Re: [galaxy-dev] Trackster error after upgrade
Hi Jeremy, Thanks for you assistance. I would love to try your suggestions, but Galaxy won't start anymore. I have found the root cause of the problems: my home partition has become too small, due to a fat 'job_working_directory'. I didn't expect it to become so big (especially with tophat output). Now I have the job_working_directory mounted on our network share. So I restart Galaxy, and got this error: Traceback (most recent call last): File /home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/buildapp.py, line 36, in app_factory app = UniverseApplication( global_conf = global_conf, **kwargs ) File /home/galaxy/galaxy-dist/lib/galaxy/app.py, line 85, in __init__ self.toolbox = tools.ToolBox( tool_configs, self.config.tool_path, self ) File /home/galaxy/galaxy-dist/lib/galaxy/tools/__init__.py, line 84, in __init__ self.load_integrated_tool_panel_keys() File /home/galaxy/galaxy-dist/lib/galaxy/tools/__init__.py, line 236, in load_integrated_tool_panel_keys tree = util.parse_xml( self.integrated_tool_panel_config ) File /home/galaxy/galaxy-dist/lib/galaxy/util/__init__.py, line 143, in parse_xml tree = ElementTree.parse(fname) File /home/galaxy/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.6.egg/elementtree/ElementTree.py, line 859, in parse tree.parse(source, parser) File /home/galaxy/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.6.egg/elementtree/ElementTree.py, line 584, in parse self._root = parser.close() File /home/galaxy/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.6.egg/elementtree/ElementTree.py, line 1251, in close self._parser.Parse(, 1) # end of data ExpatError: unclosed token: line 109, column 4 Removing PID file main.pid Before dragging up my backup, any idea how to fix this otherwise? I suspect that mercurial could not pull all changes in, is that possible? Cheers, Joachim On Wed 14 Nov 2012 04:25:53 AM CET, Jeremy Goecks wrote: One dataset I want to view in Trackster has an error ConverterDependencyException: 'A dependency (bgzip) was in an error state. I've seen this once or twice before but haven't been able to track down the issue yet. Here are two workaround that may help you out: (1) Add the dataset to a new/saved visualization and then click 'try again' to try reindexing the dataset; (2) copy the dataset using History Options -- Copy Datasets, then delete the failing dataset and try indexing the new dataset. If the dataset continues to fail, please make it available to me and I'll take a look. 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/
Re: [galaxy-dev] Can't edit galaxy workflow
This changeset is only in galaxy-central, at the moment, and not galaxy-dist. You have a few options here: Pull directly from -central to the revision indicated (though this means you will be updating your instance to less thoroughly tested galaxy-central code): hg pull -u -r 5013377e0bf7 http://bitbucket.org/galaxy/galaxy-central/ Or, probably preferable to that, you could apply just the individual changeset as a patch (which will merge in silently when you do update -dist). Simply execute the following within your galaxy-dist directory: curl https://bitbucket.org/galaxy/galaxy-central/changeset/5013377e0bf7/raw modulefix.patch hg patch --no-commit modulefix.patch -Dannon On Nov 14, 2012, at 8:04 AM, Sanjarbek Hudaiberdiev hudai...@icgeb.org wrote: Thanks a lot Dannon, for your reply. But hg keeps saying following when I try to pull: abort: unknown revision '5013377e0bf7'! Is there any other way of manually getting it? (Sorry, I'm not an expert on those new SCMs) Sanjar. On 11/13/2012 06:33 PM, Dannon Baker wrote: Sanjar, This is fixed as of 5013377e0bf7. This may not be in the next distribution, but will be in the one after that. Of course, you can manually pull the change from galaxy-central at any time. -Dannon On Nov 13, 2012, at 9:45 AM, Sanjarbek Hudaiberdiev hudai...@icgeb.org wrote: I tried to reply to similar posts, but couldn't figure out how to do it. So posting again: Galaxy giving this error when editing workflow, just after creating workflow from existing history: URL: http://localhost/galaxy/workflow/load_workflow?id=df7a1f0c02a5b08e_=1352817462148 Module weberror.evalexception.middleware:364 in respond app_iter = self.application(environ, detect_start_response) Module paste.debug.prints:98 in __call__ environ, self.app) Module paste.wsgilib:539 in intercept_output app_iter = application(environ, replacement_start_response) Module paste.recursive:80 in __call__ return self.application(environ, start_response) Module paste.httpexceptions:632 in __call__ return self.application(environ, start_response) Module galaxy.web.framework.base:160 in __call__ body = method( trans, **kwargs ) Module galaxy.web.framework:73 in decorator return simplejson.dumps( func( self, trans, *args, **kwargs ) ) Module galaxy.webapps.galaxy.controllers.workflow:733 in load_workflow 'tooltip': module.get_tooltip( static_path=url_for( '/static' ) ), Module galaxy.workflow.modules:258 in get_tooltip return self.tool.help.render( static_path=static_path ) AttributeError: 'NoneType' object has no attribute 'render' Could anyone help me to solve this problem? Thanks, Sanjar. ___ 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/ ___ 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/
Re: [galaxy-dev] Can't edit galaxy workflow
Thanks a lot Dannon, for your reply. But hg keeps saying following when I try to pull: abort: unknown revision '5013377e0bf7'! Is there any other way of manually getting it? (Sorry, I'm not an expert on those new SCMs) Sanjar. On 11/13/2012 06:33 PM, Dannon Baker wrote: Sanjar, This is fixed as of 5013377e0bf7. This may not be in the next distribution, but will be in the one after that. Of course, you can manually pull the change from galaxy-central at any time. -Dannon On Nov 13, 2012, at 9:45 AM, Sanjarbek Hudaiberdiev hudai...@icgeb.org wrote: I tried to reply to similar posts, but couldn't figure out how to do it. So posting again: Galaxy giving this error when editing workflow, just after creating workflow from existing history: URL: http://localhost/galaxy/workflow/load_workflow?id=df7a1f0c02a5b08e_=1352817462148 Module weberror.evalexception.middleware:364 in respond app_iter = self.application(environ, detect_start_response) Module paste.debug.prints:98 in __call__ environ, self.app) Module paste.wsgilib:539 in intercept_output app_iter = application(environ, replacement_start_response) Module paste.recursive:80 in __call__ return self.application(environ, start_response) Module paste.httpexceptions:632 in __call__ return self.application(environ, start_response) Module galaxy.web.framework.base:160 in __call__ body = method( trans, **kwargs ) Module galaxy.web.framework:73 in decorator return simplejson.dumps( func( self, trans, *args, **kwargs ) ) Module galaxy.webapps.galaxy.controllers.workflow:733 in load_workflow 'tooltip': module.get_tooltip( static_path=url_for( '/static' ) ), Module galaxy.workflow.modules:258 in get_tooltip return self.tool.help.render( static_path=static_path ) AttributeError: 'NoneType' object has no attribute 'render' Could anyone help me to solve this problem? Thanks, Sanjar. ___ 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/ ___ 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/
[galaxy-dev] Galaxy tool error report from yaxi...@gmail.com
GALAXY TOOL ERROR REPORT This error report was sent from the Galaxy instance hosted on the server 127.0.0.1:7070 - This is in reference to dataset id 13 from history id 6 - You should be able to view the history containing the related history item 13: FastQC_SC2T252P15_S1_L001_R1_001.fastq.html by logging in as a Galaxy admin user to the Galaxy instance referenced above and pointing your browser to the following link. 127.0.0.1:7070/history/view?id=e03374982e5c9d8a - The user 'yaxi...@gmail.com' provided the following information: This was returned upon attempt to run FasQC on one Illumina gromed dataset. Local galaxy install on RHEL58 - job id: 7 tool id: fastqc - job command line: python /home/galaxy/galaxy-dist/tools/rgenetics/rgFastQC.py -i /home/GalaxyUpload/SC2T252P15_S1_L001_R1_001.fastq -d /home/galaxy/galaxy-dist/database/job_working_directory/000/7/dataset_13_files -o /home/galaxy/galaxy-dist/database/files/000/dataset_13.dat -n FastQC -f fastq -j SC2T252P15_S1_L001_R1_001.fastq -e /home/galaxy/galaxy-dist/tool-data/shared/jars/FastQC/fastqc - job stderr: Traceback (most recent call last): File /home/galaxy/galaxy-dist/tools/rgenetics/rgFastQC.py, line 158, in module assert os.path.isfile(opts.executable),'##rgFastQC.py error - cannot find executable %s' % opts.executable AssertionError: ##rgFastQC.py error - cannot find executable /home/galaxy/galaxy-dist/tool-data/shared/jars/FastQC/fastqc - job stdout: - job info: None - job traceback: None - (This is an automated message). ___ 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/
[galaxy-dev] Working with files outside galaxy without copying?
Hi, We are looking into ways to integrate galaxy into the workflows of users at our cluster, with lots of NGS users running all and any kind of analyses on their typically huge amounts of data. For this we use a parallel file system, available on all compute nodes. This file system, although approx 1PB in size, is constantly filling up, and thus we are not very attracted by the idea of copying files into/out of galaxy for each analysis. Thus, we would be interested to know what are the options for working with existing/external(to galaxy) file systems? Eg. would it be possible to link files into some kind of galaxy file system (I'm not totally clear about how galaxy stores it's data, although I found out that stuff is created in database/files), from outside? ... or is there any work going on for selecting any file system path as input in galaxy workflows? ... or any other hints? As said, I'm quite new to galaxy, trying to grok my head around how we can use it, so all hints are welcome. Best Regards // Samuel -- Developer at SNIC-UPPMAX www.uppmax.uu.se Developer at Dept of Pharm Biosciences www.farmbio.uu.se Twitter - twitter.com/samuellampa Blog - saml.rilspace.org G+ - gplus.to/saml ___ 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/
Re: [galaxy-dev] Working with files outside galaxy without copying?
This may be implemented, I believe some people run Galaxy on the cluster, but if not: Galaxy normally operates on files stored in the database/files folder. If your Galaxy instance has access to the files you need on your parallel fs, I guess you could start by writing a tool that creates links to your files when given the path to the input file. Another tool may then move the dataset into the desired place while creating a link in the database folder. Sounds like a hack to me, but may work. cheers, jorrit On Wed, Nov 14, 2012 at 2:52 PM, Samuel Lampa samuel.la...@gmail.comwrote: Hi, We are looking into ways to integrate galaxy into the workflows of users at our cluster, with lots of NGS users running all and any kind of analyses on their typically huge amounts of data. For this we use a parallel file system, available on all compute nodes. This file system, although approx 1PB in size, is constantly filling up, and thus we are not very attracted by the idea of copying files into/out of galaxy for each analysis. Thus, we would be interested to know what are the options for working with existing/external(to galaxy) file systems? Eg. would it be possible to link files into some kind of galaxy file system (I'm not totally clear about how galaxy stores it's data, although I found out that stuff is created in database/files), from outside? ... or is there any work going on for selecting any file system path as input in galaxy workflows? ... or any other hints? As said, I'm quite new to galaxy, trying to grok my head around how we can use it, so all hints are welcome. Best Regards // Samuel -- Developer at SNIC-UPPMAX www.uppmax.uu.se Developer at Dept of Pharm Biosciences www.farmbio.uu.se Twitter - twitter.com/samuellampa Blog - saml.rilspace.org G+ - gplus.to/saml __**_ 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/ ___ 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/
Re: [galaxy-dev] Working with files outside galaxy without copying?
Hi Jorrit, thanks for the input! On 11/14/2012 03:12 PM, Jorrit Boekel wrote: This may be implemented, I believe some people run Galaxy on the cluster, Yes, but AFAIK, most cluster job runners use some kind of file staging (copying) into local storage on the compute nodes OR, require you do have the data uploaded in the galaxy file area, and to have this file are availble NFS mounted on all compute nodes. It would be very interesting if there is an existing solution for running jobs on files without moving/copying them at all, though! Best // Samuel Galaxy normally operates on files stored in the database/files folder. If your Galaxy instance has access to the files you need on your parallel fs, I guess you could start by writing a tool that creates links to your files when given the path to the input file. Another tool may then move the dataset into the desired place while creating a link in the database folder. Sounds like a hack to me, but may work. cheers, jorrit On Wed, Nov 14, 2012 at 2:52 PM, Samuel Lampa samuel.la...@gmail.com mailto:samuel.la...@gmail.com wrote: Hi, We are looking into ways to integrate galaxy into the workflows of users at our cluster, with lots of NGS users running all and any kind of analyses on their typically huge amounts of data. For this we use a parallel file system, available on all compute nodes. This file system, although approx 1PB in size, is constantly filling up, and thus we are not very attracted by the idea of copying files into/out of galaxy for each analysis. Thus, we would be interested to know what are the options for working with existing/external(to galaxy) file systems? Eg. would it be possible to link files into some kind of galaxy file system (I'm not totally clear about how galaxy stores it's data, although I found out that stuff is created in database/files), from outside? ... or is there any work going on for selecting any file system path as input in galaxy workflows? ... or any other hints? As said, I'm quite new to galaxy, trying to grok my head around how we can use it, so all hints are welcome. Best Regards // Samuel -- Developer at SNIC-UPPMAX www.uppmax.uu.se http://www.uppmax.uu.se Developer at Dept of Pharm Biosciences www.farmbio.uu.se http://www.farmbio.uu.se Twitter - twitter.com/samuellampa http://twitter.com/samuellampa Blog - saml.rilspace.org http://saml.rilspace.org G+ - gplus.to/saml http://gplus.to/saml ___ 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/ -- Developer at SNIC-UPPMAX www.uppmax.uu.se Developer at Dept of Pharm Biosciences www.farmbio.uu.se Twitter - twitter.com/samuellampa Blog - saml.rilspace.org G+ - gplus.to/saml ___ 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/
Re: [galaxy-dev] Trackster error after upgrade
Hi Joachim, It looks like your integrated_tool_panel.xml file has been corrupted somehow. You can move this file to a backup location (or delete) and it should be automatically regenerated on Galaxy startup. If this fixes the issue, could you share a copy of the file? It might be helpful for us to try to figure out what happened to it. Thanks for using Galaxy, Dan On Nov 14, 2012, at 4:25 AM, Joachim Jacob wrote: Hi Jeremy, Thanks for you assistance. I would love to try your suggestions, but Galaxy won't start anymore. I have found the root cause of the problems: my home partition has become too small, due to a fat 'job_working_directory'. I didn't expect it to become so big (especially with tophat output). Now I have the job_working_directory mounted on our network share. So I restart Galaxy, and got this error: Traceback (most recent call last): File /home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/buildapp.py, line 36, in app_factory app = UniverseApplication( global_conf = global_conf, **kwargs ) File /home/galaxy/galaxy-dist/lib/galaxy/app.py, line 85, in __init__ self.toolbox = tools.ToolBox( tool_configs, self.config.tool_path, self ) File /home/galaxy/galaxy-dist/lib/galaxy/tools/__init__.py, line 84, in __init__ self.load_integrated_tool_panel_keys() File /home/galaxy/galaxy-dist/lib/galaxy/tools/__init__.py, line 236, in load_integrated_tool_panel_keys tree = util.parse_xml( self.integrated_tool_panel_config ) File /home/galaxy/galaxy-dist/lib/galaxy/util/__init__.py, line 143, in parse_xml tree = ElementTree.parse(fname) File /home/galaxy/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.6.egg/elementtree/ElementTree.py, line 859, in parse tree.parse(source, parser) File /home/galaxy/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.6.egg/elementtree/ElementTree.py, line 584, in parse self._root = parser.close() File /home/galaxy/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.6.egg/elementtree/ElementTree.py, line 1251, in close self._parser.Parse(, 1) # end of data ExpatError: unclosed token: line 109, column 4 Removing PID file main.pid Before dragging up my backup, any idea how to fix this otherwise? I suspect that mercurial could not pull all changes in, is that possible? Cheers, Joachim On Wed 14 Nov 2012 04:25:53 AM CET, Jeremy Goecks wrote: One dataset I want to view in Trackster has an error ConverterDependencyException: 'A dependency (bgzip) was in an error state. I've seen this once or twice before but haven't been able to track down the issue yet. Here are two workaround that may help you out: (1) Add the dataset to a new/saved visualization and then click 'try again' to try reindexing the dataset; (2) copy the dataset using History Options -- Copy Datasets, then delete the failing dataset and try indexing the new dataset. If the dataset continues to fail, please make it available to me and I'll take a look. 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/ ___ 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/
Re: [galaxy-dev] [galaxy-user] Warning message
Hi Rolando, Please keep all replies on list. Without a little more information its hard to guess what is happening. Can you provide the log output for when you try to start the server? Is this a cloud instance? If I had to make a guess, it would be that there is a permissions problem due to the copy. Can you make sure that when you copied the .sample file over the .xml file that you did it as the galaxy user? Thanks for using Galaxy, Dan On Nov 13, 2012, at 10:08 PM, rolandomantil...@gmail.com wrote: I just copy the file datatypes_conf.xml.sample over datatypes_conf.xml like you told me and now I can't start galaxy it tells me Galaxy deamon not running,please help Sent from my Verizon Wireless BlackBerry From: Daniel Blankenberg d...@bx.psu.edu Date: Tue, 13 Nov 2012 10:10:43 -0500 To: Rolando Mantillarolandomantil...@gmail.com Cc: galaxy-u...@lists.bx.psu.edu Subject: Re: [galaxy-user] Warning message Hi Rolando, You'll need to remove the old blast datatypes from your datatypes_conf.xml file. If you haven't added any new datatypes manually yourself, you can copy the datatypes_conf.xml.sample file over of your datatypes_conf.xml file. Also, in the future questions about local Galaxy instances should be sent to the galaxy-dev mailing list. Thanks for using Galaxy, Dan On Nov 12, 2012, at 10:31 PM, Rolando Mantilla wrote: I'm having issues with the FASTQ_Groomer. What I have done it first I downloaded an SRA file created by an Ion torrent sequencer from the NCBI site. Then used the fastq-dump app from the NCBI site to covert the .sra file to .fastq file. When I uploaded the data into galaxy it recognized it as a fastq(as it should) but when I try to run the FASTQ groomer I get the message and warnings below. I also have already downloaded the the blast_datatypes tool from the tool_shed. I truly don't know what the issue is, any help An error occurred running this job: Groomed 12376 sanger reads into sanger reads. WARNING:galaxy.datatypes.registry:Error loading datatype with extension 'blastxml': 'module' object has no attribute 'BlastXml' WARNING:galaxy.datatypes.registry:Overriding conflicting datatype with extension 'blastxml', using datatype from /mnt/galaxyData/tmp/tmpdP_cZ7. ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ 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/
Re: [galaxy-dev] Working with files outside galaxy without copying?
Hi Samuel Have you looked at Data Libraries ? (http://wiki.galaxyproject.org/Admin/Data%20Libraries/Libraries ) also look at the configurations in universe_wsgi.ini: library_import_dir user_library_import_dir allow_library_path_paste which gives you many option to access data out side of the Galaxy database/ folder - without duplicating the data. Regards, Hans-Rudolf On 11/14/2012 03:23 PM, Samuel Lampa wrote: Hi Jorrit, thanks for the input! On 11/14/2012 03:12 PM, Jorrit Boekel wrote: This may be implemented, I believe some people run Galaxy on the cluster, Yes, but AFAIK, most cluster job runners use some kind of file staging (copying) into local storage on the compute nodes OR, require you do have the data uploaded in the galaxy file area, and to have this file are availble NFS mounted on all compute nodes. It would be very interesting if there is an existing solution for running jobs on files without moving/copying them at all, though! Best // Samuel Galaxy normally operates on files stored in the database/files folder. If your Galaxy instance has access to the files you need on your parallel fs, I guess you could start by writing a tool that creates links to your files when given the path to the input file. Another tool may then move the dataset into the desired place while creating a link in the database folder. Sounds like a hack to me, but may work. cheers, jorrit On Wed, Nov 14, 2012 at 2:52 PM, Samuel Lampa samuel.la...@gmail.com mailto:samuel.la...@gmail.com wrote: Hi, We are looking into ways to integrate galaxy into the workflows of users at our cluster, with lots of NGS users running all and any kind of analyses on their typically huge amounts of data. For this we use a parallel file system, available on all compute nodes. This file system, although approx 1PB in size, is constantly filling up, and thus we are not very attracted by the idea of copying files into/out of galaxy for each analysis. Thus, we would be interested to know what are the options for working with existing/external(to galaxy) file systems? Eg. would it be possible to link files into some kind of galaxy file system (I'm not totally clear about how galaxy stores it's data, although I found out that stuff is created in database/files), from outside? ... or is there any work going on for selecting any file system path as input in galaxy workflows? ... or any other hints? As said, I'm quite new to galaxy, trying to grok my head around how we can use it, so all hints are welcome. Best Regards // Samuel -- Developer at SNIC-UPPMAX www.uppmax.uu.se http://www.uppmax.uu.se Developer at Dept of Pharm Biosciences www.farmbio.uu.se http://www.farmbio.uu.se Twitter - twitter.com/samuellampa http://twitter.com/samuellampa Blog - saml.rilspace.org http://saml.rilspace.org G+ - gplus.to/saml http://gplus.to/saml ___ 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/ ___ 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/
Re: [galaxy-dev] Can't edit galaxy workflow
Make sure that you are pulling from galaxy-central and not galaxy-dist. I believe something like: hg pull -r rev# -u http://bitbucket.org/galaxy/galaxy-central should work. The problem may be that you are pointing to galaxy-dist by default, which will not know about that revision (yet). -Scott - Original Message - Thanks a lot Dannon, for your reply. But hg keeps saying following when I try to pull: abort: unknown revision '5013377e0bf7'! Is there any other way of manually getting it? (Sorry, I'm not an expert on those new SCMs) Sanjar. On 11/13/2012 06:33 PM, Dannon Baker wrote: Sanjar, This is fixed as of 5013377e0bf7. This may not be in the next distribution, but will be in the one after that. Of course, you can manually pull the change from galaxy-central at any time. -Dannon On Nov 13, 2012, at 9:45 AM, Sanjarbek Hudaiberdiev hudai...@icgeb.org wrote: I tried to reply to similar posts, but couldn't figure out how to do it. So posting again: Galaxy giving this error when editing workflow, just after creating workflow from existing history: URL: http://localhost/galaxy/workflow/load_workflow?id=df7a1f0c02a5b08e_=1352817462148 Module weberror.evalexception.middleware:364 in respond app_iter = self.application(environ, detect_start_response) Module paste.debug.prints:98 in __call__ environ, self.app) Module paste.wsgilib:539 in intercept_output app_iter = application(environ, replacement_start_response) Module paste.recursive:80 in __call__ return self.application(environ, start_response) Module paste.httpexceptions:632 in __call__ return self.application(environ, start_response) Module galaxy.web.framework.base:160 in __call__ body = method( trans, **kwargs ) Module galaxy.web.framework:73 in decorator return simplejson.dumps( func( self, trans, *args, **kwargs ) ) Module galaxy.webapps.galaxy.controllers.workflow:733 in load_workflow 'tooltip': module.get_tooltip( static_path=url_for( '/static' ) ), Module galaxy.workflow.modules:258 in get_tooltip return self.tool.help.render( static_path=static_path ) AttributeError: 'NoneType' object has no attribute 'render' Could anyone help me to solve this problem? Thanks, Sanjar. ___ 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/ ___ 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/ ___ 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/
[galaxy-dev] Galaxy November 14, 2012 Distribution News Brief
*Galaxy November 14, 2012 Distribution News Brief http://wiki.galaxyproject.org/News/2012_11_14_DistributionNewsBrief* * Complete News Brief http://wiki.galaxyproject.org/DevNewsBriefs/2012_11_14 * *Highlights:* * *NGS: Picard (beta)* have moved from the *Galaxy distribution https://bitbucket.org/galaxy/galaxy-dist* to the*Galaxy Main Tool Shed* http://toolshed.g2.bx.psu.edu/. * The *Galaxy Project* is now using /Sphinx http://sphinx-doc.org/ Python/ to document the *galaxy-central http://galaxy-central.readthedocs.org* and *galaxy-dist* http://galaxy-dist.readthedocs.org code base. * The *Intergalactic Utilities Commission* http://wiki.g2.bx.psu.edu/ReviewingToolShedRepositories will soon begin reviewing repositories in the *Galaxy Main Tool Shed http://toolshed.g2.bx.psu.edu/* (better repos, better tools) * *Tool Shed http://toolshed.g2.bx.psu.edu/* *best practice* advice: a single tool or a suite of tools per repository? http://wiki.galaxyproject.org/AToolOrASuitePerRepository * *Tophat http://tophat.cbcb.umd.edu/*, *Tophat2 http://tophat.cbcb.umd.edu/manual.html*, and *Cuffdiff http://cufflinks.cbcb.umd.edu/manual.html#cuffdiff* *updated* to accept gene annotations in *GFF3 http://wiki.galaxyproject.org/Learn/Datatypes#GFF3* format. * Multiple *enhancements* to the *API* http://wiki.galaxyproject.org/DevNewsBriefs/2012_11_14#APItargeting user and history actions. * Plus *updates to* *CloudLaunch http://usegalaxy.org/cloud*, new *Security Fixes* http://wiki.galaxyproject.org/DevNewsBriefs/2012_11_14#Security_Fixes, and several usability enhancements for *Datasets*, *Datatypes*, *Tools*, and *Tool Shed* functions. / http://getgalaxy.org/// /http://bitbucket.org/galaxy/galaxy-dist/ /http://galaxy-dist.readthedocs.org/ new: $ hg clone http://www.bx.psu.edu/hg/galaxy galaxy-dist upgrade: $ hg pull -u -r 5dcbbdfe1087 *Thanks for using Galaxy!* Jennifer Jackson http://wiki.galaxyproject.org/JenniferJackson the Galaxy Team http://wiki.galaxyproject.org/Galaxy%20Team /http://galaxyproject.org/ ___ 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/
[galaxy-dev] Join (Operate on Genomic Intervals)
Hello, I am using the Galaxy public server to conduct a join operating on genomic intervals. However, my job has not completed in over 2 days. Is there a bug, and what can I do to speed up the process? Thank you, George ___ 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/
[galaxy-dev] Galaxy-related job opening at the FMI in Basel, Switzerland
Hi I apologize for abusing the list for a job add: We are looking for a R/Bioconductor person which is familiar with Galaxy to help us expanding our sets of NGS tools in Galaxy, see http://www.fmi.ch/Careers/JobDetails.html?jobID=158 Please feel free to contact me for more details Regards, Hans-Rudolf Hans-Rudolf Hotz, PhD Bioinformatics Support Friedrich Miescher Institute for Biomedical Research Maulbeerstrasse 66 4058 Basel/Switzerland ___ 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/
[galaxy-dev] ftp file upload error question
Dear Galaxy Devs, I have tried to upload 2 files though the ftp upload using FileZila. I have been getting the following error: Response: 220 ProFTPD 1.3.4b Server (Galaxy Main Server FTP) [:::128.118.250.4] Command:USER ** Response: 331 Password required for ** Command:PASS * Response: 530 Sorry, the maximum number of clients (3) for this user are already connected. Error: Critical error Error: Could not connect to server I have seen that some one else had this issue and posted online. What should I do to try to get around this issue? Thank you Tony Szempruch ___ 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/
