu/&name=blast_datatypes&owner=devteam&changese… >> ' >> REMOTE_ADDR: '222.28.170.89' >> REQUEST_METHOD: 'GET' >> SERVER_NAME: '127.0.0.1' >> SERVER_PORT: '8080' >> SERVER_PROTOCOL: 'HTTP/1.0' >> >> >> WSGI Variables >> -------------- >> application: <paste.recursive.RecursiveMiddleware object at 0xd888510> >> is_api_request: False >> paste.cookies: (<SimpleCookie: >> galaxysession='c6ca0ddb55be603a23b93349895e875da395c1164de6cfc693d5dd79dc3d9d2edcd8d527c7310424'>, >> 'galaxysession=c6ca0ddb55be603a23b93349895e875da395c1164de6cfc693d5dd79dc3d9d2edcd8d527c7310424') >> paste.expected_exceptions: [<class >> 'paste.httpexceptions.HTTPException'>] >> paste.httpexceptions: <paste.httpexceptions.HTTPExceptionHandler object >> at 0xd888fd0> >> paste.httpserver.thread_pool: <paste.httpserver.ThreadPool object at >> 0xdcf8650> >> paste.parsed_querystring: ([('tool_shed_url', ' >> https://toolshed.g2.bx.psu.edu/'), ('name', 'blast_datatypes'), >> ('owner', 'devteam'), ('changeset_revision', 'de11e1a921c4'), >> ('latest_changeset_revision', '5482a8cd0f36'), ('latest_ctx_rev', '10')], >> 'tool_shed_url= >> https://toolshed.g2.bx.psu.edu/&name=blast_datatypes&owner=devteam&changese… >> ') >> paste.recursive.forward: <paste.recursive.Forwarder from /> >> paste.recursive.include: <paste.recursive.Includer from /> >> paste.recursive.include_app_iter: <paste.recursive.IncluderAppIter from >> /> >> paste.recursive.script_name: '' >> paste.throw_errors: True >> request_id: 'a12a5604dce911e4a05000215e543aa8' >> webob._parsed_query_vars: (MultiDict([('tool_shed_url', ' >> https://toolshed.g2.bx.psu.edu/'), ('name', 'blast_datatypes'), >> ('owner', 'devteam'), ('changeset_revision', 'de11e1a921c4'), >> ('latest_changeset_revision', '5482a8cd0f36'), ('latest_ctx_rev', '10')]), >> 'tool_shed_url= >> https://toolshed.g2.bx.psu.edu/&name=blast_datatypes&owner=devteam&changese… >> ') >> wsgi process: 'Multithreaded' >> ------------------------------------------------------------ >> ---------------------------------------- >> Exception happened during processing of request from ('127.0.0.1', 39438) >> Traceback (most recent call last): >> File >> "/share/apps/galaxy/Galaxy_Test2015/galaxy-dist/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpserver.py", >> line 1068, in process_request_in_thread >> self.finish_request(request, client_address) >> File "/usr/lib64/python2.6/SocketServer.py", line 322, in finish_request >> self.RequestHandlerClass(request, client_address, self) >> File "/usr/lib64/python2.6/SocketServer.py", line 618, in __init__ >> self.finish() >> File "/usr/lib64/python2.6/SocketServer.py", line 661, in finish >> self.wfile.flush() >> File "/usr/lib64/python2.6/socket.py", line 303, in flush >> self._sock.sendall(buffer(data, write_offset, buffer_size)) >> error: [Errno 32] Broken pipe >> ---------------------------------------- >> 222.28.170.89 - - [07/Apr/2015:13:47:59 +0800] "GET >> /admin_toolshed/update_to_changeset_revision?tool_shed_url= >> https://toolshed.g2.bx.psu.edu/&name=blast_datatypes&owner=devteam&changese… >> HTTP/1.0" 500 - " >> http://222.28.163.110/admin_toolshed/browse_repositories?status=done&messag…." >> "Mozilla/5.0 (Windows NT 5.1) AppleWebKit/537.36 (KHTML, like Gecko) >> Chrome/34.0.1847.116 Safari/537.36" >> Error - <type 'exceptions.AttributeError'>: 'NoneType' object has no >> attribute 'get' >> URL: >> http://222.28.163.110/admin_toolshed/update_to_changeset_revision?tool_shed… >> File >> '/share/apps/galaxy/Galaxy_Test2015/galaxy-dist/lib/galaxy/web/framework/middleware/error.py', >> line 149 in __call__ >> app_iter = self.application(environ, sr_checker) >> File >> '/share/apps/galaxy/Galaxy_Test2015/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 >> '/share/apps/galaxy/Galaxy_Test2015/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 >> '/share/apps/galaxy/Galaxy_Test2015/galaxy-dist/lib/galaxy/web/framework/base.py', >> line 133 in __call__ >> return self.handle_request( environ, start_response ) >> File >> '/share/apps/galaxy/Galaxy_Test2015/galaxy-dist/lib/galaxy/web/framework/base.py', >> line 191 in handle_request >> body = method( trans, **kwargs ) >> File >> '/share/apps/galaxy/Galaxy_Test2015/galaxy-dist/lib/galaxy/web/framework/decorators.py', >> line 87 in decorator >> return func( self, trans, *args, **kwargs ) >> File >> '/share/apps/galaxy/Galaxy_Test2015/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py', >> line 1954 in update_to_changeset_revision >> persist=True ) >> File >> '/share/apps/galaxy/Galaxy_Test2015/galaxy-dist/lib/tool_shed/galaxy_install/metadata/installed_repository_metadata_manager.py', >> line 31 in __init__ >> metadata_dict=metadata_dict, user=None ) >> File >> '/share/apps/galaxy/Galaxy_Test2015/galaxy-dist/lib/tool_shed/metadata/metadata_generator.py', >> line 60 in __init__ >> self.metadata_dict = { 'shed_config_filename' : >> self.shed_config_dict.get( 'config_filename', None ) } >> AttributeError: 'NoneType' object has no attribute 'get' >> >> >> CGI Variables >> ------------- >> CONTENT_LENGTH: '0' >> HTTP_ACCEPT: >> 'text/html,application/xhtml+xml,application/xml;q=0.9,image/webp,*/*;q=0.8' >> HTTP_ACCEPT_ENCODING: 'gzip,deflate,sdch' >> HTTP_ACCEPT_LANGUAGE: 'zh-CN,zh;q=0.8' >> HTTP_CONNECTION: 'close' >> HTTP_COOKIE: >> 'galaxysession=c6ca0ddb55be603a23b93349895e875da395c1164de6cfc693d5dd79dc3d9d2edcd8d527c7310424' >> HTTP_HOST: '222.28.163.110' >> HTTP_REFERER: ' >> http://222.28.163.110/admin_toolshed/browse_repositories?status=done&messag… >> .' >> HTTP_USER_AGENT: 'Mozilla/5.0 (Windows NT 5.1) AppleWebKit/537.36 >> (KHTML, like Gecko) Chrome/34.0.1847.116 Safari/537.36' >> HTTP_X_FORWARDED_FOR: '222.28.170.89' >> HTTP_X_FORWARDED_HOST: '222.28.163.110' >> ORGINAL_HTTP_HOST: '127.0.0.1:8080' >> ORGINAL_REMOTE_ADDR: '127.0.0.1' >> PATH_INFO: '/admin_toolshed/update_to_changeset_revision' >> QUERY_STRING: 'tool_shed_url= >> https://toolshed.g2.bx.psu.edu/&name=blast_datatypes&owner=devteam&changese… >> ' >> REMOTE_ADDR: '222.28.170.89' >> REQUEST_METHOD: 'GET' >> SERVER_NAME: '127.0.0.1' >> SERVER_PORT: '8080' >> SERVER_PROTOCOL: 'HTTP/1.0' >> >> >> WSGI Variables >> -------------- >> application: <paste.recursive.RecursiveMiddleware object at 0xd888510> >> is_api_request: False >> paste.cookies: (<SimpleCookie: >> galaxysession='c6ca0ddb55be603a23b93349895e875da395c1164de6cfc693d5dd79dc3d9d2edcd8d527c7310424'>, >> 'galaxysession=c6ca0ddb55be603a23b93349895e875da395c1164de6cfc693d5dd79dc3d9d2edcd8d527c7310424') >> paste.expected_exceptions: [<class >> 'paste.httpexceptions.HTTPException'>] >> paste.httpexceptions: <paste.httpexceptions.HTTPExceptionHandler object >> at 0xd888fd0> >> paste.httpserver.thread_pool: <paste.httpserver.ThreadPool object at >> 0xdcf8650> >> paste.parsed_querystring: ([('tool_shed_url', ' >> https://toolshed.g2.bx.psu.edu/'), ('name', 'blast_datatypes'), >> ('owner', 'devteam'), ('changeset_revision', 'de11e1a921c4'), >> ('latest_changeset_revision', '5482a8cd0f36'), ('latest_ctx_rev', '10')], >> 'tool_shed_url= >> https://toolshed.g2.bx.psu.edu/&name=blast_datatypes&owner=devteam&changese… >> ') >> paste.recursive.forward: <paste.recursive.Forwarder from /> >> paste.recursive.include: <paste.recursive.Includer from /> >> paste.recursive.include_app_iter: <paste.recursive.IncluderAppIter from >> /> >> paste.recursive.script_name: '' >> paste.throw_errors: True >> request_id: 'a58bb404dce911e481c700215e543aa8' >> webob._parsed_query_vars: (MultiDict([('tool_shed_url', ' >> https://toolshed.g2.bx.psu.edu/'), ('name', 'blast_datatypes'), >> ('owner', 'devteam'), ('changeset_revision', 'de11e1a921c4'), >> ('latest_changeset_revision', '5482a8cd0f36'), ('latest_ctx_rev', '10')]), >> 'tool_shed_url= >> https://toolshed.g2.bx.psu.edu/&name=blast_datatypes&owner=devteam&changese… >> ') >> wsgi process: 'Multithreaded' >> ------------------------------------------------------------ >> >> Could you please give me some advise to figure out where the problem is >> and how to fix it? >> >> Thanks, >> >> >> Zhaozhen >> >> >> >> ___________________________________________________________ >> 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: >> https://lists.galaxyproject.org/ >> >> To search Galaxy mailing lists use the unified search at: >> http://galaxyproject.org/search/mailinglists/ > >

1 0

Cloning state when installing tools.
by Carlos Lijeron 08 Apr '15

08 Apr '15

Everyone, I've been encountering problems when installing particular tools in a local Galaxy instance. One such tool is Cummerbund as you can see in link below: https://www.dropbox.com/s/bmg4qcci97ayq2k/Cloning%20State.JPG?dl=0 Would you have a suggestion on how to troubleshoot failed tool installations that do not give an output error message? Thank you all ! Carlos.

2 1

restricted data upload from server folder
by De Smet Matthias 08 Apr '15

08 Apr '15

Hey Galaxy-dev’s, I’m completely new to galaxy, but I am tasked with a small scale deployment project. I am looking for an alternate option to upload data to galaxy. All data from our sequencers is stored on a NAS, which is accessible by the galaxy server. I would like to make it so that the users can only select data from that folder, to eliminate the need to transfer data through the client to the server. Is there any way to do this? Or am I making this to hard on myself? Sincerely [cid:image001.png@01D04471.1ABB7370] Matthias De Smet Centrum voor Medische Genetica De Pintelaan 185 - 9000 Gent matthias.desmet(a)uzgent.be<mailto:matthias.desmet@uzgent.be> tel.: +32 (0)9 332 0296 http://www.cmgg.be

2 1