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[GSoC2013] Week 5 Update
by Saket Choudhary 23 Jul '13

23 Jul '13

Was stuck up with my approach of wrapping the Workflows in a toolbox and hence this blog post is a bit delayed. http://galaxy-gsoc2013.blogspot.in/2013/07/week-5-update.html Saket

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HTML output with external Javascript
by Sinthong, Phanwadee 23 Jul '13

23 Jul '13

Hi galaxy-dev, I have a tool that generates a HTML output file which uses some javascript library. I cannot view the output file with the eye button in Galaxy, but it still works fine from the HTML file opened out of the file directory. I changed the sanitize_all_html = False and restarted the galaxy server as some earlier post suggested but still couldn't view the output file. What else can I do to execute Javascript in the Galaxy browser? Thanks, Gift

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Two questions
by Gromobir 23 Jul '13

23 Jul '13

Hello list, I have two questions regarding galaxy: 1.) Is it possible to configure the amount of lines listed in the tool standard output (stdout)? On my system only the last five lines of tool output are shown there. 2.) Currently I get the message "This dataset is large and only the first megabyte is shown below" every time I try to display a file, which is larger than one megabyte. Is it possible to change this size, such that I won't get this message anymore for larger files? Thank you very much in advance! Cheers, Gromobir

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Re: [galaxy-dev] Problem in uploading file
by Himanshu Gupta 23 Jul '13

23 Jul '13

Hello, It seems you are right. It has nothing to do with the SQLAlchemy. I checked the Galaxy log and didn't find any other error log. After upgrading the database to MySQL when I uploaded the first input file, job dispatched to local runner and everything was fine. But when I tried to upload another file Galaxy didn't even dispatched the Job. I am pasting below the snapshot of the Galaxy log for your reference. galaxy.jobs DEBUG 2013-07-23 09:36:15,579 job 1 ended galaxy.datatypes.metadata DEBUG 2013-07-23 09:36:15,579 Cleaning up external metadata files 10.180.4.152 - - [23/Jul/2013:09:36:15 +0600] "GET /api/histories/f2db41e1fa331b3e HTTP/1.1" 200 - " http://10.180.8.54:6080/history" "Mozilla/5.0 (X11; Linux i686) AppleWebKit/537.4 (KHTML, like Gecko) Chrome/22.0.1229.94 Safari/537.4" 10.180.4.152 - - [23/Jul/2013:09:36:15 +0600] "GET /api/users/current HTTP/1.1" 200 - "http://10.180.8.54:6080/" "Mozilla/5.0 (X11; Linux i686) AppleWebKit/537.4 (KHTML, like Gecko) Chrome/22.0.1229.94 Safari/537.4" 10.180.4.152 - - [23/Jul/2013:09:36:15 +0600] "GET /api/histories/f2db41e1fa331b3e/contents?ids=ebfb8f50c6abde6d HTTP/1.1" 200 - "http://10.180.8.54:6080/history" "Mozilla/5.0 (X11; Linux i686) AppleWebKit/537.4 (KHTML, like Gecko) Chrome/22.0.1229.94 Safari/537.4" 10.180.4.152 - - [23/Jul/2013:09:36:33 +0600] "GET /tool_runner?tool_id=upload1 HTTP/1.1" 200 - "http://10.180.8.54:6080/" "Mozilla/5.0 (X11; Linux i686) AppleWebKit/537.4 (KHTML, like Gecko) Chrome/22.0.1229.94 Safari/537.4" 10.180.4.152 - - [23/Jul/2013:09:36:38 +0600] "POST /tool_runner/upload_async_create HTTP/1.1" 200 - "http://10.180.8.54:6080/" "Mozilla/5.0 (X11; Linux i686) AppleWebKit/537.4 (KHTML, like Gecko) Chrome/22.0.1229.94 Safari/537.4" 10.180.4.152 - - [23/Jul/2013:09:36:38 +0600] "GET /tool_runner/upload_async_message HTTP/1.1" 200 - "http://10.180.8.54:6080/" "Mozilla/5.0 (X11; Linux i686) AppleWebKit/537.4 (KHTML, like Gecko) Chrome/22.0.1229.94 Safari/537.4" 10.180.4.152 - - [23/Jul/2013:09:37:01 +0600] "GET /tool_runner?tool_id=upload1 HTTP/1.1" 200 - "http://10.180.8.54:6080/" "Mozilla/5.0 (X11; Linux i686) AppleWebKit/537.4 (KHTML, like Gecko) Chrome/22.0.1229.94 Safari/537.4" 10.180.4.152 - - [23/Jul/2013:09:37:08 +0600] "POST /tool_runner/upload_async_create HTTP/1.1" 200 - "http://10.180.8.54:6080/" "Mozilla/5.0 (X11; Linux i686) AppleWebKit/537.4 (KHTML, like Gecko) Chrome/22.0.1229.94 Safari/537.4" 10.180.4.152 - - [23/Jul/2013:09:37:08 +0600] "GET /tool_runner/upload_async_message HTTP/1.1" 200 - "http://10.180.8.54:6080/" "Mozilla/5.0 (X11; Linux i686) AppleWebKit/537.4 (KHTML, like Gecko) Chrome/22.0.1229.94 Safari/537.4" 10.180.4.152 - - [23/Jul/2013:09:37:53 +0600] "GET /history HTTP/1.1" 200 - "http://10.180.8.54:6080/" "Mozilla/5.0 (X11; Linux i686) AppleWebKit/537.4 (KHTML, like Gecko) Chrome/22.0.1229.94 Safari/537.4" 10.180.4.152 - - [23/Jul/2013:09:37:53 +0600] "GET /api/histories/f2db41e1fa331b3e HTTP/1.1" 200 - " http://10.180.8.54:6080/history" "Mozilla/5.0 (X11; Linux i686) AppleWebKit/537.4 (KHTML, like Gecko) Chrome/22.0.1229.94 Safari/537.4" 10.180.4.152 - - [23/Jul/2013:09:37:53 +0600] "GET /history/get_display_application_links HTTP/1.1" 200 - " http://10.180.8.54:6080/history" "Mozilla/5.0 (X11; Linux i686) AppleWebKit/537.4 (KHTML, like Gecko) Chrome/22.0.1229.94 Safari/537.4" 10.180.4.152 - - [23/Jul/2013:09:37:57 +0600] "GET / HTTP/1.1" 200 - "-" "Mozilla/5.0 (X11; Linux i686) AppleWebKit/537.4 (KHTML, like Gecko) Chrome/22.0.1229.94 Safari/537.4" 10.180.4.152 - - [23/Jul/2013:09:37:57 +0600] "GET /root/welcome HTTP/1.1" 302 - "http://10.180.8.54:6080/" "Mozilla/5.0 (X11; Linux i686) AppleWebKit/537.4 (KHTML, like Gecko) Chrome/22.0.1229.94 Safari/537.4" 10.180.4.152 - - [23/Jul/2013:09:37:57 +0600] "GET /history HTTP/1.1" 200 - "http://10.180.8.54:6080/" "Mozilla/5.0 (X11; Linux i686) AppleWebKit/537.4 (KHTML, like Gecko) Chrome/22.0.1229.94 Safari/537.4" 10.180.4.152 - - [23/Jul/2013:09:37:57 +0600] "GET /history/get_display_application_links HTTP/1.1" 200 - " http://10.180.8.54:6080/history" "Mozilla/5.0 (X11; Linux i686) AppleWebKit/537.4 (KHTML, like Gecko) Chrome/22.0.1229.94 Safari/537.4" 10.180.4.152 - - [23/Jul/2013:09:37:57 +0600] "GET /api/histories/f2db41e1fa331b3e HTTP/1.1" 200 - " http://10.180.8.54:6080/history" "Mozilla/5.0 (X11; Linux i686) AppleWebKit/537.4 (KHTML, like Gecko) Chrome/22.0.1229.94 Safari/537.4" 10.180.4.152 - - [23/Jul/2013:09:38:02 +0600] "GET /api/histories/f2db41e1fa331b3e HTTP/1.1" 200 - " http://10.180.8.54:6080/history" "Mozilla/5.0 (X11; Linux i686) AppleWebKit/537.4 (KHTML, like Gecko) Chrome/22.0.1229.94 Safari/537.4" 10.180.4.152 - - [23/Jul/2013:09:38:06 +0600] "GET /api/histories/f2db41e1fa331b3e HTTP/1.1" 200 - " http://10.180.8.54:6080/history" "Mozilla/5.0 (X11; Linux i686) AppleWebKit/537.4 (KHTML, like Gecko) Chrome/22.0.1229.94 Safari/537.4" 10.180.4.152 - - [23/Jul/2013:09:38:10 +0600] "GET /api/histories/f2db41e1fa331b3e HTTP/1.1" 200 - " http://10.180.8.54:6080/history" "Mozilla/5.0 (X11; Linux i686) AppleWebKit/537.4 (KHTML, like Gecko) Chrome/22.0.1229.94 Safari/537.4" 10.180.4.152 - - [23/Jul/2013:09:38:14 +0600] "GET /api/histories/f2db41e1fa331b3e HTTP/1.1" 200 - " http://10.180.8.54:6080/history" "Mozilla/5.0 (X11; Linux i686) AppleWebKit/537.4 (KHTML, like Gecko) Chrome/22.0.1229.94 Safari/537.4" 10.180.4.152 - - [23/Jul/2013:09:38:18 +0600] "GET /api/histories/f2db41e1fa331b3e HTTP/1.1" 200 - " http://10.180.8.54:6080/history" "Mozilla/5.0 (X11; Linux i686) AppleWebKit/537.4 (KHTML, like Gecko) Chrome/22.0.1229.94 Safari/537.4" 10.180.4.152 - - [23/Jul/2013:09:38:22 +0600] "GET /api/histories/f2db41e1fa331b3e HTTP/1.1" 200 - " http://10.180.8.54:6080/history" "Mozilla/5.0 (X11; Linux i686) AppleWebKit/537.4 (KHTML, like Gecko) Chrome/22.0.1229.94 Safari/537.4" 10.180.4.152 - - [23/Jul/2013:09:38:24 +0600] "POST /datasets/33b43b4e7093c91f/delete_async HTTP/1.1" 200 - " http://10.180.8.54:6080/history" "Mozilla/5.0 (X11; Linux i686) AppleWebKit/537.4 (KHTML, like Gecko) Chrome/22.0.1229.94 Safari/537.4" Thanks On Mon, Jul 22, 2013 at 1:05 PM, James Taylor <james(a)jamestaylor.org> wrote: > The SQLAlchemy warning shouldn't have anything to do with uploads. > Does Galaxy still start correctly and do you see any other errors on > the log? What is logged when you try to do the upload? > > -- > James Taylor, Assistant Professor, Biology/CS, Emory University > > > On Fri, Jul 19, 2013 at 9:19 AM, Himanshu Gupta <himanshucse10(a)gmail.com> > wrote: > > Hello everyone, > > > > I had configured galaxy with MySQL database and for some time it was > working > > fine. But suddenly it started showing following warning whenever I start > > galaxy. > > > ".../galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs2.egg/sqlalchemy/sql/expression.py:1927: > > SAWarning: The IN-predicate on "request_type.id" was invoked with an > empty > > sequence. This results in a contradiction, which nonetheless can be > > expensive to evaluate. Consider alternative strategies for improved > > performance." > > > > And now I am not able to upload any file. Please help me to resolve it. > > > > Thanks > > > > ___________________________________________________________ > > 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/ > > > > To search Galaxy mailing lists use the unified search at: > > http://galaxyproject.org/search/mailinglists/ >

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Running additional services
by Rob Leclerc 23 Jul '13

23 Jul '13

We're running cloudman and I would like to run a couple of additional services alongside galaxy. Is there a elegant way/place to add/run these services to existing galaxy code/scripts? Cheers, Rob Rob Leclerc, PhD <http://www.linkedin.com/in/robleclerc> <https://twitter.com/#!/robleclerc> P: (US) +1-(917)-873-3037 P: (Shanghai) +86-1-(861)-612-5469 Personal Email: rob.leclerc(a)aya.yale.edu

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Problem with tophat in local instance
by Rainy Luo 22 Jul '13

22 Jul '13

Hi,all, I am a beginner of Galaxy.Because I need to analyze large-scale deep-seq data and the pubic Galaxy serve did not work out,I installed linux(the first time to use linux) and set up the local galaxy instance in my computer. It seemed everything worked fine until I tried to use Tophat to align the reads to the reference genome.The problem is although I have already downloaded the Refgenome from UCSC,when I use the Tophat,"select a reference genome"option is empty. is there anybody having similar problem?How to deal with it? Thanks! Rainy

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Adding files to a data library - genome option
by Lionel Guy 22 Jul '13

22 Jul '13

Hi Galaxy-devs, When adding files to a data library (as admin), I have to choose the genome corresponding to my dataset, but the drop-down list is not sorted, making it a tad annoying to scroll. In addition, by default, the homIni20 genome is selected, which seems a bit anthropocentric ;) I would suggest that the genome drop-down list has the same behavior as the one in the Upload File tool (i.e. sorted alphabetically, with "unspecified" as the default value). Not sure this is a bug or even worth a Trello card, so I post it here. I'd be happy to fill in a Trello card if requested. Cheers, Lionel

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ToolShed preview lacking controls
by Peter Cock 22 Jul '13

22 Jul '13

HI all, I just had a query about some 'missing' functionality in one of my tools, which is handled by a parameter which doesn't get shown on the preview shown in the Tool Shed - perhaps because it is inside a conditional? <conditional name="output_choice_cond"> <param name="output_choice" type="select" label="Output positive matches, negative matches, or both?"> <option value="both">Both positive matches (ID on list) and negative matches (ID not on list), as two files</option> <option value="pos">Just positive matches (ID on list), as a single file</option> <option value="neg">Just negative matches (ID not on list), as a single file</option> </param>  <when value="both" /> <when value="pos" /> <when value="neg" /> </conditional> Ideally the ToolShed preview would show the dropdown combo box allowing you to pick both files, positive only, or negative only: http://toolshed.g2.bx.psu.edu/view/peterjc/seq_filter_by_id Is this a known limitation? Is there a Trello card I should follow? Thanks, Peter

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unable to display text output
by mark.rose＠syngenta.com 22 Jul '13

22 Jul '13

Hi All I'm trying to format one of the three outputs of my galaxy tool as plain text. Thus far no matter how I specify my output format in the tool xml file I have the same problem. When I click the eye icon it opens a save dialog rather that displaying the text output in the central frame. The preview shows the text output and if I follow through and save the output and open with wordpad it is fine. Also if I edit the attributes of the output and change it to "txt" (which is one of the formats I had tried specifying in the xml) it will render in the central frame but I would rather not have to do that. Both of my other outputs (a vcf and a tab-delimited file) are rendered in the central frame properly. How do I to fix this? Thanks Mark This message may contain confidential information. If you are not the designated recipient, please notify the sender immediately, and delete the original and any copies. Any use of the message by you is prohibited.

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Manual modifications to integrated_tool_panel.xml?
by Dan Sullivan 22 Jul '13

22 Jul '13

Hi, Galaxy Developers, I have what I believe to be a basic question/problem with respect to making modifications to the integrated_tool_panel.xml (and or tool_conf.xml). Our Galaxy deployment does have some custom additions made to these files (I did not make these modifications so I am not 100% certain at this point whether or not the modifications to integrated_tool_panel.xml were manual or propagated from elsewhere) , and everything seems to work alright, although I do have a problem that I am having somewhat of a difficult time resolving. Before ask my question, I wanted to confirm my understanding of the wiki page http://wiki.galaxyproject.org/GalaxyToolPanel. I was hoping that somebody could validate the following statements; 1) The only thing that a human being should really ever change in the file "integrated_tool_panel.xml" is the ordering of the groupings (I believe I read on the developer mailing list that it was acceptable to delete sections from here as well, although I am not attempting to validate this at this time). 2) That for all intensive purposes, the integrated_tool_panel.xml should be generated automatically from the files specified in the "tool_config_file" configuration directive in universe_wsgi.ini. 3) That it is perfectly to acceptable to make manual modifications to XML files supplied in the configuration directive "tool_config_file" in the universe_wsgi.ini, or add any number additional XML files to this list (presumably I wouldn't want to make too many manual changes to the shed_tool_conf.xml file, I'm referring to the other XML files, not this one). The reason I am asking this question is a fairly simple one; every now and then, it appears that new tools are released when new versions of Galaxy are released (i.e. a slightly different default toolset is offered, and thus tool panel and or tool configuration files are generated when the new version of Galaxy is started, at least if I do a fresh install). It appears to me based on some very basic testing that once a manual modification to the tool_conf.xml is made, that the next time a pull for an update is run and Galaxy is restarted, that these files remain as-is; basically, what appears to be happening is that we are running a new version of Galaxy with what seems to be an out-of-date integrated_tool_panel.xml, at least in terms of the tools that are configured as part of the default install; this, in a nutshell, is the fundamental problem I am currently dealing with. Here is what I'm thinking is the "correct" way to solve my problem; 1) Since we are manually modifying the tools_conf.xml, It seems to me that we are kind of shooting ourselves in the foot in terms of our ability to delete this file and have Galaxy update it when we do an upgrade . Based on what I know I feel that we should do is take all of our custom tools modifications and put them in a separate file called uofc_custom_tools.xml, and then add that to "tool_config_file" to abstract away our custom tool configurations from the default tool_conf.xml. 2) When we upgrade galaxy, delete the tools_conf.xml, and when galaxy starts, let it replace this file with the default from the current changeset. 3) As long as we didn't need to do any manually reordering of elements in the integrated_tool_panel.xml, just delete the integrated_tool_panel.xml, and allow it to be manually re-generated from tool_conf.xml and uofc_custom_tools.xml. Does this solution sound reasonable? I would be very grateful on any insight anybody could provide in the best way to address this problem. I wish you a wonderful day. Dan Sullivan

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