[galaxy-dev] Displayed versions of tools in Galaxy
Hi guys, I wasn't sure if I should send this one to galaxy-user. I have just confused myself about the versions of tools displayed within Galaxy. If I select the TopHat tool, the tool UI says Tophat for Illumina (version 1.5.0). After I have run the job, the step panel in the History window says Info: TopHat v1.4.1 If I select the Cufflinks tool, the tool UI says Cufflinks (version 0.0.5) After running the job, the step panel says Info: cufflinks v1.3.0. Looking at the xml files, it does look like the version displayed before running is the wrapper and the version displayed on the resulting dataset is that of the command-line tool. tool id=tophat name=Tophat for Illumina version=1.5.0 !-- Wrapper compatible with Tophat versions 1.3.0 to 1.4.1 -- tool id=cufflinks name=Cufflinks version=0.0.5 !-- Wrapper supports Cufflinks versions v1.3.0 and newer -- So looking at the XML it's very clear, but from the versions displayed in Galaxy I was completely confused, particularly since the two tophat version numbers happened to be similar (1.4.1 and 1.5.0). Maybe we should change it so that when Galaxy says version it is always explicit about whether it's wrapper version or just version? It also seems like there's no way for a user to discover the command-line tool version without actually running the tool (or is there)? Is this because Galaxy itself does not know this information? All this came about because I'm trying to specify to users which versions of tools my exported Workflow was built with, and I'm not sure how to do it without confusing them. Thanks, Clare -- Clare Sloggett Research Fellow / Bioinformatician Life Sciences Computation Centre Victorian Life Sciences Computation Initiative University of Melbourne, Parkville Campus 187 Grattan Street, Carlton, Melbourne Victoria 3010, Australia Ph: 03 903 53357 M: 0414 854 759 ___ 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] Trying to Run MegaBlast
On Monday, December 10, 2012, Jeremy Goecks wrote: Decompress and unpack the file and you'll find the relevant files (though everything now has extensions with p* rather than n*); add an entry to blastdb pointing to the directory with these files and you should be good to go. J. Not quite - blastdb.loc is for nucleotide databases only (needed for megablast), and NR is proteins. For that use blastdb_p.loc and blastp or blastx from the NCBI BLAST+ wrappers. Peter ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] Displayed versions of tools in Galaxy
This has been confusing for me also. Perhaps if we had a way to distinguish between the two by prefixing the tool version of a wrapper with w0.0.5 and the actual tool version with v1.3.0? I think that Galaxy determines the versions of the tools it loads at startup in lib/galaxy/tools/__init__.py ToolBox::__add_tool_to_tool_panel() - log.debug( Loaded tool id: %s, version: %s into tool panel. % ( tool.id, tool.version ) ) - Also check out class Tool which is in the same file...probably requires a bit more code reading to fully understand the underlying layers in question... On Tue, Dec 11, 2012 at 6:43 PM, Clare Sloggett s...@unimelb.edu.au wrote: Hi guys, I wasn't sure if I should send this one to galaxy-user. I have just confused myself about the versions of tools displayed within Galaxy. If I select the TopHat tool, the tool UI says Tophat for Illumina (version 1.5.0). After I have run the job, the step panel in the History window says Info: TopHat v1.4.1 If I select the Cufflinks tool, the tool UI says Cufflinks (version 0.0.5) After running the job, the step panel says Info: cufflinks v1.3.0. Looking at the xml files, it does look like the version displayed before running is the wrapper and the version displayed on the resulting dataset is that of the command-line tool. tool id=tophat name=Tophat for Illumina version=1.5.0 !-- Wrapper compatible with Tophat versions 1.3.0 to 1.4.1 -- tool id=cufflinks name=Cufflinks version=0.0.5 !-- Wrapper supports Cufflinks versions v1.3.0 and newer -- So looking at the XML it's very clear, but from the versions displayed in Galaxy I was completely confused, particularly since the two tophat version numbers happened to be similar (1.4.1 and 1.5.0). Maybe we should change it so that when Galaxy says version it is always explicit about whether it's wrapper version or just version? It also seems like there's no way for a user to discover the command-line tool version without actually running the tool (or is there)? Is this because Galaxy itself does not know this information? All this came about because I'm trying to specify to users which versions of tools my exported Workflow was built with, and I'm not sure how to do it without confusing them. Thanks, Clare -- Clare Sloggett Research Fellow / Bioinformatician Life Sciences Computation Centre Victorian Life Sciences Computation Initiative University of Melbourne, Parkville Campus 187 Grattan Street, Carlton, Melbourne Victoria 3010, Australia Ph: 03 903 53357 M: 0414 854 759 ___ 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] some problem with the fastq interlacer
Hi all, I ran the fastq interlacer with a fastq encoding 1.8+ data, the interlacer seems do not reganize the name of the pair-end reads, and treat the pair-end reads as non-pair-edn reads. Best regards___ 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] Public Tool Shed Error
Hi, I have been using the tool shed recently and come across a problem. When a searching for valid tools within the Public Tool Shed, it seems that if the search should return nothing found, it is instead displaying a Server Error page instead. For example: http://toolshed.g2.bx.psu.edu/repository/find_tools?tool_name=wibble Is currently returning an HTTP status code of 500 Internal Server Error. [cid:image001.png@01CDD78F.1E47CE90] --- Adam Carr Linux Support Developmnent E adam.c...@nbi.ac.uk T +44 1603 450161 W jic.ac.uk ifr.ac.uk tgac.ac.uk tsl.ac.uk NBI Partnership Ltd Norwich Research Park Norwich NR4 7UH The NBI Partnership Ltd provides non-scientific services to the Institute of Food Research, the John Innes Centre, The Genome Analysis Centre and The Sainsbury Laboratory inline: image001.png___ 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] Server Error / Edit attribut of a dataset generated by a tool
Hello, One of my users gets the following message when he wishes to edit the attribute of a dataset which is generated by using a tool (same problem as it is a tool provided by Galaxy or a tool coded by us). Do you have any idea? Thanks in advance, Sarah Maman URL: http://sigenae-workbench.toulouse.inra.fr/galaxy/datasets/b9580783e2098a2b/edit File '/usr/local/bioinfo/src/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/exceptions/errormiddleware.py', line 143 in __call__ app_iter = self.application(environ, start_response) File '/usr/local/bioinfo/src/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/debug/prints.py', line 98 in __call__ environ, self.app) File '/usr/local/bioinfo/src/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/wsgilib.py', line 539 in intercept_output app_iter = application(environ, replacement_start_response) File '/usr/local/bioinfo/src/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response) File '/usr/local/bioinfo/src/galaxy/galaxy-dist/lib/galaxy/web/framework/middleware/remoteuser.py', line 111 in __call__ return self.app( environ, start_response ) File '/usr/local/bioinfo/src/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py', line 632 in __call__ return self.application(environ, start_response) File '/usr/local/bioinfo/src/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 160 in __call__ body = method( trans, **kwargs ) File '/usr/local/bioinfo/src/galaxy/galaxy-dist/lib/galaxy/web/controllers/dataset.py', line 600 in edit refresh_frames=refresh_frames ) File '/usr/local/bioinfo/src/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 722 in fill_template return self.fill_template_mako( filename, **kwargs ) File '/usr/local/bioinfo/src/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 733 in fill_template_mako return template.render( **data ) File '/usr/local/bioinfo/src/galaxy/galaxy-dist/eggs/Mako-0.4.1-py2.6.egg/mako/template.py', line 296 in render return runtime._render(self, self.callable_, args, data) File '/usr/local/bioinfo/src/galaxy/galaxy-dist/eggs/Mako-0.4.1-py2.6.egg/mako/runtime.py', line 660 in _render **_kwargs_for_callable(callable_, data)) File '/usr/local/bioinfo/src/galaxy/galaxy-dist/eggs/Mako-0.4.1-py2.6.egg/mako/runtime.py', line 692 in _render_context _exec_template(inherit, lclcontext, args=args, kwargs=kwargs) File '/usr/local/bioinfo/src/galaxy/galaxy-dist/eggs/Mako-0.4.1-py2.6.egg/mako/runtime.py', line 718 in _exec_template callable_(context, *args, **kwargs) File '/usr/local/bioinfo/src/galaxy/galaxy-dist/database/compiled_templates/base.mako.py', line 42 in render_body __M_writer(unicode(next.body())) File '/usr/local/bioinfo/src/galaxy/galaxy-dist/database/compiled_templates/dataset/edit_attributes.mako.py', line 95 in render_body __M_writer(filters.html_escape(unicode(data.info ))) UnicodeDecodeError: 'ascii' codec can't decode byte 0xc3 in position 31: ordinal not in range(128) ___ 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] Impossible to add a (new) tool in a workflow (in edition mode)
Hello, For one of my tools that I have added to my local instance of Galaxy, I can not add this tool in the editing workflow. When I click on the tool name in the tools windows on the left, it does not appear in the editing workflow. Do you have any idea? Thank you in advance, Sarah Maman ___ 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] Installation issue on EC2
Hi, Dannon. Thanks for the tip. No, I was not reusing the cluster names exactly to avoid previous data to mess up with my fresh new deployments. There were indeed about 8 buckets referring to clusters that don`t exist anymore. Write now I can`t remove my current cluster by the web interface because it never comes up. What would be the safe way to allow you to see my instance? Cheers, F. -Original Message- From: Dannon Baker [mailto:dannonba...@me.com] Sent: Monday, December 10, 2012 3:36 PM To: Fabiano Lucchese Cc: Brad Chapman; galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] Installation issue on EC2 On Dec 10, 2012, at 6:17 PM, Fabiano Lucchese fabiano.lucch...@hds.com wrote: I appreciate your effort to help me, but it looks like my AWS account has some serious hidden issues going on. I completely wiped out CloudMan/Galaxy instances from my EC2 environment as well as their volumes, and waited a couple of hours for the instances to disappear from the instances list. After that, I repeated the whole process twice, trying to create a Galaxy cluster with 10 and then 15 Gb of storage space, but the result was equally frustrating with some minor differences. PS: Dannon, one thing that intrigues me is how the web form manages to find out the names of the previous clusters that I tried to instantiate. Where does it get this information from if all the respective instances have been terminated and wiped out? Did you reuse the same cluster name for either of these? This would explain conflicting settings - there's more to a cluster than just the running instances and persistent volumes. That form retrieves those listings from the S3 buckets in your account. Each cluster has its own S3 bucket -- you can identify them with the yourCluster.clusterName files in the listing. These contain lots of information about your galaxy clusters (references to volumes, universe settings, etc.), and if you're attempting to eliminate a cluster completely (you never want to restart it and don't want *anything* preserved), you should delete the buckets referring to them as well. When you ask Cloudman to terminate and remove a cluster permanently, it removes all of this for you, and I'd recommend always using the interface to do this and not doing it manually. Definitely let me know what else I can do to help. If you have a running instance you'd like for me to look at directly I'd be happy to do so -- maybe this is indeed some weird issue that we can work around better. ___ 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] About the output
Thx Hans-Rudolf But I did write /output in the xml file Here is just a mistake In ~in ~/database/files/ folder there is just a folder named 000 and there are lots of *.dat file in 000 folder From: Hans-Rudolf Hotz h...@fmi.ch To: Chenhao windfl...@yahoo.co.uk Cc: galaxy-dev@lists.bx.psu.edu Sent: Tuesday, 11 December 2012, 8:36 Subject: Re: [galaxy-dev] About the output On 12/10/2012 11:26 PM, Chenhao wrote: I made a galaxy tool which is just create a txt file. When I use this tool , I wish to let it show the detail of the txt. In the xml file I use : output data name=”test” format=”txt”output/ I assume, this should be written: outputs data name=”test” format=”txt” / /outputs I am surprised, your tool doesn't create an error much earlier. How does the actual data file (in ~/database/files/ ) in look like? Regards, Hans-Rudolf But it does not work, when I click the “eye” button in galaxy, a download dialog appear, but it is just a empty file. Could somebody tell me what should I do , I want show the txt detail in the galaxy. ___ 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] Impossible to add a (new) tool in a workflow (in edition mode)
Thanks Danon, But I have no error generated in my error log file (logs of run.sh): [11/Dec/2012:16:39:09 +0200] GET /galaxy/workflow HTTP/1.1 200 - http://URL/galaxy/root; Mozilla/5.0 (Windows NT 6.1; WOW64; rv:17.0) Gecko/20100101 Firefox/17.0 IP - - [11/Dec/2012:16:39:11 +0200] GET /galaxy/workflow/editor?id=7085c9c37b8829fc HTTP/1.1 200 - http://URL/galaxy/workflow; Mozilla/5.0 (Windows NT 6.1; WOW64; rv:17.0) Gecko/20100101 Firefox/17.0 IP - - [11/Dec/2012:16:39:12 +0200] GET /galaxy/workflow/get_datatypes?_=1355240375711 HTTP/1.1 200 - http://URL/galaxy/workflow/editor?id=7085c9c37b8829fc; Mozilla/5.0 (Windows NT 6.1; WOW64; rv:17.0) Gecko/20100101 Firefox/17.0 IP - - [11/Dec/2012:16:39:12 +0200] GET /galaxy/workflow/load_workflow?id=7085c9c37b8829fc_=1355240375756 HTTP/1.1 200 - http://URL/galaxy/workflow/editor?id=7085c9c37b8829fc; Mozilla/5.0 (Windows NT 6.1; WOW64; rv:17.0) Gecko/20100101 Firefox/17.0 IP - - [11/Dec/2012:16:39:17 +0200] GET /galaxy/workflow/get_new_module_info?type=tooltool_id=BWA_miRNA_=true HTTP/1.1 200 - http://URL/galaxy/workflow/editor?id=7085c9c37b8829fc; Mozilla/5.0 (Windows NT 6.1; WOW64; rv:17.0) Gecko/20100101 Firefox/17.0 Others actions are listed by not my click on this tool's name. Is paster.log file a default file of Galaxy? Where could I find this file ? Sarah Dannon Baker a écrit : Do you see any errors in Galaxy's paster.log, or in the javascript console? -Dannon On Dec 11, 2012, at 8:40 AM, Sarah Maman sarah.ma...@toulouse.inra.fr wrote: Hello, For one of my tools that I have added to my local instance of Galaxy, I can not add this tool in the editing workflow. When I click on the tool name in the tools windows on the left, it does not appear in the editing workflow. Do you have any idea? Thank you in advance, Sarah Maman ___ 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] Impossible to add a (new) tool in a workflow (in edition mode)
The paster.log is just the file for the output you've copied below when running daemonized -- if you're running in the foreground it just gets sent there instead of to the file. So, no obvious errors there. Could you check for javascript console errors? And, if you'd like, feel free to send the tool xml to me directly and I'll try to see if I can reproduce the issue. -Dannon On Dec 11, 2012, at 10:47 AM, Sarah Maman sarah.ma...@toulouse.inra.fr wrote: Thanks Danon, But I have no error generated in my error log file (logs of run.sh): [11/Dec/2012:16:39:09 +0200] GET /galaxy/workflow HTTP/1.1 200 - http://URL/galaxy/root; Mozilla/5.0 (Windows NT 6.1; WOW64; rv:17.0) Gecko/20100101 Firefox/17.0 IP - - [11/Dec/2012:16:39:11 +0200] GET /galaxy/workflow/editor?id=7085c9c37b8829fc HTTP/1.1 200 - http://URL/galaxy/workflow; Mozilla/5.0 (Windows NT 6.1; WOW64; rv:17.0) Gecko/20100101 Firefox/17.0 IP - - [11/Dec/2012:16:39:12 +0200] GET /galaxy/workflow/get_datatypes?_=1355240375711 HTTP/1.1 200 - http://URL/galaxy/workflow/editor?id=7085c9c37b8829fc; Mozilla/5.0 (Windows NT 6.1; WOW64; rv:17.0) Gecko/20100101 Firefox/17.0 IP - - [11/Dec/2012:16:39:12 +0200] GET /galaxy/workflow/load_workflow?id=7085c9c37b8829fc_=1355240375756 HTTP/1.1 200 - http://URL/galaxy/workflow/editor?id=7085c9c37b8829fc; Mozilla/5.0 (Windows NT 6.1; WOW64; rv:17.0) Gecko/20100101 Firefox/17.0 IP - - [11/Dec/2012:16:39:17 +0200] GET /galaxy/workflow/get_new_module_info?type=tooltool_id=BWA_miRNA_=true HTTP/1.1 200 - http://URL/galaxy/workflow/editor?id=7085c9c37b8829fc; Mozilla/5.0 (Windows NT 6.1; WOW64; rv:17.0) Gecko/20100101 Firefox/17.0 Others actions are listed by not my click on this tool's name. Is paster.log file a default file of Galaxy? Where could I find this file ? Sarah Dannon Baker a écrit : Do you see any errors in Galaxy's paster.log, or in the javascript console? -Dannon On Dec 11, 2012, at 8:40 AM, Sarah Maman sarah.ma...@toulouse.inra.fr wrote: Hello, For one of my tools that I have added to my local instance of Galaxy, I can not add this tool in the editing workflow. When I click on the tool name in the tools windows on the left, it does not appear in the editing workflow. Do you have any idea? Thank you in advance, Sarah Maman ___ 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] Impossible to add a (new) tool in a workflow (in edition mode)
Dannon, Here is myjavascript console errors : SyntaxError: missing ) after argument list : /* ool( 'sm_miRNA_join_annot', '* Construction de la matrice d'annotations' ) */ /*editor...8829fc# (ligne 1, col. 60)*/ I replaced this syntax Construction de la matrice d'annotations by the latter Construction de la matrice d annotations, and thank you, now it works! Thanks a lot, Sarah Dannon Baker a écrit : The paster.log is just the file for the output you've copied below when running daemonized -- if you're running in the foreground it just gets sent there instead of to the file. So, no obvious errors there. Could you check for javascript console errors? And, if you'd like, feel free to send the tool xml to me directly and I'll try to see if I can reproduce the issue. -Dannon On Dec 11, 2012, at 10:47 AM, Sarah Maman sarah.ma...@toulouse.inra.fr wrote: Thanks Danon, But I have no error generated in my error log file (logs of run.sh): [11/Dec/2012:16:39:09 +0200] GET /galaxy/workflow HTTP/1.1 200 - http://URL/galaxy/root; Mozilla/5.0 (Windows NT 6.1; WOW64; rv:17.0) Gecko/20100101 Firefox/17.0 IP - - [11/Dec/2012:16:39:11 +0200] GET /galaxy/workflow/editor?id=7085c9c37b8829fc HTTP/1.1 200 - http://URL/galaxy/workflow; Mozilla/5.0 (Windows NT 6.1; WOW64; rv:17.0) Gecko/20100101 Firefox/17.0 IP - - [11/Dec/2012:16:39:12 +0200] GET /galaxy/workflow/get_datatypes?_=1355240375711 HTTP/1.1 200 - http://URL/galaxy/workflow/editor?id=7085c9c37b8829fc; Mozilla/5.0 (Windows NT 6.1; WOW64; rv:17.0) Gecko/20100101 Firefox/17.0 IP - - [11/Dec/2012:16:39:12 +0200] GET /galaxy/workflow/load_workflow?id=7085c9c37b8829fc_=1355240375756 HTTP/1.1 200 - http://URL/galaxy/workflow/editor?id=7085c9c37b8829fc; Mozilla/5.0 (Windows NT 6.1; WOW64; rv:17.0) Gecko/20100101 Firefox/17.0 IP - - [11/Dec/2012:16:39:17 +0200] GET /galaxy/workflow/get_new_module_info?type=tooltool_id=BWA_miRNA_=true HTTP/1.1 200 - http://URL/galaxy/workflow/editor?id=7085c9c37b8829fc; Mozilla/5.0 (Windows NT 6.1; WOW64; rv:17.0) Gecko/20100101 Firefox/17.0 Others actions are listed by not my click on this tool's name. Is paster.log file a default file of Galaxy? Where could I find this file ? Sarah Dannon Baker a écrit : Do you see any errors in Galaxy's paster.log, or in the javascript console? -Dannon On Dec 11, 2012, at 8:40 AM, Sarah Maman sarah.ma...@toulouse.inra.fr wrote: Hello, For one of my tools that I have added to my local instance of Galaxy, I can not add this tool in the editing workflow. When I click on the tool name in the tools windows on the left, it does not appear in the editing workflow. Do you have any idea? Thank you in advance, Sarah Maman ___ 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] Mutation/SNP detection RNA-Seq
Hi, I am trying to look mutations/SNPs in RNA-Seq data. Can anyone suggest me a workflow in Galaxy on how to detect SNPs and mutations Thanks in advance Suz ___ 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] Downloading datasets without username/password when login is required
Hi, Is it possible to download a dataset when require_login=True in universe_wsgi.ini using the API key? Thanks, Ilya ___ 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] Impersonate a User
Hi guys, I tried the impersonate a user feature, but I don't know how to stop impersonating a user? I tried going back to the impersonate a user feature and selecting myself but it's not clear if it changed anything, and I no longer see the History items I had before I did the impersonation. Thanks, Greg ___ 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] Re-installing error persists
Hi Franco, I'm not quite sure what page you'r eon, but if you're looking at the page that has the tool dependency with the error status, you should be able to click the link of the tool dependency and see the error, log, etc. If this is not the page you're referring to, then I'll have to take a look and see if I can reproduce this. I'm swamped right now, but I'll get to this as soon as possible. Greg Von Kuster On Dec 11, 2012, at 1:17 AM, Franco Caramia wrote: Hi Greg, list When installing a tool dependency, and the Installation Status shows : Error In what log would the actual error be specified?? Thanks, Franco On 5/12/12 9:10 PM, Greg Von Kuster g...@bx.psu.edu wrote: If you have not yet updated your Galaxy instance to the revision from the galaxy-dist repository in bitbucket, then that is most likely the cause of the behavior you are seeing. Greg Von Kuster On Dec 5, 2012, at 12:52 AM, Franco Caramia wrote: Re-installing error persists Hi Greg, I have now modified the tool_dependencies.xml thank you for that.. I still have problems re-installing the tool... (need to reinstall to update the tool dependency and test it correctly) Is the reinstalling failure related to my galaxy version?? Here is the error: Server Error URL: http://bioinf-galaxy/admin_toolshed/browse_repositories?operation=activate+or+reinstallid=88ee2d7021e4dc1a Module paste.exceptions.errormiddleware:143 in __call__ http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=activate+or+reinstallid=88ee2d7021e4dc1a# app_iter = self.application(environ, start_response) Module paste.debug.prints:98 in __call__ http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=activate+or+reinstallid=88ee2d7021e4dc1a# environ, self.app) Module paste.wsgilib:539 in intercept_output http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=activate+or+reinstallid=88ee2d7021e4dc1a# app_iter = application(environ, replacement_start_response) Module paste.recursive:80 in __call__ http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=activate+or+reinstallid=88ee2d7021e4dc1a# return self.application(environ, start_response) Module paste.httpexceptions:632 in __call__ http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=activate+or+reinstallid=88ee2d7021e4dc1a# return self.application(environ, start_response) Module galaxy.web.framework.base:160 in __call__ http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=activate+or+reinstallid=88ee2d7021e4dc1a# body = method( trans, **kwargs ) Module galaxy.web.framework:184 in decorator http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=activate+or+reinstallid=88ee2d7021e4dc1a# return func( self, trans, *args, **kwargs ) Module galaxy.web.controllers.admin_toolshed:350 in browse_repositories http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=activate+or+reinstallid=88ee2d7021e4dc1a# return self.reselect_tool_panel_section( trans, **kwd ) Module galaxy.web.framework:184 in decorator http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=activate+or+reinstallid=88ee2d7021e4dc1a# return func( self, trans, *args, **kwargs ) Module galaxy.web.controllers.admin_toolshed:1352 in reselect_tool_panel_section http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=activate+or+reinstallid=88ee2d7021e4dc1a# status=status ) Module galaxy.web.framework:746 in fill_template http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=activate+or+reinstallid=88ee2d7021e4dc1a# return self.fill_template_mako( filename, **kwargs ) Module galaxy.web.framework:757 in fill_template_mako http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=activate+or+reinstallid=88ee2d7021e4dc1a# return template.render( **data ) Module mako.template:296 in render http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=activate+or+reinstallid=88ee2d7021e4dc1a# return runtime._render(self, self.callable_, args, data) Module mako.runtime:660 in _render http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=activate+or+reinstallid=88ee2d7021e4dc1a# **_kwargs_for_callable(callable_, data)) Module mako.runtime:692 in _render_context http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=activate+or+reinstallid=88ee2d7021e4dc1a# _exec_template(inherit, lclcontext, args=args, kwargs=kwargs) Module mako.runtime:718 in _exec_template http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=activate+or+reinstallid=88ee2d7021e4dc1a# callable_(context, *args, **kwargs) Module _base_mako:42 in render_body
[galaxy-dev] Extra files saved outside of Galaxy's history?
Hi all, I have a pipeline involving a series of scripts, which creates directories (and many subdirectories), that I'd like to wrap for use in Galaxy. Although the contents of the folders are not the primary output of the pipeline, (and I don't want them as history items), I'd still like them to be accessible for users to double-check the contents if they so desire. However, I'm not sure where a good place to create/persist the folders would be. Although I'm running a local install on my own machine for the moment, the goal will be to move to a cluster in the near future. Does anyone have experience with this kind of thing or have any ideas? Apologies if I've missed something; I haven't found anything related on the mailing list or the wiki, except for this thread that suggests disabling the cleanup method of the JobWrapper for debugging purposes: http://dev.list.galaxyproject.org/persisting-job-working-directory-td413 8922.html. Thanks for your consideration, Ann ___ 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] problem with uploading data
Hi Nate, I loaded the file named s_6_1_sequence.txt.gz (Illumni file) under the login name abdul.ban...@uconn.edumailto:abdul.ban...@uconn.edu as FTP.ftp://ftp.R Whenever I am trying to load it as history so that I can run it for analysis, the file upload is showing error and massage comes as data cannot be uncompressed. I have been trying to contact you guys from five days now. In one email you told me as soon as you have ftp transfer let me know. Could you check my file and see what is the problem. Thanking in anticipation. Postdoc at Uconn Rouf Banday ___ 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] Impersonate a User
Hi Greg, Try clicking the logout button. That should logout of the user you are impersonating and back into you. Although, this does have a few quirks also and may log you right out. Don't forget that when you are impersonating someone the history may not be automatically loaded and you will have to do that manually. Cheers, Ed ___ 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] Installing Job Runners on a Cluster
Hi all, I could use some help getting DMRAA to run. We already have a galaxy instance with pbs running, but I'd like to connect to Torque using dmraa because we eventually intend to port over to a different resource manager. I've followed these instructions: http://apps.man.poznan.pl/trac/pbs-drmaa/wiki#Introduction http://wiki.galaxyproject.org/Admin/Config/Performance/Cluster Got dmraa installed and exported a path in my shell config: (PREFIX is long so I omitted it) DRMAA_LIBRARY_PATH=PREFIX/drmaa/lib/libdrmaa.so.1.0.12 in my universe_wsgi.ini: start_job_runners = drmaa default_cluster_job_runner = drmaa://-q tstgalxy -V/ addValue = drmaa:/// Here's my pbs_drmaa.conf: wait_thread: 0, pool_delay: 5, keep_completed: 60, user_state_dir: PREFIX/%s/jobs, I tried something simple like the add value tool. When I run it, I get the following error state: perl: warning: Setting locale failed. perl: warning: Please check that your locale settings: LANGUAGE = (unset), LC_ALL = (unset), LC_CTYPE = en_US, LANG = C are supported and installed on your system. perl: warning: Falling back to the standard locale (C). The output file is actually correct, Galaxy just thinks there's an error. I get 2 files in user_state_dir with a job number and .started (empty) and .exitcode (0). Sounds like an env issue? If I run the perl script generated in the .sh file, it works fine. Output as expected. If I use local:/// it works fine with no error. I couldn't find any documentation on how to actually link dmraa to torque. Am I missing something major? Thanks in advance, Carrie Ganote ___ 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] Job is waiting to run
I have a local galaxy server, and I built a workflow, it got stuck in one step in the middle. The computer is a 64 cores server, and no other jobs running in this server. Any idea how to trouble shooting? Thanks, Fenglou ___ 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-bugs] galaxy.genenetwork.org
有olb吃掉 Yunbo Xu 817 Hickman rd, Apt A-23 Augusta,GA 30904 706 - 877 3892 On Dec 11, 2012, at 4:13 PM, Lei Yan leiyan2...@gmail.com wrote: Dear Dannon and James, On Mon, Dec 10, 2012 at 8:04 AM, Dannon Baker dannonba...@me.com wrote: • I installed a Cloud Galaxy instance one month ago, and a user reported that it still has some problems. At that time, I found that it can be upgraded to new version in the administration page, so I did so. But its log showed that it “has error”, and the service cannot start. I then tried to reboot the machine, but Galaxy still could not start and the service is not responding. Can you share the cloud log? This would be the best place to look to find out what the errors are. For this Cloud Galaxy instance, I can boot it, but the Galaxy service could not start. So I logged in this server by SSH to get the log files from file system. And I found a strange thing, this server doesn’t mount the three partitions of Galaxy (/dev/xvdg1, /dev/xvdg2, /dev/xvdg3) automatically when booting. I thought this should be automatically, so need I setup something for mounting automatically? I attached the log files, and they are compressed to a zip file “1.log.zip”. • Then I tried to build a new Cloud Galaxy, but after trying at least 8 times it still didn’t work. Each time, after I launched the Cloud Galaxy instance, even its State is running and the Status Checks is 2/2 checks passed”, but it would still not respond if I opened “http://**.amazonaws.com/cloud”; I never even get to Welcome to Galaxy on the cloud. Can you share any more information about this? Can you confirm that you're using the supported AMI, have launched with the correct security groups, etc? For future reference, just using usegalaxy.org/cloudlaunch is probably the easiest way to make sure you avoid any launch issues. Are you able to SSH in to the instance? I am using ami-78a00411. I attached three other files, and they are the AMI I am using, the security groups I am using, and the instance configurations. I never used this usegalaxy.org/cloudlaunch. But it looks good, and I will try this later. Yes, I can login this instance by SSH. But I never even get to Welcome to Galaxy on the cloud. Could you please give us some suggestions or let us know who we should contact about this issue? Sending email directly to galaxy-bugs, as you have, for stuff you'd rather not share with the wider community is the best bet. For anything that isn't sensitive, emailing galaxy-dev is useful if you're working with customized or local/cloud installs. I cannot find any telephone number on the Galaxy community pages, and it would be better if I could talk to someone about the problem over the phone. Would it be helpful to chat over IRC and debug this? See the IRC Channel information on http://wiki.galaxyproject.org/Get%20Involved. -Dannon Thanks so much for your help. Lei Yan leiyan2...@gmail.com UTHSC 1.log.zip 2.ami.png 2.instanceconfiguration.png 2.securitygroups.png ___ 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] Tool dependency installation fail, any documentation?
Hi list, I got the following tool_dependencies.xml file failing: ?xml version=1.0? tool_dependency package name=bedtools version=2.17.0 install version=1.0 actions action type=download_by_url target_filename=bedtools-2.17.0.tar. gz http://bedtools.googlecode.com/files/BEDTools.v2.17.0.tar.gz/action action type=shell_commandmake clean/action action type=shell_commandmake all/action action type=move_directory_files source_directorybin/source_directory destination_directory$INSTALL_DIR/bin/destination_directory /action action type=set_environment environment_variable name=PATH action=prepend_to$INSTALL_DI R/bin/environment_variable /action /actions /install readme GCC version 4.1 or greater is recommended. 3.x versions will typically not c ompile BEDTools /readme /package /tool_dependency The error given is: # make clean STDOUT # # make clean STDERR make: *** No rule to make target clean'. Stop. # I basically just copied the example code from the Galaxy wiki for R: ?xml version=1.0? tool_dependency set_environment version=1.0 environment_variable name=R_SCRIPT_PATH action=set_to$REPOSITORY_INSTALL_DIR/environment_variable /set_environment package name=R version=2.15.1 install version=1.0 actions action type=download_by_urlhttp://CRAN.R-project.org/src/base/R-2/R-2.15.1.tar.g z/action action type=shell_command./configure --prefix=$INSTALL_DIR/action action type=shell_commandmake/action action type=set_environment environment_variable name=PATH action=prepend_to$INSTALL_DIR/bin/environment_variable /action /actions /install readme You need a FORTRAN compiler or perhaps f2c in addition to a C compiler to build R. /readme /package /tool_dependency I have found no documentation to what the tag action type=download_by_url does... I have asumed it downloads, unzips and moves into the unzipped directory.. But apparently it doesn¹t.. Any advice on this or at least a link to the pertinent documentation?? Thanks a lot in advance... Franco This email (including any attachments or links) may contain confidential and/or legally privileged information and is intended only to be read or used by the addressee. If you are not the intended addressee, any use, distribution, disclosure or copying of this email is strictly prohibited. Confidentiality and legal privilege attached to this email (including any attachments) are not waived or lost by reason of its mistaken delivery to you. If you have received this email in error, please delete it and notify us immediately by telephone or email. Peter MacCallum Cancer Centre provides no guarantee that this transmission is free of virus or that it has not been intercepted or altered and will not be liable for any delay in its receipt. ___ 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] Tool dependency installation fail, any documentation?
Franco, BEDTools, unlike some other packages, does not require the 'make clean' shell command to compile. If you remove that line, the dependency should install without problems. --Dave B. On 2012-12-11 21:16, Franco Caramia wrote: Hi list, I got the following tool_dependencies.xml file failing: ?xml version=1.0? tool_dependency package name=bedtools version=2.17.0 install version=1.0 actions action type=download_by_url target_filename=bedtools-2.17.0.tar.gz http://bedtools.googlecode.com/files/BEDTools.v2.17.0.tar.gz/action action type=shell_commandmake clean/action action type=shell_commandmake all/action action type=move_directory_files source_directorybin/source_directory destination_directory$INSTALL_DIR/bin/destination_directory /action action type=set_environment environment_variable name=PATH action=prepend_to$INSTALL_DIR/bin/environment_variable /action /actions /install readme GCC version 4.1 or greater is recommended. 3.x versions will typically not compile BEDTools /readme /package /tool_dependency The error given is: # make clean STDOUT # # make clean STDERR make: *** No rule to make target clean'. Stop. # I basically just copied the example code from the Galaxy wiki for R: ?xml version=1.0? tool_dependency set_environment version=1.0 environment_variable name=R_SCRIPT_PATH action=set_to$REPOSITORY_INSTALL_DIR/environment_variable /set_environment package name=R version=2.15.1 install version=1.0 actions action type=download_by_urlhttp://CRAN.R-project.org/src/base/R-2/R-2.15.1.tar.gz/action action type=shell_command./configure --prefix=$INSTALL_DIR/action action type=shell_commandmake/action action type=set_environment environment_variable name=PATH action=prepend_to$INSTALL_DIR/bin/environment_variable /action /actions /install readme You need a FORTRAN compiler or perhaps f2c in addition to a C compiler to build R. /readme /package /tool_dependency I have found no documentation to what the tag action type=download_by_url does... I have asumed it downloads, unzips and moves into the unzipped directory.. But apparently it doesn’t.. Any advice on this or at least a link to the pertinent documentation?? Thanks a lot in advance... Franco This email (including any attachments or links) may contain confidential and/or legally privileged information and is intended only to be read or used by the addressee. If you are not the intended addressee, any use, distribution, disclosure or copying of this email is strictly prohibited. Confidentiality and legal privilege attached to this email (including any attachments) are not waived or lost by reason of its mistaken delivery to you. If you have received this email in error, please delete it and notify us immediately by telephone or email. Peter MacCallum Cancer Centre provides no guarantee that this transmission is free of virus or that it has not been intercepted or altered and will not be liable for any delay in its receipt. ___ 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 doesn't detect the file when we add dataset to a library under Manage data libraries
Hi list, We have found that, in Galaxy, when we add dataset to a library under Manage data libraries, Galaxy sometimes detects the type of the file and sometimes does not. What I have noticed is that it detects the type of the file when we select Copy file into Galaxy under Copy data into Galaxy? option and does not detect it when we select Link to files ... Is this a known issue? If it is, is there any workaround to solve the issue? Thanks Regards, Sachit ___ 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] pbs_python and torque 4.x
Hi all, We are trying to get our instance of Galaxy submitting jobs to a cluster a using the staged method referred to at http://wiki.galaxyproject.org/Admin/Config/Performance/Cluster. Our cluster is running Torque 4.1.3. We need to use Torque 4.x clients to be able to submit jobs to it. I've set up our Galaxy server to be able to submit jobs and stage data in and out. Galaxy can't submit jobs to the cluster, however. The problem seems to be with pbs_python. On the associated wiki there is a ticket for the problem and I have been able to reproduce it. https://oss.trac.sara.nl/pbs_python/ticket/31 Has anyone had any experience with getting pbs_python to work with Torque 4.x? Regards. Steve McMahon Solutions architect senior systems administrator ASC Cluster Services Information Management Technology (IMT) CSIRO Phone: +61-2-62142968 | Mobile: +61-4-00779318 steve.mcma...@csiro.aumailto:steve.mcma...@csiro.au | www.csiro.auhttp://www.csiro.au/ PO Box 225, DICKSON ACT 2602 1 Wilf Crane Crescent, Yarralumla ACT 2600 ___ 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] Tool dependency installation fail, any documentation?
Franco, You're right, I see a both clean and all rules in the makefile. It looks almost like it's not finding the expected makefile, I'll have to look into that in the morning. As for the download_by_url action, it downloads and extracts the specified file, then changes to the extracted directory. Could you remind me which changeset revision you're trying to install this repository in? --Dave B. On 2012-12-11 23:10, Franco Caramia wrote: Hi Dave, It does not require it, but it should not fail either as the clean rule is in the makefile.. By removing it I get: make: *** No rule to make target `all'. Stop. Same problem as before but this time with the 'all' rule... I'm not sure what the action type=download_by_url tag does.. Do I need to 'cd' into the unzipped directory? Thanks, Franco On 12/12/12 1:03 PM, Dave Bouvier d...@bx.psu.edu wrote: Franco, BEDTools, unlike some other packages, does not require the 'make clean' shell command to compile. If you remove that line, the dependency should install without problems. --Dave B. On 2012-12-11 21:16, Franco Caramia wrote: Hi list, I got the following tool_dependencies.xml file failing: ?xml version=1.0? tool_dependency package name=bedtools version=2.17.0 install version=1.0 actions action type=download_by_url target_filename=bedtools-2.17.0.tar.gz http://bedtools.googlecode.com/files/BEDTools.v2.17.0.tar.gz/action action type=shell_commandmake clean/action action type=shell_commandmake all/action action type=move_directory_files source_directorybin/source_directory destination_directory$INSTALL_DIR/bin/destination_directory /action action type=set_environment environment_variable name=PATH action=prepend_to$INSTALL_DIR/bin/environment_variable /action /actions /install readme GCC version 4.1 or greater is recommended. 3.x versions will typically not compile BEDTools /readme /package /tool_dependency The error given is: # make clean STDOUT # # make clean STDERR make: *** No rule to make target clean'. Stop. # I basically just copied the example code from the Galaxy wiki for R: ?xml version=1.0? tool_dependency set_environment version=1.0 environment_variable name=R_SCRIPT_PATH action=set_to$REPOSITORY_INSTALL_DIR/environment_variable /set_environment package name=R version=2.15.1 install version=1.0 actions action type=download_by_urlhttp://CRAN.R-project.org/src/base/R-2/R-2.15.1.tar.gz /action action type=shell_command./configure --prefix=$INSTALL_DIR/action action type=shell_commandmake/action action type=set_environment environment_variable name=PATH action=prepend_to$INSTALL_DIR/bin/environment_variable /action /actions /install readme You need a FORTRAN compiler or perhaps f2c in addition to a C compiler to build R. /readme /package /tool_dependency I have found no documentation to what the tag action type=download_by_url does... I have asumed it downloads, unzips and moves into the unzipped directory.. But apparently it doesn¹t.. Any advice on this or at least a link to the pertinent documentation?? Thanks a lot in advance... Franco This email (including any attachments or links) may contain confidential and/or legally privileged information and is intended only to be read or used by the addressee. If you are not the intended addressee, any use, distribution, disclosure or copying of this email is strictly prohibited. Confidentiality and legal privilege attached to this email (including any attachments) are not waived or lost by reason of its mistaken delivery to you. If you have received this email in error, please delete it and notify us immediately by telephone or email. Peter MacCallum Cancer Centre provides no guarantee that this transmission is free of virus or that it has not been intercepted or altered and will not be liable for any delay in its receipt. ___ 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/ This email (including any attachments or links) may contain confidential
