Re: [galaxy-dev] nice quality Galaxy logo and name
Hi Leandro, I apologize for the delay in answering this. The highest resolution logo I have is at http://gmod.org/wiki/File:GalaxyLogoBigger.png, which may not be big enough for some purposes, but will look much better than what you have been using. Sometime in the near future I hope to get a page like this http://gmod.org/wiki/GMOD_Promotion up for Galaxy. Thanks, Dave C. On Thu, May 19, 2011 at 12:15 PM, Leandro Hermida soft...@leandrohermida.com wrote: Hi there, Would anyone have a nice quality Galaxy logo and name image for presentations and posters? I've been using the one in the left hand corner of the server which ok but wondering if there is a better official one or something regards, leandro ___ 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/ -- http://galaxy.psu.edu/gcc2011/ http://getgalaxy.org http://usegalaxy.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/
Re: [galaxy-dev] Uploading Binary Files into Galaxy
Hi, Have you tried grep'ing the error message in the lib files to see where Galaxy goes to during the upload of these files? like: grep /The uploaded binary file contains inappropriate content/ `find *` I had a similar problem when I modified Galaxy to manage .gz files without uncompressing them automatically (I had to add a new file type too), and diving into the code to see what is actually executed really helped. Good luck, L-A Le 24/05/2011 04:40, darren.culle...@csiro.au a écrit : Hi All, Sorry for the delay, I have had a couple of other projects on the go. Still no good. I have made the data type unsniffable and added what I thought was the correct information. I have also added the extension (sfx) to the list of unsniffable binary formats in binary.py but it does not make a difference. Code is as follows: ./datatypes_conf.xml datatype extension=sfx type=galaxy.datatypes.binary:Sfx display_in_upload=true/ ./lib/galaxy/datatypes/binary.py class Sfx( Binary ): Kanga and uAssembler Suffix Array file_ext = sfx def __init__( self, **kwd ): Binary.__init__( self, **kwd ) def set_peek( self, dataset, is_multi_byte=False ): if not dataset.dataset.purged: dataset.peek = 'Suffix Array sfx' dataset.blurb = 'binary data' else: dataset.peek = 'file does not exist' dataset.blurb = 'file purged from disk' My gut feeling is that this is related to the fact that Galaxy wants to look in the file, but as soon as its opened, it can't recognise the characters and it reports /The uploaded binary file contains inappropriate content/. I thought the set_peekmethod I have above would override the one described in the Class Binary. I have tried adding a sniffer tag into datatypes_conf.xml, but I get the same result whether the sniffer tag is there or not. I am sure I have missed a step or piece of content but I have no idea what I am missing... Thanks again for your time, Darren Cullerne Computational Biology CSIRO Plant Industry x5042 +61 2 62465042 darren.culle...@csiro.au mailto:darren.culle...@csiro.au ___ 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] Follow the 2011 Galaxy Community Conference on Twitter
Hello all, The 2011 Galaxy Community Conference starts in about 10 hours with the sold out Introduction to Galaxy session, and then gets fully rolling Wednesday morning with the main meeting. See the schedule ( http://galaxy.psu.edu/gcc2011/Programme.html) for full details. If you want to follow the meeting on Twitter, we are encouraging copious tweeting by participants using the #usegalaxy hashtag. You can follow at https://twitter.com/#!/search/%23usegalaxy or http://galaxy.psu.edu/gcc2011/Home.html In addition, NBIC, the conference host, is also sponsoring the videotaping of all 23 talks. These will be placed online after the conference and will be open to anyone. We have 148 registered attendees (about twice as many as last year) form 19 countries (6 continents!) Well over 100 different organizations will have representatives at the meeting. I'm expecting great things. Thanks, Dave C -- http://galaxy.psu.edu/gcc2011/ http://getgalaxy.org http://usegalaxy.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/
Re: [galaxy-dev] Uploading Binary Files into Galaxy
darren.culle...@csiro.au wrote: Hi All, Sorry for the delay, I have had a couple of other projects on the go. Still no good. I have made the data type unsniffable and added what I thought was the correct information. I have also added the extension (sfx) to the list of unsniffable binary formats in binary.py but it does not make a difference. Hi Darren, Please have a look in tools/data_source/upload.py, you'll need to bypass the binary test for your new datatype. Eventually this test should be moved up to the datatype code, but for now this extra step is required. --nate Code is as follows: ./datatypes_conf.xml datatype extension=sfx type=galaxy.datatypes.binary:Sfx display_in_upload=true/ ./lib/galaxy/datatypes/binary.py class Sfx( Binary ): Kanga and uAssembler Suffix Array file_ext = sfx def __init__( self, **kwd ): Binary.__init__( self, **kwd ) def set_peek( self, dataset, is_multi_byte=False ): if not dataset.dataset.purged: dataset.peek = 'Suffix Array sfx' dataset.blurb = 'binary data' else: dataset.peek = 'file does not exist' dataset.blurb = 'file purged from disk' My gut feeling is that this is related to the fact that Galaxy wants to look in the file, but as soon as its opened, it can't recognise the characters and it reports The uploaded binary file contains inappropriate content. I thought the set_peek method I have above would override the one described in the Class Binary. I have tried adding a sniffer tag into datatypes_conf.xml, but I get the same result whether the sniffer tag is there or not. I am sure I have missed a step or piece of content but I have no idea what I am missing... Thanks again for your time, Darren Cullerne Computational Biology CSIRO Plant Industry x5042 +61 2 62465042 darren.culle...@csiro.aumailto:darren.culle...@csiro.au ___ 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] AttributeError: 'list' object has no attribute 'missing_meta' when doing multiple=true input datasets
Hi Leandro, The Galaxy Team has recently been preparing for and traveling in advance of the Galaxy Community Conference, which begins today. Unfortunately I don't have an answer for you, but when we're all back at work next week, someone should be able to respond. Thanks, --nate Leandro Hermida wrote: Hi again, Very sorry to ask again, just gotten no repsonse, but is this a Galaxy bug or does anyone have a functioning tool that takes multiple datasets as an input parameter??? i.e. param type=data multiple=true ... / regards, Leandro On Thu, May 19, 2011 at 7:15 PM, Leandro Hermida soft...@leandrohermida.com wrote: Hi again, I tried changing the format to txt and tabular which I have other datasets in my history and still the same error and stack trace in Galaxy. Is it possible at all to have a select multiple of datasets as an input parameter?? best, Leandro On Thu, May 19, 2011 at 6:59 PM, Leandro Hermida soft...@leandrohermida.com wrote: Hi Galaxy developers, Something seems maybe to be wrong with the format=html type... I forgot to add before that my tool input param the format=html attribute: param type=data multiple=true format=html name=input1 / In another tool I have it outputs format=html and this works and displays in Galaxy just fine. I would like to use multiple of these output datasets in my history as the input for this other tool but something seems to be wrong if you try to do this? a bit lost, Leandro On Thu, May 19, 2011 at 3:30 PM, Leandro Hermida soft...@leandrohermida.com wrote: Hi, I have a tool where the input is multi-select of datasets, e.g.: param type=data multiple=true name=input1 / I tested it to see what it would pass to my command and I get the following debug page and error in Galaxy: AttributeError: 'list' object has no attribute 'missing_meta' The last part of the stack trace looks like: validator.validate( value, history ) Module galaxy.tools.parameters.validation:185 in validate history galaxy.model.History object at 0xb8ea190 selfgalaxy.tools.parameters.validation.MetadataValidator object at 0xb8e6250 value [galaxy.model.HistoryDatasetAssociation object at 0xa20, galaxy.model.HistoryDataset ... Association object at 0xb8ea210] if value and value.missing_meta( check = self.check, skip = self.skip ): AttributeError: 'list' object has no attribute 'missing_meta' What am I doing wrong? regards, Leandro ___ 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] Checkboxes/booleans in tools, again
Thanks! This has been fixed in changeset 5594:2f84c42a548a. Also, if I could ask for a minor thing to assist us with list maintenance: when starting a new thread on the list, please create a brand new email to galaxy-dev rather than replying to an existing message. Replying includes headers that reference the message you replied to, which means it threads with the original thread in mail readers and the list archive. Thanks, --nate Louise-Amélie Schmitt wrote: Yeah, and I fixed it... somehow. In the lib/galaxy/web/form_builder.py I added the import on string_as_bool from galaxy.util, then I modified the code as follows: 126 @staticmethod 127 def is_checked( value ): 128 if value == True: 129 return True 130 # This may look strange upon initial inspection, but see the comments in the get_html() method 131 # above for clarification. Basically, if value is not True, then it will always be a list with 132 # 2 input fields ( a checkbox and a hidden field ) if the checkbox is checked. If it is not 133 # checked, then value will be only the hidden field. 134 if isinstance(value, basestring): 135 return string_as_bool( value ) 136 return isinstance( value, list ) and len( value ) == 2 (see l.134 and 135) The value variable actually contained something else than True or a list, namely the string true. Now it seems to work fine. Cheers, L-A Le 23/05/2011 18:26, Peter Cock a écrit : 2011/5/23 Louise-Amélie Schmittlouise-amelie.schm...@embl.de: @ Peter: I'm not sure I can get more precise... the checked attribute has no effect whatsoever, the boxes are always unchecked when I open the tool. I tried the yes and the true values to no avail. @ Leandro: Yes I already saw that ... But that's actually not the issue here. I just want my checkboxes to be checked by default, and it appears not to work. To give an example, here is one of the lines of my tool XML file: param name=SQA type=boolean label=Run SolexaQA checked=true / This checkbox remains unchecked at tool opening. As far as I know, some people managed to get it working and I'd like to know how. Any suggestion? I think you've found a bug :( I found two working examples, Filter out low complexity regions (with DUST) parameter in tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml and the scaffolding parameter in sr_assembly/velvetg.xml - however they are both within a conditional parameter section (only shown in advanced mode). Have a look at sr_mapping/bwa_color_wrapper.xml which has a Suppress the header in the output SAM file boolean which should be checked by default: param name=suppressHeader type=boolean truevalue=true falsevalue=false checked=true label=Suppress the header in the output SAM file help=BWA produces SAM with several lines of header information / It's not working on http://usegalaxy.org - the box isn't checked. If you can verify that, please file an issue on bitbucket: https://bitbucket.org/galaxy/galaxy-central/issues/new 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/ ___ 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] Load balanced configuration unable to access Admin - Manage jobs?
Olen Vance Sluder Jr wrote: Problem solved: I found this stack trace in the job runner's log: Traceback (most recent call last): File ./scripts/paster.py, line 34, in module command.run() File /home/galaxy/galaxy-dist/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/command.py, line 84, in run invoke(command, command_name, options, args[1:]) File /home/galaxy/galaxy-dist/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/command.py, line 123, in invoke exit_code = runner.run(args) File /home/galaxy/galaxy-dist/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/command.py, line 218, in run result = self.command() File /home/galaxy/galaxy-dist/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/serve.py, line 303, in command serve() File /home/galaxy/galaxy-dist/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/serve.py, line 287, in serve server(app) File /home/galaxy/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py, line 151, in server_wrapper **context.local_conf) File /home/galaxy/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/util/fixtypeerror.py, line 57, in fix_call val = callable(*args, **kw) File /home/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpserver.py, line 1314, in server_runner serve(wsgi_app, **kwargs) File /home/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpserver.py, line 1264, in serve threadpool_options=threadpool_options) File /home/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpserver.py, line 1118, in __init__ **threadpool_options) File /home/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpserver.py, line 1024, in __init__ **threadpool_options) File /home/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpserver.py, line 588, in __init__ % (spawn_if_under, nworkers)) AssertionError: spawn_if_under (5) should be less than nworkers (3) Per the Scaling and Load Balancing instructions [1], I had used the following stanza for the job runner: [server:runner0] use = egg:Paste#http port = 8079 #host = 127.0.0.1 use_threadpool = true threadpool_workers = 3 The value for threadpool_workers (3) conflicted with the default value for local_job_queue_workers (5). When I increased the value of threadpool_workers to 5, the runner's web interface came right up. Hi Olen, Thanks for finding this! I've increased the value in the documentation to 5. --nate -- Olen [1] https://bitbucket.org/galaxy/galaxy-central/wiki/Config/WebApplicationScaling On Mon, May 23, 2011 at 08:53, Olen Vance Sluder Jr o...@acm.org wrote: I have had good success in setting up a load balanced configuration with nginx except that I get the following error when accessing Admin - Manage jobs: This Galaxy instance is not configured to run jobs. If using multiple servers, please directly access the job running instance to manage jobs. When I access the runner instance directly at http://localhost:8079/admin/jobs, the browser just hangs with no response. A quick search of the wiki and the dev mailing list archive didn't turn up a solution, so any help would be appreciated. Thanks, Olen ___ 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] multiple cluster job runners?
Shantanu Pavgi wrote: I am looking at options to configure settings such as wall-time, memory, and number of cores etc. for each tool and wondering if this can be done using multiple cluster job runner configurations. Is it possible to define multiple cluster job runner configurations for each tool? In the universe_wsgi.ini file it is mentioned that individual per-tool job runners can be specified, however I don't see any example other than 'default_cluster_job_runner'. So is there any key-value syntax for defining it in the ini file? I appreciate any comments or suggestions regarding this issue. Hi Shantanu, Please have a look at the examples in the [galaxy:tool_runners] section at the bottom of universe_wsgi.ini and let us know if this suits your needs. Thanks, --nate -- Thanks, Shantanu. ___ 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] nice quality Galaxy logo and name
Hi Dave, thank you much appreciated! On Tue, May 24, 2011 at 9:43 AM, Dave Clements cleme...@galaxyproject.orgwrote: Hi Leandro, I apologize for the delay in answering this. The highest resolution logo I have is at http://gmod.org/wiki/File:GalaxyLogoBigger.png, which may not be big enough for some purposes, but will look much better than what you have been using. Sometime in the near future I hope to get a page like this http://gmod.org/wiki/GMOD_Promotion up for Galaxy. Thanks, Dave C. On Thu, May 19, 2011 at 12:15 PM, Leandro Hermida soft...@leandrohermida.com wrote: Hi there, Would anyone have a nice quality Galaxy logo and name image for presentations and posters? I've been using the one in the left hand corner of the server which ok but wondering if there is a better official one or something regards, leandro ___ 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/ -- http://galaxy.psu.edu/gcc2011/ http://getgalaxy.org http://usegalaxy.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/
Re: [galaxy-dev] AttributeError: 'list' object has no attribute 'missing_meta' when doing multiple=true input datasets
Hi Nate, Thanks for the ping, have fun at the conference! On Tue, May 24, 2011 at 11:22 AM, Nate Coraor n...@bx.psu.edu wrote: Hi Leandro, The Galaxy Team has recently been preparing for and traveling in advance of the Galaxy Community Conference, which begins today. Unfortunately I don't have an answer for you, but when we're all back at work next week, someone should be able to respond. Thanks, --nate Leandro Hermida wrote: Hi again, Very sorry to ask again, just gotten no repsonse, but is this a Galaxy bug or does anyone have a functioning tool that takes multiple datasets as an input parameter??? i.e. param type=data multiple=true ... / regards, Leandro On Thu, May 19, 2011 at 7:15 PM, Leandro Hermida soft...@leandrohermida.com wrote: Hi again, I tried changing the format to txt and tabular which I have other datasets in my history and still the same error and stack trace in Galaxy. Is it possible at all to have a select multiple of datasets as an input parameter?? best, Leandro On Thu, May 19, 2011 at 6:59 PM, Leandro Hermida soft...@leandrohermida.com wrote: Hi Galaxy developers, Something seems maybe to be wrong with the format=html type... I forgot to add before that my tool input param the format=html attribute: param type=data multiple=true format=html name=input1 / In another tool I have it outputs format=html and this works and displays in Galaxy just fine. I would like to use multiple of these output datasets in my history as the input for this other tool but something seems to be wrong if you try to do this? a bit lost, Leandro On Thu, May 19, 2011 at 3:30 PM, Leandro Hermida soft...@leandrohermida.com wrote: Hi, I have a tool where the input is multi-select of datasets, e.g.: param type=data multiple=true name=input1 / I tested it to see what it would pass to my command and I get the following debug page and error in Galaxy: AttributeError: 'list' object has no attribute 'missing_meta' The last part of the stack trace looks like: validator.validate( value, history ) Module galaxy.tools.parameters.validation:185 in validate history galaxy.model.History object at 0xb8ea190 selfgalaxy.tools.parameters.validation.MetadataValidator object at 0xb8e6250 value [galaxy.model.HistoryDatasetAssociation object at 0xa20, galaxy.model.HistoryDataset ... Association object at 0xb8ea210] if value and value.missing_meta( check = self.check, skip = self.skip ): AttributeError: 'list' object has no attribute 'missing_meta' What am I doing wrong? regards, Leandro ___ 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 download
Hi, I am a new linux user, would like to use galaxy directly on my computer could you instruct me how to download galaxy? thanks Jasmine Jacob-Hirsch Functional Genomics Cancer Research Center Sheba Medical Center 972-3-5302147 972-523790500 ___ 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] Uploading Binary Files into Galaxy
Hi All, Sorry for the delay, I have had a couple of other projects on the go. Still no good. I have made the data type unsniffable and added what I thought was the correct information. I have also added the extension (sfx) to the list of unsniffable binary formats in binary.py but it does not make a difference. Code is as follows: ./datatypes_conf.xml datatype extension=sfx type=galaxy.datatypes.binary:Sfx display_in_upload=true/ ./lib/galaxy/datatypes/binary.py class Sfx( Binary ): Kanga and uAssembler Suffix Array file_ext = sfx def __init__( self, **kwd ): Binary.__init__( self, **kwd ) def set_peek( self, dataset, is_multi_byte=False ): if not dataset.dataset.purged: dataset.peek = 'Suffix Array sfx' dataset.blurb = 'binary data' else: dataset.peek = 'file does not exist' dataset.blurb = 'file purged from disk' My gut feeling is that this is related to the fact that Galaxy wants to look in the file, but as soon as its opened, it can't recognise the characters and it reports The uploaded binary file contains inappropriate content. I thought the set_peek method I have above would override the one described in the Class Binary. I have tried adding a sniffer tag into datatypes_conf.xml, but I get the same result whether the sniffer tag is there or not. I am sure I have missed a step or piece of content but I have no idea what I am missing... Thanks again for your time, Darren Cullerne Computational Biology CSIRO Plant Industry x5042 +61 2 62465042 darren.culle...@csiro.aumailto:darren.culle...@csiro.au ___ 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 download
Hello Jasmine, Please see http://getgalaxy.org On May 24, 2011, at 1:21 AM, jasmine jacob wrote: Hi, I am a new linux user, would like to use galaxy directly on my computer could you instruct me how to download galaxy? thanks Jasmine Jacob-Hirsch Functional Genomics Cancer Research Center Sheba Medical Center 972-3-5302147 972-523790500 ___ 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/ Greg Von Kuster Galaxy Development Team g...@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 download
Hi Jasmin, at first you need to install mercurial. Under debian/ubuntu install it with: sudo apt-get mercurial Then you can check out all the necessary stuff with: hg clone https://bitbucket.org/galaxy/galaxy-dist You can start galaxy with: ./run.sh For more information, please see the wiki page. https://bitbucket.org/galaxy/galaxy-central/wiki/Home Ciao, Bjoern Am Dienstag, den 24.05.2011, 08:21 +0300 schrieb jasmine jacob: Hi, I am a new linux user, would like to use galaxy directly on my computer could you instruct me how to download galaxy? thanks Jasmine Jacob-Hirsch Functional Genomics Cancer Research Center Sheba Medical Center 972-3-5302147 972-523790500 ___ 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/ -- Björn Grüning Albert-Ludwigs-Universität Freiburg Institut für Pharmazeutische Wissenschaften Pharmazeutische Bioinformatik Hermann-Herder-Strasse 9 D-79104 Freiburg i. Br. Tel.: +49 761 203-4872 Fax.: +49 761 203-6366 E-Mail: bjoern.gruen...@pharmazie.uni-freiburg.de Web: http://www.pharmaceutical-bioinformatics.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/
Re: [galaxy-dev] Display column headers in data_column parameter
On Tue, May 24, 2011 at 3:12 PM, Johannes Eichner johannes.eich...@uni-tuebingen.de wrote: Dear Galaxy-Dev Team, is it possible to display the headers of the columns which can be selected in a data_column parameter? Currently, only the column index (e.g., c1, c2, etc.) is displayed in Galaxy. If it would be possible to additionally display the column headers, the selection of the desired columns would be easier for the user. Is there a way to do this using the current version of Galaxy? Kind regards, Johannes I completely agree that in general the UI for column parameter isn't as user friendly as it could be. The filter data UI is even worse for non-programmers, but due to its complexity and flexibility, that is harder to improve too. This was one of the things I wanted to bring up with the Galaxy team at the conference (starting tonight). Unfortunately due to the Grimsvotn Volcano's cloud of ash I won't be there. In some cases yes, Galaxy knows the column meaning. In many of my data files there is a # header line with tab separated column names, which could be detected and shown. Given there may or not be suitable column meta data, what I was picturing was an expanded column picking dialogue that could show the first few rows of data in each column (not using a simple HTML widget anymore), or simply the first value (less drastic change). So, rather than having as now something like: Pick column(s): [ ] c1 [ ] c2 [ ] c3 [ ] c4 [ ] c5 If Galaxy has names in the column meta data you might have Pick columns(s): [ ] c1 - Identifier [ ] c2 - Start [ ] c3 - End [ ] c4 - Strand [ ] c5 - Sequence Or, showing the first data entry: Pick columns(s): [ ] c1, e.g. gi|12345678 [ ] c2, e.g. 123 [ ] c3, e.g. 456 [ ] c4, e.g. + [ ] c4, e.g. ACGTACTGT... In the final example I envision truncating very long values with an ellipsis. Both the above proposals don't require drastic changes to the HTML widget and layout. I guess we should file an enhancement issue on bitbucket: https://bitbucket.org/galaxy/galaxy-central/issues/new 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] multiple cluster job runners?
On May 24, 2011, at 4:49 AM, Nate Coraor wrote:
Shantanu Pavgi wrote:
I am looking at options to configure settings such as wall-time, memory, and
number of cores etc. for each tool and wondering if this can be done using
multiple cluster job runner configurations. Is it possible to define
multiple cluster job runner configurations for each tool? In the
universe_wsgi.ini file it is mentioned that individual per-tool job runners
can be specified, however I don't see any example other than
'default_cluster_job_runner'. So is there any key-value syntax for defining
it in the ini file? I appreciate any comments or suggestions regarding this
issue.
Hi Shantanu,
Please have a look at the examples in the [galaxy:tool_runners] section
at the bottom of universe_wsgi.ini and let us know if this suits your
needs.
Yes, that should work for me.
I was wondering if I need to define job runners first and then specify it for
each tool: e.g.
{{{
$job_runner_one = drmaa:// -V /
$job_runner_two = drmaa:// -V -l h_rt=00:10:00 /
...
...
$galaxy_tool_one = $job_runner_one
...
}}}
But current configuration syntax should work. Thanks for the help.
--
Shantanu.
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Re: [galaxy-dev] galaxy download
See this page for the official installation instructions https://bitbucket.org/galaxy/galaxy-central/wiki/GetGalaxy 2011/5/24 Björn Grüning bjoern.gruen...@pharmazie.uni-freiburg.de Hi Jasmin, at first you need to install mercurial. Under debian/ubuntu install it with: sudo apt-get mercurial Then you can check out all the necessary stuff with: hg clone https://bitbucket.org/galaxy/galaxy-dist You can start galaxy with: ./run.sh For more information, please see the wiki page. https://bitbucket.org/galaxy/galaxy-central/wiki/Home Ciao, Bjoern Am Dienstag, den 24.05.2011, 08:21 +0300 schrieb jasmine jacob: Hi, I am a new linux user, would like to use galaxy directly on my computer could you instruct me how to download galaxy? thanks Jasmine Jacob-Hirsch Functional Genomics Cancer Research Center Sheba Medical Center 972-3-5302147 972-523790500 ___ 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/ -- Björn Grüning Albert-Ludwigs-Universität Freiburg Institut für Pharmazeutische Wissenschaften Pharmazeutische Bioinformatik Hermann-Herder-Strasse 9 D-79104 Freiburg i. Br. Tel.: +49 761 203-4872 Fax.: +49 761 203-6366 E-Mail: bjoern.gruen...@pharmazie.uni-freiburg.de Web: http://www.pharmaceutical-bioinformatics.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/ ___ 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] cluster files directory configuration
On May 19, 2011, at 4:05 PM, Shantanu Pavgi wrote: I have configured custom cluster_files_directory in universe_wsgi.ini file. The cluster jobs are running fine, however job scripts, stdout and stderr are being written in default database/pbs location. Am I missing something in the configuration here? Any help on what might be wrong here? Is this option getting overridden by some other config? -- Thanks, Shantanu. ___ 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] Error getting to http://galaxy/user/create on local instance
We upgraded our Galaxy instance to the current Dist build at the end of last week. Since then we've had a couple new users attempt to create accounts. When they go to the create user page (http://galaxy.jax.org/user/create) they get a 500 Server Error. The message in the error log is: 10.30.34.254 - - [24/May/2011:15:54:24 -0400] GET /user/create HTTP/1.0 500 - http://galaxy/user/login; Mozilla/5.0 (Macintosh; U; Intel Mac OS X 10.6; en-US; rv:1.9.1.2) Gecko/20090729 Firefox/3.5.2 Error - type 'exceptions.TypeError': create() takes at least 3 arguments (2 given) Glen is traveling to the Galaxy Community Conference, he's the one that did the upgrade, but as far as I know, he did a pretty straight forward upgrade. Did something change, in configuration of the create user page? Any thoughts what might be causing this? Thanks, Dave ___ 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] Getting binary programs into Galaxy distribution?
There is a C program for merging Gzip files (gzjoin) that I'd love to rely on for a core Galaxy capability. Is there a standard way to get things like this included in Galaxy? Recoding it in Python would be a bit of a pain, and might be a lot slower due to the IO layer not allowing the reuse of buffers. Thanks - John Duddy Sr. Staff Software Engineer Illumina, Inc. 9885 Towne Centre Drive San Diego, CA 92121 Tel: 858-736-3584 E-mail: jdu...@illumina.commailto:jdu...@illumina.com ___ 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] Error getting to http://galaxy/user/create on local instance
Greg, We've tried just reloading the browser and that didn't do anything. As for deleting the cached templates, on our development server I tried deleting everything under the database/compiled_templates directory (I even restarted my server) and it appeared to have no affect. We still get the error message. Maybe I misunderstood you. The only cache related variable in my universe_wsgi files is static_cache_time = 360. Thanks, Dave On 5/24/11 4:27 PM, Greg Von Kuster g...@bx.psu.edu wrote: Hello Dave, The index method signature of the user controller changed, so this is a template cache issue. It may work to simply have your users refresh their Galaxy masthead ( the top menu banner that includes the login in the User pop-up ). However, sometimes this isn't enough to clear the cache, so you can fix things for sure by deleting the cached templates in ~//database/compiled_templates/user assuming you have not changed the setting for the template cache in your universe_wsgi.ini file. If you have, delete the files in the user directory where you have them stored. Greg Von Kuster On May 24, 2011, at 4:02 PM, Dave Walton wrote: We upgraded our Galaxy instance to the current Dist build at the end of last week. Since then we've had a couple new users attempt to create accounts. When they go to the create user page (http://galaxy.jax.org/user/create) they get a 500 Server Error. The message in the error log is: 10.30.34.254 - - [24/May/2011:15:54:24 -0400] GET /user/create HTTP/1.0 500 - http://galaxy/user/login; Mozilla/5.0 (Macintosh; U; Intel Mac OS X 10.6; en-US; rv:1.9.1.2) Gecko/20090729 Firefox/3.5.2 Error - type 'exceptions.TypeError': create() takes at least 3 arguments (2 given) Glen is traveling to the Galaxy Community Conference, he's the one that did the upgrade, but as far as I know, he did a pretty straight forward upgrade. Did something change, in configuration of the create user page? Any thoughts what might be causing this? Thanks, Dave ___ 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/ Greg Von Kuster Galaxy Development Team g...@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] Error getting to http://galaxy/user/create on local instance
Hi Dave, If you do not have a template_cache_path config setting in universe_wsgi.ini, then your cached templates are stored in the default directory of ~/database/compiled_templates. Deleting your cached templates in ~/database/compiled_templates should have corrected the problem, assuming there are no other issues within your Galaxy environment, so let's begin down the path of determining the cause. You mention your development server in your response. Are you running only 1 Galaxy instance, or more than 1? Is the behavior occurring for all of your users or just a few? Does it occur with different browsers, or is it related to a certain browser brand? What version of Galaxy are your running? Thanks Dave, Greg Von Kuster On May 24, 2011, at 6:06 PM, Dave Walton wrote: Greg, We've tried just reloading the browser and that didn't do anything. As for deleting the cached templates, on our development server I tried deleting everything under the database/compiled_templates directory (I even restarted my server) and it appeared to have no affect. We still get the error message. Maybe I misunderstood you. The only cache related variable in my universe_wsgi files is static_cache_time = 360. Thanks, Dave On 5/24/11 4:27 PM, Greg Von Kuster g...@bx.psu.edu wrote: Hello Dave, The index method signature of the user controller changed, so this is a template cache issue. It may work to simply have your users refresh their Galaxy masthead ( the top menu banner that includes the login in the User pop-up ). However, sometimes this isn't enough to clear the cache, so you can fix things for sure by deleting the cached templates in ~//database/compiled_templates/user assuming you have not changed the setting for the template cache in your universe_wsgi.ini file. If you have, delete the files in the user directory where you have them stored. Greg Von Kuster On May 24, 2011, at 4:02 PM, Dave Walton wrote: We upgraded our Galaxy instance to the current Dist build at the end of last week. Since then we've had a couple new users attempt to create accounts. When they go to the create user page (http://galaxy.jax.org/user/create) they get a 500 Server Error. The message in the error log is: 10.30.34.254 - - [24/May/2011:15:54:24 -0400] GET /user/create HTTP/1.0 500 - http://galaxy/user/login; Mozilla/5.0 (Macintosh; U; Intel Mac OS X 10.6; en-US; rv:1.9.1.2) Gecko/20090729 Firefox/3.5.2 Error - type 'exceptions.TypeError': create() takes at least 3 arguments (2 given) Glen is traveling to the Galaxy Community Conference, he's the one that did the upgrade, but as far as I know, he did a pretty straight forward upgrade. Did something change, in configuration of the create user page? Any thoughts what might be causing this? Thanks, Dave ___ 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/ Greg Von Kuster Galaxy Development Team g...@bx.psu.edu Greg Von Kuster Galaxy Development Team g...@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/
