Re: [galaxy-dev] conda management of tools dependent on python3
I'm not quite sure if I understand you correctly, but let's see. The original tool wrapper stated python3 as a dependency. This did not work with at runtime installation at all because conda cannot resolve python3 and the requirement got ignored by Galaxy. I changed the requirement tag now to: python and now Galaxy happily installs a __python@3.4 environment, but then it tries to set up a *new* environment for my package, which is still based on python2.7 and fails as before. On the bioconda side, all the recipe does is to declare that it shouldn't be built under python2 using skip: True # [py2k] in the build section of the recipe. On 03.11.2016 21:36, Björn Grüning wrote: Hi, can you check the package? The package should have a dependency on python3, if not the package seems to be broken :( Ciao, Bjoern Am 03.11.2016 um 21:32 schrieb Wolfgang Maier: Hi Björn, Hmm, I guess I should have phrased my question more clearly. What I'm trying to do is to get Galaxy to satisfy a missing tool dependency at *tool runtime* using a bioconda package that is only available for Python3. I am able to satisfy the dependency *manually* by running: conda create --name __@ ==https://docs.galaxyproject.org/en/master/admin/conda_faq.html#how-do-conda-dependencies-work-where-do-things-get-installed), but when I let *Galaxy autoinstall* the package it will use python2.7 for the environment, then fail with: Error: Unsatisfiable package specifications. and a hint that conflicts with python 2.7. So my question is: is there any way to inform Galaxy that the dependency requires a conda environment based on python3? Best, Wolfgang On 28.10.2016 19:14, Björn Grüning wrote: Hi Wolfgang, can you describe step by step what you are trying to do? A conda package ships it's own python version, you can see this in the build-string py35_0 for example. So conda can handle all python version independent of the python version of miniconda. Cheers, Bjoern Dear all, I'm still pretty new to conda tool dependencies management and there is one thing I cannot find documented anywhere: How can I let conda manage tool dependencies that involve python3? If I let Galaxy install conda for me, it creates an environment with python2, then if there is a tool dependency that has a conda package built for only python3 I'm getting an error because of a conflict between that package and python2 (not surprisingly), but AFAIU conda environments are bound to one particular version of python (or is that incorrect?). Thanks for any help with this and best wishes, Wolfgang ___ 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/ ___ 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/
Re: [galaxy-dev] conda management of tools dependent on python3
Hi, can you check the package? The package should have a dependency on python3, if not the package seems to be broken :( Ciao, Bjoern Am 03.11.2016 um 21:32 schrieb Wolfgang Maier: > Hi Björn, > > Hmm, I guess I should have phrased my question more clearly. What I'm > trying to do is to get Galaxy to satisfy a missing tool dependency at > *tool runtime* using a bioconda package that is only available for > Python3. I am able to satisfy the dependency *manually* by running: > > conda create --name __@ > == > (following the example at > https://docs.galaxyproject.org/en/master/admin/conda_faq.html#how-do-conda-dependencies-work-where-do-things-get-installed), > but when I let *Galaxy autoinstall* the package it will use python2.7 > for the environment, then fail with: > > Error: Unsatisfiable package specifications. > > and a hint that conflicts with python 2.7. So my question is: > is there any way to inform Galaxy that the dependency requires a conda > environment based on python3? > > Best, > Wolfgang > > > On 28.10.2016 19:14, Björn Grüning wrote: >> Hi Wolfgang, >> >> can you describe step by step what you are trying to do? >> >> A conda package ships it's own python version, you can see this in the >> build-string py35_0 for example. So conda can handle all python version >> independent of the python version of miniconda. >> >> Cheers, >> Bjoern >> >>> Dear all, >>> >>> I'm still pretty new to conda tool dependencies management and there is >>> one thing I cannot find documented anywhere: >>> How can I let conda manage tool dependencies that involve python3? >>> If I let Galaxy install conda for me, it creates an environment with >>> python2, then if there is a tool dependency that has a conda package >>> built for only python3 I'm getting an error because of a conflict >>> between that package and python2 (not surprisingly), but AFAIU conda >>> environments are bound to one particular version of python (or is that >>> incorrect?). >>> >>> Thanks for any help with this and best wishes, >>> Wolfgang >>> ___ >>> 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/ ___ 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/
Re: [galaxy-dev] conda management of tools dependent on python3
Hi Björn, Hmm, I guess I should have phrased my question more clearly. What I'm trying to do is to get Galaxy to satisfy a missing tool dependency at *tool runtime* using a bioconda package that is only available for Python3. I am able to satisfy the dependency *manually* by running: conda create --name __@ == (following the example at https://docs.galaxyproject.org/en/master/admin/conda_faq.html#how-do-conda-dependencies-work-where-do-things-get-installed), but when I let *Galaxy autoinstall* the package it will use python2.7 for the environment, then fail with: Error: Unsatisfiable package specifications. and a hint that conflicts with python 2.7. So my question is: is there any way to inform Galaxy that the dependency requires a conda environment based on python3? Best, Wolfgang On 28.10.2016 19:14, Björn Grüning wrote: Hi Wolfgang, can you describe step by step what you are trying to do? A conda package ships it's own python version, you can see this in the build-string py35_0 for example. So conda can handle all python version independent of the python version of miniconda. Cheers, Bjoern Dear all, I'm still pretty new to conda tool dependencies management and there is one thing I cannot find documented anywhere: How can I let conda manage tool dependencies that involve python3? If I let Galaxy install conda for me, it creates an environment with python2, then if there is a tool dependency that has a conda package built for only python3 I'm getting an error because of a conflict between that package and python2 (not surprisingly), but AFAIU conda environments are bound to one particular version of python (or is that incorrect?). Thanks for any help with this and best wishes, Wolfgang ___ 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/ ___ 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/
Re: [galaxy-dev] galaxy - velvet devteam revision 08256557922f
Hey everyone, I haven’t got a feedback from you. If you have any suggestions, I’m a little bit confused with this problem. Thank you very much! Edgar Fernandez System Administrator (Linux) Direction Générale des Technologies de l'Information et de la Communication Université de Montréal PAVILLON ROGER-GAUDRY, bureau X-210 • Bur. : 1-514-343-6111 poste 16568 From: Fernandez Edgar Sent: October-31-16 11:40 AM To: galaxy-...@bx.psu.edu Subject: [galaxy-dev] galaxy - velvet devteam revision 08256557922f Hey Guys, I need your help understanding what’s happening with velvet devteam revision 08256557922f. After installing it, velvet was giving me the following error: galaxy.jobs.handler WARNING 2016-10-20 12:15:11,986 (1599) Tool 'toolshed.g2.bx.psu.edu/repos/devteam/velvet/velveth/1.2.10.0' removed from tool config, unable to run job galaxy.jobs.handler ERROR 2016-10-20 12:15:12,165 (1599) Error checking job readiness galaxy.jobs.handler ERROR 2016-10-20 12:15:12,165 (1599) Error checking job readiness I realized velvet needed that galaxy was restarted. Now, velvet finishes his jobs (becomes green) however, the following message is on galaxy’s Job output not returned from cluster And you can see in the logs of the handler: galaxy.jobs DEBUG 2016-10-31 10:17:08,548 (1669) Working directory for job is: /home/galaxy/galaxy-16.04/database/jobs_directory/001/1669 galaxy.jobs.handler DEBUG 2016-10-31 10:17:08,567 (1669) Dispatching to drmaa runner galaxy.jobs DEBUG 2016-10-31 10:17:08,621 (1669) Persisting job destination (destination id: torque) galaxy.jobs.runners DEBUG 2016-10-31 10:17:08,630 Job [1669] queued (63.397 ms) galaxy.jobs.handler INFO 2016-10-31 10:17:08,652 (1669) Job dispatched galaxy.tools.deps DEBUG 2016-10-31 10:17:08,891 Building dependency shell command for dependency 'velvet' galaxy.tools.deps DEBUG 2016-10-31 10:17:08,891 Find dependency velvet version 1.2.10 galaxy.tools.deps DEBUG 2016-10-31 10:17:08,896 Resolver tool_shed_packages returned (isnull? False) galaxy.jobs.command_factory INFO 2016-10-31 10:17:08,945 Built script [/home/galaxy/galaxy-16.04/database/jobs_directory/001/1669/tool_script.sh] for tool command[PACKAGE_BASE=/home/galaxy/galaxy-prod/tool-data/toolshed.dependency.dir/velvet/1.2.10/devteam/velvet/08256557922f; export PACKAGE_BASE; . /home/galaxy/galaxy-prod/tool-data/toolshed.dependency.dir/velvet/1.2.10/devteam/velvet/08256557922f/env.sh; velveth 2>&1 | grep "Version" | sed -e 's/Version //' > /home/galaxy/galaxy-prod/database/tmp/GALAXY_VERSION_STRING_1669 2>&1; python /home/galaxy/galaxy-prod/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/velvet/08256557922f/velvet/velveth_wrapper.py '/home/galaxy/galaxy-prod/database/files/004/dataset_4306.dat' '/home/galaxy/galaxy-16.04/database/jobs_directory/001/1669/dataset_4306_files' 21 -fasta -short /home/galaxy/galaxy-prod/database/files/003/dataset_3537.dat] galaxy.tools.deps DEBUG 2016-10-31 10:17:09,144 Building dependency shell command for dependency 'samtools' galaxy.tools.deps DEBUG 2016-10-31 10:17:09,144 Find dependency samtools version None galaxy.tools.deps DEBUG 2016-10-31 10:17:09,144 Resolver tool_shed_packages returned (isnull? True) galaxy.tools.deps DEBUG 2016-10-31 10:17:09,144 Resolver galaxy_packages returned (isnull? True) galaxy.tools.deps DEBUG 2016-10-31 10:17:09,144 Resolver galaxy_packages returned (isnull? True) galaxy.tools.deps DEBUG 2016-10-31 10:17:09,145 Resolver conda returned (isnull? True) galaxy.tools.deps DEBUG 2016-10-31 10:17:09,145 Resolver conda returned (isnull? True) galaxy.tools.deps WARNING 2016-10-31 10:17:09,145 Failed to resolve dependency on 'samtools', ignoring galaxy.jobs.runners DEBUG 2016-10-31 10:17:09,153 (1669) command is: mkdir -p working; cd working; /home/galaxy/galaxy-16.04/database/jobs_directory/001/1669/tool_script.sh; return_code=$?; cd '/home/galaxy/galaxy-16.04/database/jobs_directory/001/1669'; python "/home/galaxy/galaxy-16.04/database/jobs_directory/001/1669/set_metadata_KQTExg.py" "/home/galaxy/galaxy-prod/database/tmp/tmpLU0HQy" "/home/galaxy/galaxy-16.04/database/jobs_directory/001/1669/working/galaxy.json" "/home/galaxy/galaxy-16.04/database/jobs_directory/001/1669/metadata_in_HistoryDatasetAssociation_4437_kIYXWa,/home/galaxy/galaxy-16.04/database/jobs_directory/001/1669/metadata_kwds_HistoryDatasetAssociation_4437_ArCXyb,/home/galaxy/galaxy-16.04/database/jobs_directory/001/1669/metadata_out_HistoryDatasetAssociation_4437_l28qWr,/home/galaxy/galaxy-16.04/database/jobs_directory/001/1669/metadata_results_HistoryDatasetAssociation_4437_oTDjOd,/home/galaxy/galaxy-prod/database/files/004/dataset_4306.dat,/home/galaxy/galaxy-16.04/database/jobs_directory/001/1669/metadata_override_HistoryDatasetAssociation_4437_8VzdJw" 5242880; sh -c "exit $return_code" galaxy.jobs.runners.drmaa DEBUG 2016-10-31 10:17:09,202 (1669) submitting file /home/galaxy/galaxy-16.04/database/jobs_directory/001/1669/gala
Re: [galaxy-dev] Installing ToolShed Tools into Galaxy via Browser Interface Exception Thrown
Awesome! After changing “&” to “and”, it worked! Thank you! > On Nov 3, 2016, at 12:59 PM, Peter Cock wrote: > > Good news - this is the bug I though it was, the ampersand > should be escaped as & in the XML file: > > https://github.com/galaxyproject/galaxy/issues/3084 > > More good news: This will likely be fixed in the next release > of Galaxy: > > https://github.com/galaxyproject/galaxy/pull/3122 > > Right now I suggest you manually edit these XML files to > use the word "and" instead of "&". > > Peter > > > On Thu, Nov 3, 2016 at 2:36 PM, Yip, Miu ki wrote: >> Hi Peter, >> >> Line 44 is oddly specific. Nevertheless, we have this as the 44th line in >> the xml file. >> >> > version="" /> >> >> This tool is not the one trying to be installed. >> >> Thanks, >> Miuki >> On Nov 3, 2016, at 10:28 AM, Peter Cock >> mailto:p.j.a.c...@googlemail.com>> wrote: >> >> I think you may have hit the same bug I found recently: >> >> https://github.com/galaxyproject/galaxy/issues/3084 >> >> What is line 44 of your integrated_tool_panel.xml file? >> >> Peter >> >> On Thu, Nov 3, 2016 at 2:16 PM, Yip, Miu ki wrote: >> Hi all, >> >> While trying to install tools from the toolshed via the browser interface, >> an error keeps appearing and nothing is abled to be installed. Currently >> using the latest version of Galaxy and having tried to install several >> different tools, the following error keeps appearing in the log file. >> >> galaxy.queue_worker DEBUG 2016-11-03 13:08:32,425 Executing toolbox reload >> on 'main' >> Exception in thread Thread-2: >> Traceback (most recent call last): >> File "/usr/lib64/python2.7/threading.py", line 811, in __bootstrap_inner >> self.run() >> File "/usr/lib64/python2.7/threading.py", line 764, in run >> self.__target(*self.__args, **self.__kwargs) >> File >> "/mnt/sdd1/nondocker_galaxy/galaxy/lib/galaxy/tools/toolbox/watcher.py", >> line 147, in on_any_event >> self._handle(event) >> File >> "/mnt/sdd1/nondocker_galaxy/galaxy/lib/galaxy/tools/toolbox/watcher.py", >> line 150, in _handle >> self.reload_callback() >> File "/mnt/sdd1/nondocker_galaxy/galaxy/lib/galaxy/tools/toolbox/base.py", >> line 78, in >> self._tool_conf_watcher = get_tool_conf_watcher( lambda: >> reload_toolbox(app)) >> File "/mnt/sdd1/nondocker_galaxy/galaxy/lib/galaxy/queue_worker.py", line >> 56, in reload_toolbox >> app.toolbox = _get_new_toolbox(app) >> File "/mnt/sdd1/nondocker_galaxy/galaxy/lib/galaxy/queue_worker.py", line >> 72, in _get_new_toolbox >> new_toolbox = tools.ToolBox(tool_configs, app.config.tool_path, app, >> app.toolbox._tool_conf_watcher) >> File "/mnt/sdd1/nondocker_galaxy/galaxy/lib/galaxy/tools/__init__.py", line >> 110, in __init__ >> tool_conf_watcher=tool_conf_watcher >> File "/mnt/sdd1/nondocker_galaxy/galaxy/lib/galaxy/tools/toolbox/base.py", >> line 1037, in __init__ >> super(BaseGalaxyToolBox, self).__init__(config_filenames, tool_root_dir, >> app, tool_conf_watcher=tool_conf_watcher) >> File "/mnt/sdd1/nondocker_galaxy/galaxy/lib/galaxy/tools/toolbox/base.py", >> line 69, in __init__ >> self._init_integrated_tool_panel( app.config ) >> File >> "/mnt/sdd1/nondocker_galaxy/galaxy/lib/galaxy/tools/toolbox/integrated_panel.py", >> line 36, in _init_integrated_tool_panel >> self._load_integrated_tool_panel_keys() >> File "/mnt/sdd1/nondocker_galaxy/galaxy/lib/galaxy/tools/toolbox/base.py", >> line 368, in _load_integrated_tool_panel_keys >> tree = parse_xml( self._integrated_tool_panel_config ) >> File "/mnt/sdd1/nondocker_galaxy/galaxy/lib/galaxy/util/__init__.py", line >> 211, in parse_xml >> root = tree.parse( fname, parser=ElementTree.XMLParser( >> target=DoctypeSafeCallbackTarget() ) ) >> File "/usr/lib64/python2.7/xml/etree/ElementTree.py", line 656, in parse >> parser.feed(data) >> File "/usr/lib64/python2.7/xml/etree/ElementTree.py", line 1642, in feed >> self._raiseerror(v) >> File "/usr/lib64/python2.7/xml/etree/ElementTree.py", line 1506, in >> _raiseerror >> raise err >> ParseError: not well-formed (invalid token): line 44, column 71 >> >> Is there an XML or configuration file which needs to be changed for this to >> work? Not sure how to proceed. >> >> Thanks! >> Miuki >> ___ >> 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/ >> ___ 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://galaxyproj
Re: [galaxy-dev] Installing ToolShed Tools into Galaxy via Browser Interface Exception Thrown
Good news - this is the bug I though it was, the ampersand should be escaped as & in the XML file: https://github.com/galaxyproject/galaxy/issues/3084 More good news: This will likely be fixed in the next release of Galaxy: https://github.com/galaxyproject/galaxy/pull/3122 Right now I suggest you manually edit these XML files to use the word "and" instead of "&". Peter On Thu, Nov 3, 2016 at 2:36 PM, Yip, Miu ki wrote: > Hi Peter, > > Line 44 is oddly specific. Nevertheless, we have this as the 44th line in the > xml file. > > version="" /> > > This tool is not the one trying to be installed. > > Thanks, > Miuki > On Nov 3, 2016, at 10:28 AM, Peter Cock > mailto:p.j.a.c...@googlemail.com>> wrote: > > I think you may have hit the same bug I found recently: > > https://github.com/galaxyproject/galaxy/issues/3084 > > What is line 44 of your integrated_tool_panel.xml file? > > Peter > > On Thu, Nov 3, 2016 at 2:16 PM, Yip, Miu ki wrote: > Hi all, > > While trying to install tools from the toolshed via the browser interface, an > error keeps appearing and nothing is abled to be installed. Currently using > the latest version of Galaxy and having tried to install several different > tools, the following error keeps appearing in the log file. > > galaxy.queue_worker DEBUG 2016-11-03 13:08:32,425 Executing toolbox reload on > 'main' > Exception in thread Thread-2: > Traceback (most recent call last): > File "/usr/lib64/python2.7/threading.py", line 811, in __bootstrap_inner >self.run() > File "/usr/lib64/python2.7/threading.py", line 764, in run >self.__target(*self.__args, **self.__kwargs) > File > "/mnt/sdd1/nondocker_galaxy/galaxy/lib/galaxy/tools/toolbox/watcher.py", line > 147, in on_any_event >self._handle(event) > File > "/mnt/sdd1/nondocker_galaxy/galaxy/lib/galaxy/tools/toolbox/watcher.py", line > 150, in _handle >self.reload_callback() > File "/mnt/sdd1/nondocker_galaxy/galaxy/lib/galaxy/tools/toolbox/base.py", > line 78, in >self._tool_conf_watcher = get_tool_conf_watcher( lambda: > reload_toolbox(app)) > File "/mnt/sdd1/nondocker_galaxy/galaxy/lib/galaxy/queue_worker.py", line > 56, in reload_toolbox >app.toolbox = _get_new_toolbox(app) > File "/mnt/sdd1/nondocker_galaxy/galaxy/lib/galaxy/queue_worker.py", line > 72, in _get_new_toolbox >new_toolbox = tools.ToolBox(tool_configs, app.config.tool_path, app, > app.toolbox._tool_conf_watcher) > File "/mnt/sdd1/nondocker_galaxy/galaxy/lib/galaxy/tools/__init__.py", line > 110, in __init__ >tool_conf_watcher=tool_conf_watcher > File "/mnt/sdd1/nondocker_galaxy/galaxy/lib/galaxy/tools/toolbox/base.py", > line 1037, in __init__ >super(BaseGalaxyToolBox, self).__init__(config_filenames, tool_root_dir, > app, tool_conf_watcher=tool_conf_watcher) > File "/mnt/sdd1/nondocker_galaxy/galaxy/lib/galaxy/tools/toolbox/base.py", > line 69, in __init__ >self._init_integrated_tool_panel( app.config ) > File > "/mnt/sdd1/nondocker_galaxy/galaxy/lib/galaxy/tools/toolbox/integrated_panel.py", > line 36, in _init_integrated_tool_panel >self._load_integrated_tool_panel_keys() > File "/mnt/sdd1/nondocker_galaxy/galaxy/lib/galaxy/tools/toolbox/base.py", > line 368, in _load_integrated_tool_panel_keys >tree = parse_xml( self._integrated_tool_panel_config ) > File "/mnt/sdd1/nondocker_galaxy/galaxy/lib/galaxy/util/__init__.py", line > 211, in parse_xml >root = tree.parse( fname, parser=ElementTree.XMLParser( > target=DoctypeSafeCallbackTarget() ) ) > File "/usr/lib64/python2.7/xml/etree/ElementTree.py", line 656, in parse >parser.feed(data) > File "/usr/lib64/python2.7/xml/etree/ElementTree.py", line 1642, in feed >self._raiseerror(v) > File "/usr/lib64/python2.7/xml/etree/ElementTree.py", line 1506, in > _raiseerror >raise err > ParseError: not well-formed (invalid token): line 44, column 71 > > Is there an XML or configuration file which needs to be changed for this to > work? Not sure how to proceed. > > Thanks! > Miuki > ___ > 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/ > ___ 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/
[galaxy-dev] purge dataset at a different location
Dear Galaxy Developers, Because of specific use case, our transfer tool need to keep the datasets in a different location instead of the default location, so we'd like to purge datasets according to its "external_filename" (we found this column in the dataset table in the database). Is there a way or some code to modify so that when we try to purge a dataset or a history in Galaxy, the file located at a dataset's external_filename can also be deleted? Thanks in advance, Mark Xiao ___ 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/
Re: [galaxy-dev] Installing ToolShed Tools into Galaxy via Browser Interface Exception Thrown
Hi Marius, Thanks for the reply! I have tried moving the file and just deleting the file all together. I am still running into this error. Thanks, Miuki > On Nov 3, 2016, at 10:29 AM, Marius van den Beek > wrote: > > Hello Miuki, > > this looks like your integrated_tool_panel.xml file has some problems. > Can you try to move this file to a different location and try the > installation again? > It should be located in your galaxy directory. > > Best, > Marius > > > On 11/03/2016 03:16 PM, Yip, Miu ki wrote: >> Hi all, >> >> While trying to install tools from the toolshed via the browser interface, >> an error keeps appearing and nothing is abled to be installed. Currently >> using the latest version of Galaxy and having tried to install several >> different tools, the following error keeps appearing in the log file. >> >> galaxy.queue_worker DEBUG 2016-11-03 13:08:32,425 Executing toolbox reload >> on 'main' >> Exception in thread Thread-2: >> Traceback (most recent call last): >> File "/usr/lib64/python2.7/threading.py", line 811, in __bootstrap_inner >> self.run() >> File "/usr/lib64/python2.7/threading.py", line 764, in run >> self.__target(*self.__args, **self.__kwargs) >> File >> "/mnt/sdd1/nondocker_galaxy/galaxy/lib/galaxy/tools/toolbox/watcher.py", >> line 147, in on_any_event >> self._handle(event) >> File >> "/mnt/sdd1/nondocker_galaxy/galaxy/lib/galaxy/tools/toolbox/watcher.py", >> line 150, in _handle >> self.reload_callback() >> File "/mnt/sdd1/nondocker_galaxy/galaxy/lib/galaxy/tools/toolbox/base.py", >> line 78, in >> self._tool_conf_watcher = get_tool_conf_watcher( lambda: >> reload_toolbox(app)) >> File "/mnt/sdd1/nondocker_galaxy/galaxy/lib/galaxy/queue_worker.py", line >> 56, in reload_toolbox >> app.toolbox = _get_new_toolbox(app) >> File "/mnt/sdd1/nondocker_galaxy/galaxy/lib/galaxy/queue_worker.py", line >> 72, in _get_new_toolbox >> new_toolbox = tools.ToolBox(tool_configs, app.config.tool_path, app, >> app.toolbox._tool_conf_watcher) >> File "/mnt/sdd1/nondocker_galaxy/galaxy/lib/galaxy/tools/__init__.py", >> line 110, in __init__ >> tool_conf_watcher=tool_conf_watcher >> File "/mnt/sdd1/nondocker_galaxy/galaxy/lib/galaxy/tools/toolbox/base.py", >> line 1037, in __init__ >> super(BaseGalaxyToolBox, self).__init__(config_filenames, tool_root_dir, >> app, tool_conf_watcher=tool_conf_watcher) >> File "/mnt/sdd1/nondocker_galaxy/galaxy/lib/galaxy/tools/toolbox/base.py", >> line 69, in __init__ >> self._init_integrated_tool_panel( app.config ) >> File >> "/mnt/sdd1/nondocker_galaxy/galaxy/lib/galaxy/tools/toolbox/integrated_panel.py", >> line 36, in _init_integrated_tool_panel >> self._load_integrated_tool_panel_keys() >> File "/mnt/sdd1/nondocker_galaxy/galaxy/lib/galaxy/tools/toolbox/base.py", >> line 368, in _load_integrated_tool_panel_keys >> tree = parse_xml( self._integrated_tool_panel_config ) >> File "/mnt/sdd1/nondocker_galaxy/galaxy/lib/galaxy/util/__init__.py", line >> 211, in parse_xml >> root = tree.parse( fname, parser=ElementTree.XMLParser( >> target=DoctypeSafeCallbackTarget() ) ) >> File "/usr/lib64/python2.7/xml/etree/ElementTree.py", line 656, in parse >> parser.feed(data) >> File "/usr/lib64/python2.7/xml/etree/ElementTree.py", line 1642, in feed >> self._raiseerror(v) >> File "/usr/lib64/python2.7/xml/etree/ElementTree.py", line 1506, in >> _raiseerror >> raise err >> ParseError: not well-formed (invalid token): line 44, column 71 >> >> Is there an XML or configuration file which needs to be changed for this to >> work? Not sure how to proceed. >> >> Thanks! >> Miuki >> ___ >> 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/ > ___ 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/
Re: [galaxy-dev] Installing ToolShed Tools into Galaxy via Browser Interface Exception Thrown
I think you may have hit the same bug I found recently: https://github.com/galaxyproject/galaxy/issues/3084 What is line 44 of your integrated_tool_panel.xml file? Peter On Thu, Nov 3, 2016 at 2:16 PM, Yip, Miu ki wrote: > Hi all, > > While trying to install tools from the toolshed via the browser interface, an > error keeps appearing and nothing is abled to be installed. Currently using > the latest version of Galaxy and having tried to install several different > tools, the following error keeps appearing in the log file. > > galaxy.queue_worker DEBUG 2016-11-03 13:08:32,425 Executing toolbox reload on > 'main' > Exception in thread Thread-2: > Traceback (most recent call last): > File "/usr/lib64/python2.7/threading.py", line 811, in __bootstrap_inner > self.run() > File "/usr/lib64/python2.7/threading.py", line 764, in run > self.__target(*self.__args, **self.__kwargs) > File > "/mnt/sdd1/nondocker_galaxy/galaxy/lib/galaxy/tools/toolbox/watcher.py", line > 147, in on_any_event > self._handle(event) > File > "/mnt/sdd1/nondocker_galaxy/galaxy/lib/galaxy/tools/toolbox/watcher.py", line > 150, in _handle > self.reload_callback() > File "/mnt/sdd1/nondocker_galaxy/galaxy/lib/galaxy/tools/toolbox/base.py", > line 78, in > self._tool_conf_watcher = get_tool_conf_watcher( lambda: > reload_toolbox(app)) > File "/mnt/sdd1/nondocker_galaxy/galaxy/lib/galaxy/queue_worker.py", line > 56, in reload_toolbox > app.toolbox = _get_new_toolbox(app) > File "/mnt/sdd1/nondocker_galaxy/galaxy/lib/galaxy/queue_worker.py", line > 72, in _get_new_toolbox > new_toolbox = tools.ToolBox(tool_configs, app.config.tool_path, app, > app.toolbox._tool_conf_watcher) > File "/mnt/sdd1/nondocker_galaxy/galaxy/lib/galaxy/tools/__init__.py", line > 110, in __init__ > tool_conf_watcher=tool_conf_watcher > File "/mnt/sdd1/nondocker_galaxy/galaxy/lib/galaxy/tools/toolbox/base.py", > line 1037, in __init__ > super(BaseGalaxyToolBox, self).__init__(config_filenames, tool_root_dir, > app, tool_conf_watcher=tool_conf_watcher) > File "/mnt/sdd1/nondocker_galaxy/galaxy/lib/galaxy/tools/toolbox/base.py", > line 69, in __init__ > self._init_integrated_tool_panel( app.config ) > File > "/mnt/sdd1/nondocker_galaxy/galaxy/lib/galaxy/tools/toolbox/integrated_panel.py", > line 36, in _init_integrated_tool_panel > self._load_integrated_tool_panel_keys() > File "/mnt/sdd1/nondocker_galaxy/galaxy/lib/galaxy/tools/toolbox/base.py", > line 368, in _load_integrated_tool_panel_keys > tree = parse_xml( self._integrated_tool_panel_config ) > File "/mnt/sdd1/nondocker_galaxy/galaxy/lib/galaxy/util/__init__.py", line > 211, in parse_xml > root = tree.parse( fname, parser=ElementTree.XMLParser( > target=DoctypeSafeCallbackTarget() ) ) > File "/usr/lib64/python2.7/xml/etree/ElementTree.py", line 656, in parse > parser.feed(data) > File "/usr/lib64/python2.7/xml/etree/ElementTree.py", line 1642, in feed > self._raiseerror(v) > File "/usr/lib64/python2.7/xml/etree/ElementTree.py", line 1506, in > _raiseerror > raise err > ParseError: not well-formed (invalid token): line 44, column 71 > > Is there an XML or configuration file which needs to be changed for this to > work? Not sure how to proceed. > > Thanks! > Miuki > ___ > 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/ ___ 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/
Re: [galaxy-dev] Installing ToolShed Tools into Galaxy via Browser Interface Exception Thrown
Hello Miuki, this looks like your integrated_tool_panel.xml file has some problems. Can you try to move this file to a different location and try the installation again? It should be located in your galaxy directory. Best, Marius On 11/03/2016 03:16 PM, Yip, Miu ki wrote: Hi all, While trying to install tools from the toolshed via the browser interface, an error keeps appearing and nothing is abled to be installed. Currently using the latest version of Galaxy and having tried to install several different tools, the following error keeps appearing in the log file. galaxy.queue_worker DEBUG 2016-11-03 13:08:32,425 Executing toolbox reload on 'main' Exception in thread Thread-2: Traceback (most recent call last): File "/usr/lib64/python2.7/threading.py", line 811, in __bootstrap_inner self.run() File "/usr/lib64/python2.7/threading.py", line 764, in run self.__target(*self.__args, **self.__kwargs) File "/mnt/sdd1/nondocker_galaxy/galaxy/lib/galaxy/tools/toolbox/watcher.py", line 147, in on_any_event self._handle(event) File "/mnt/sdd1/nondocker_galaxy/galaxy/lib/galaxy/tools/toolbox/watcher.py", line 150, in _handle self.reload_callback() File "/mnt/sdd1/nondocker_galaxy/galaxy/lib/galaxy/tools/toolbox/base.py", line 78, in self._tool_conf_watcher = get_tool_conf_watcher( lambda: reload_toolbox(app)) File "/mnt/sdd1/nondocker_galaxy/galaxy/lib/galaxy/queue_worker.py", line 56, in reload_toolbox app.toolbox = _get_new_toolbox(app) File "/mnt/sdd1/nondocker_galaxy/galaxy/lib/galaxy/queue_worker.py", line 72, in _get_new_toolbox new_toolbox = tools.ToolBox(tool_configs, app.config.tool_path, app, app.toolbox._tool_conf_watcher) File "/mnt/sdd1/nondocker_galaxy/galaxy/lib/galaxy/tools/__init__.py", line 110, in __init__ tool_conf_watcher=tool_conf_watcher File "/mnt/sdd1/nondocker_galaxy/galaxy/lib/galaxy/tools/toolbox/base.py", line 1037, in __init__ super(BaseGalaxyToolBox, self).__init__(config_filenames, tool_root_dir, app, tool_conf_watcher=tool_conf_watcher) File "/mnt/sdd1/nondocker_galaxy/galaxy/lib/galaxy/tools/toolbox/base.py", line 69, in __init__ self._init_integrated_tool_panel( app.config ) File "/mnt/sdd1/nondocker_galaxy/galaxy/lib/galaxy/tools/toolbox/integrated_panel.py", line 36, in _init_integrated_tool_panel self._load_integrated_tool_panel_keys() File "/mnt/sdd1/nondocker_galaxy/galaxy/lib/galaxy/tools/toolbox/base.py", line 368, in _load_integrated_tool_panel_keys tree = parse_xml( self._integrated_tool_panel_config ) File "/mnt/sdd1/nondocker_galaxy/galaxy/lib/galaxy/util/__init__.py", line 211, in parse_xml root = tree.parse( fname, parser=ElementTree.XMLParser( target=DoctypeSafeCallbackTarget() ) ) File "/usr/lib64/python2.7/xml/etree/ElementTree.py", line 656, in parse parser.feed(data) File "/usr/lib64/python2.7/xml/etree/ElementTree.py", line 1642, in feed self._raiseerror(v) File "/usr/lib64/python2.7/xml/etree/ElementTree.py", line 1506, in _raiseerror raise err ParseError: not well-formed (invalid token): line 44, column 71 Is there an XML or configuration file which needs to be changed for this to work? Not sure how to proceed. Thanks! Miuki ___ 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/ ___ 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/
[galaxy-dev] Installing ToolShed Tools into Galaxy via Browser Interface Exception Thrown
Hi all, While trying to install tools from the toolshed via the browser interface, an error keeps appearing and nothing is abled to be installed. Currently using the latest version of Galaxy and having tried to install several different tools, the following error keeps appearing in the log file. galaxy.queue_worker DEBUG 2016-11-03 13:08:32,425 Executing toolbox reload on 'main' Exception in thread Thread-2: Traceback (most recent call last): File "/usr/lib64/python2.7/threading.py", line 811, in __bootstrap_inner self.run() File "/usr/lib64/python2.7/threading.py", line 764, in run self.__target(*self.__args, **self.__kwargs) File "/mnt/sdd1/nondocker_galaxy/galaxy/lib/galaxy/tools/toolbox/watcher.py", line 147, in on_any_event self._handle(event) File "/mnt/sdd1/nondocker_galaxy/galaxy/lib/galaxy/tools/toolbox/watcher.py", line 150, in _handle self.reload_callback() File "/mnt/sdd1/nondocker_galaxy/galaxy/lib/galaxy/tools/toolbox/base.py", line 78, in self._tool_conf_watcher = get_tool_conf_watcher( lambda: reload_toolbox(app)) File "/mnt/sdd1/nondocker_galaxy/galaxy/lib/galaxy/queue_worker.py", line 56, in reload_toolbox app.toolbox = _get_new_toolbox(app) File "/mnt/sdd1/nondocker_galaxy/galaxy/lib/galaxy/queue_worker.py", line 72, in _get_new_toolbox new_toolbox = tools.ToolBox(tool_configs, app.config.tool_path, app, app.toolbox._tool_conf_watcher) File "/mnt/sdd1/nondocker_galaxy/galaxy/lib/galaxy/tools/__init__.py", line 110, in __init__ tool_conf_watcher=tool_conf_watcher File "/mnt/sdd1/nondocker_galaxy/galaxy/lib/galaxy/tools/toolbox/base.py", line 1037, in __init__ super(BaseGalaxyToolBox, self).__init__(config_filenames, tool_root_dir, app, tool_conf_watcher=tool_conf_watcher) File "/mnt/sdd1/nondocker_galaxy/galaxy/lib/galaxy/tools/toolbox/base.py", line 69, in __init__ self._init_integrated_tool_panel( app.config ) File "/mnt/sdd1/nondocker_galaxy/galaxy/lib/galaxy/tools/toolbox/integrated_panel.py", line 36, in _init_integrated_tool_panel self._load_integrated_tool_panel_keys() File "/mnt/sdd1/nondocker_galaxy/galaxy/lib/galaxy/tools/toolbox/base.py", line 368, in _load_integrated_tool_panel_keys tree = parse_xml( self._integrated_tool_panel_config ) File "/mnt/sdd1/nondocker_galaxy/galaxy/lib/galaxy/util/__init__.py", line 211, in parse_xml root = tree.parse( fname, parser=ElementTree.XMLParser( target=DoctypeSafeCallbackTarget() ) ) File "/usr/lib64/python2.7/xml/etree/ElementTree.py", line 656, in parse parser.feed(data) File "/usr/lib64/python2.7/xml/etree/ElementTree.py", line 1642, in feed self._raiseerror(v) File "/usr/lib64/python2.7/xml/etree/ElementTree.py", line 1506, in _raiseerror raise err ParseError: not well-formed (invalid token): line 44, column 71 Is there an XML or configuration file which needs to be changed for this to work? Not sure how to proceed. Thanks! Miuki ___ 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/
