Re: [galaxy-dev] Role-based tool availability.
Hi Luca, I think we have a nice feature for you: https://wiki.galaxyproject.org/UserDefinedToolboxFilters Thanks for using Galaxy, Bjoern Am 19.02.2014 08:54, schrieb Luca Toldo: dear Galaxians, the users of my galaxy service are quite eterogenous, and would like to have the toolbar customised only with subsets of the available tools. Such customisation should be possible a) at user group level b) at individual level A possibility for group-level tool availability could be to create separate galaxy sites and then upon login redirect the user to the specific one. For individual level customisation of the toolbar, one would need a different infrastructure, i guess. I would appreciate learning your views / experiences on the topic. Sincerely your Luca ___ 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/ ___ 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/
Re: [galaxy-dev] Nightly testing status on the (Test) Tool Shed
On Tue, Feb 18, 2014 at 11:41 AM, Greg Von Kuster g...@bx.psu.edu wrote: Hi Peter, We'll try to get some time to look at your tool_dependencies.xml recipe as soon as possible. Greg Von Kuster Hi Greg, Overnight this has gone back to the previously observed missing data problem (e.g. email of 4th Feb) - no test results at all: http://testtoolshed.g2.bx.psu.edu/view/peterjc/mira4_assembler Test runs 2014-02-18 16:15:52 Automated test environment Time tested: 2014-02-18 16:15:52 System: Architecture: Python version: Galaxy revision: Galaxy database version: Tool shed revision: 12485:64e6873c8825 Tool shed database version: 22 Tool shed mercurial version: 2.2.3 Tools missing tests or test data Tool id: mira_4_0_mapping Tool version: 0.0.2 Tool guid: testtoolshed.g2.bx.psu.edu/repos/peterjc/mira4_assembler/mira_4_0_mapping/0.0.2 Missing components: Functional test definitions missing for mira_4_0_mapping. i.e. No test successes or failures reported. Collapsing the sections a bit: Test runs * 2014-02-18 16:15:52 *Automated test environment This was on Firefox (logged in, or logged out of the Tool Shed). Oddly, switching to Safari (not logged into the Tool Shed) on the same machine, or Chrome on a second machine, I also see an older test run's information where there is test output: Test runs * 2014-02-18 16:15:52 *Automated test environment * Tools missing tests or test data * 2014-02-18 03:40:12 * Automated test environment * Tests that failed * Tools missing tests or test data * Successful installation Might some strange cache or Firefox issue be hiding data? Thanks, 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] package_r_xx problem: X11 is not available
Hi Geert, I tried to update the R package to include the libpng dependency, if you like to test it ... http://testtoolshed.g2.bx.psu.edu/view/iuc/package_r_3_0_2 Do you know if cairo is really needed? If I can I would omit to have a dependency on cairo :) Cheers, Bjoern Hi all, I installed to package_r_2.11 and r_3x from the devteam to use as tool dependency. All installation goes fine, but when I run my tool I get the following error: Error in png(file = ../Plots/outname.png, bg = white, width = 480, : X11 is not available The tool uses the installed R : /galaxy/galaxy_tool_binaries/R/2.11.0/devteam/package_r_2_11_0/8d0a55bf7aaf/lib/R/bin/R If I force the tool to use the system installed version of R, it works fine. Are there packages available in the toolsheds that allow the 'png' function to work? I already tried the R-packages from boris, but they gave compilation errors... I also tried to install the R-png package from cran as a galaxy dependency, but that didn't help either. Thanks for the help, Geert ___ 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/
[galaxy-dev] Tools with multiple input files, and multiple output files
Hi all, I'm looking for examples of tools which take multiple input files (one or more, determined at run time) and produce multiple output files (one for each input file). Any specific suggestions? I have a number of sequence filtering/renaming tools where this might be useful - in some cases taking multiple input files and producing a single output is fine, but in general I'd like to know how to preserve a one to one mapping from input files to output files. I realise this may overlap slightly with the work John is doing on dataset collections, but for now I'd like to target the current Galaxy feature set. In some of the simpler cases, if I have N input datasets and want N output files, I can just run the tool N times . This means more steps in the Galaxy GUI, but it isn't very complicated. However, for the current problem I need access to all the inputs at once for setting overall data derived parameters. Regards, 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] Sending tool output to input parameters of downstream tool(s)
Hi all, I was recently wondering how it might be possible for an output from tool A to be used as a parameter when calling tool B (without modifying tool B to take a data configuration file or anything like that). To clarify, I'm thinking about simple parameters like a single integer/float/string like median insert size or average coverage which map to a single input parameter in a downstream tool. Workflow parameters basic $variable support is similar to what I'm thinking about here, see: https://wiki.galaxyproject.org/DevNewsBriefs/2011_01_31 Perhaps one day in addition to tool outputs being files, they can include setting $variables (local to the history), which could then be used within downstream tools? I can see this has downsides with tracking the providence of each variable though... thus: Another idea would be extra filetypes for each parameter type (Unix philosophy - make everything into a file), e.g. integer_parameter, float_parameter, ... which Tool A could define as an output, and write to. Galaxy would then need to offer these history entries to the user when a later tool (e.g. Tool B) asked for a parameter of that type (e.g. an integer, or a float). (This idea could be extended further, with data files using JSON or something to hold a structured set of parameter values which Galaxy could then offer to fill later tool's inputs.) Crazy, or is there some mileage in this idea? 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Tools with multiple input files, and multiple output files
Hey Peter, Have you seen this solution? https://wiki.galaxyproject.org/Admin/Tools/Multiple%20Output%20Files#Number_of_Output_datasets_cannot_be_determined_until_tool_run It always seems to get mentioned when this topic is brought up. It has serious limitations in terms or workflow running, but it can probably be made to work for individual tool executions. Otherwise I would wait for future feature sets :), maybe other people have some good ideas however. -John On Wed, Feb 19, 2014 at 7:16 AM, Peter Cock p.j.a.c...@googlemail.com wrote: Hi all, I'm looking for examples of tools which take multiple input files (one or more, determined at run time) and produce multiple output files (one for each input file). Any specific suggestions? I have a number of sequence filtering/renaming tools where this might be useful - in some cases taking multiple input files and producing a single output is fine, but in general I'd like to know how to preserve a one to one mapping from input files to output files. I realise this may overlap slightly with the work John is doing on dataset collections, but for now I'd like to target the current Galaxy feature set. In some of the simpler cases, if I have N input datasets and want N output files, I can just run the tool N times . This means more steps in the Galaxy GUI, but it isn't very complicated. However, for the current problem I need access to all the inputs at once for setting overall data derived parameters. Regards, 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] Galaxy-LIMS and multiple sample
Dear all, I don't have an instance of galaxy that manages sequencing requests. I would like to, but I would like to know a single thing: Is the interface friendly enough to make me define multiple sample at once in a single request? Thanks d ___ 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/
Re: [galaxy-dev] Tools with multiple input files, and multiple output files
On Wed, Feb 19, 2014 at 2:16 PM, John Chilton jmchil...@bx.psu.edu wrote: Hey Peter, Have you seen this solution? https://wiki.galaxyproject.org/Admin/Tools/Multiple%20Output%20Files#Number_of_Output_datasets_cannot_be_determined_until_tool_run It always seems to get mentioned when this topic is brought up. It has serious limitations in terms or workflow running, but it can probably be made to work for individual tool executions. Hmm. Any real life examples of this in use? I guess looking for the magic string $__new_file_path__ in the command tag is the only way to identify this? Otherwise I would wait for future feature sets :), maybe other people have some good ideas however. I'll ponder this a bit more then... thanks. 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Tools with multiple input files, and multiple output files
On Wednesday, February 19, 2014, Peter Cock p.j.a.c...@googlemail.com wrote: On Wed, Feb 19, 2014 at 2:16 PM, John Chilton jmchil...@bx.psu.edujavascript:; wrote: Hey Peter, Have you seen this solution? https://wiki.galaxyproject.org/Admin/Tools/Multiple%20Output%20Files#Number_of_Output_datasets_cannot_be_determined_until_tool_run It always seems to get mentioned when this topic is brought up. It has serious limitations in terms or workflow running, but it can probably be made to work for individual tool executions. Hmm. Any real life examples of this in use? I guess looking for the magic string $__new_file_path__ in the command tag is the only way to identify this? Hi Peter, I used the current functionality here: http://toolshed.g2.bx.psu.edu/view/cjav/split_by_barcode The code for the underlining tool is available here: https://github.com/cjav/ngs-tools Hope it helps, Carlos ___ 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/
Re: [galaxy-dev] Local Galaxy web layout
Hi Shenwiyn, Can you specify what is not working? Did you find the file? Thanks, Sam On Wed, Feb 19, 2014 at 1:42 AM, shenw...@gmail.com shenw...@gmail.comwrote: Hi Sam and Hans-Rudolf， Thank you very much for your help.It seems that the static/scripts/galaxy.menu.js fail to work in my local Galaxy.As a result,would you please show me some more details about this? Regards, Shenwiyn *From:* sam guerler aysam.guer...@gmail.com *Date:* 2014-02-18 01:20 *To:* Hans-Rudolf Hotz h...@fmi.ch *CC:* shenw...@gmail.com; galaxy-dev galaxy-dev@lists.bx.psu.edu *Subject:* Re: [galaxy-dev] Local Galaxy web layout Hi Shenwiyn, This has changed recently. Please take a look at: static/scripts/galaxy.menu.js Using that file, you can add/remove/change labels and their position. It is recommended to run pack_scripts.py after changing the source file. Regards, Sam On Mon, Feb 17, 2014 at 11:33 AM, Hans-Rudolf Hotz h...@fmi.ch wrote: Hi Shenwiyn Have a look at: ~/galaxy_dist/database/compiled_templates/base_panels.mako.py Regards, Hans-Rudolf On 02/17/2014 08:04 AM, shenw...@gmail.com wrote: Galaxy developers: I want to change my local Galaxy web layout,for example,delete the top button of Visualization and Cloud or change their positions.Could anyone show me some details about this? Thank you very much. shenw...@gmail.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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] Galaxy-LIMS and multiple sample
Dear all, I don't have an instance of galaxy that manages sequencing requests. I would like to, but I would like to know a single thing: Is the interface friendly enough to make me define multiple sample at once in a single request? Thanks d ___ 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/
Re: [galaxy-dev] Tools with multiple input files, and multiple output files
FYI: it is my understanding that such tools cannot be used in a workflow at this time. On Feb 19, 2014 10:08 AM, Carlos Borroto carlos.borr...@gmail.com wrote: On Wednesday, February 19, 2014, Peter Cock p.j.a.c...@googlemail.com wrote: On Wed, Feb 19, 2014 at 2:16 PM, John Chilton jmchil...@bx.psu.edu wrote: Hey Peter, Have you seen this solution? https://wiki.galaxyproject.org/Admin/Tools/Multiple%20Output%20Files#Number_of_Output_datasets_cannot_be_determined_until_tool_run It always seems to get mentioned when this topic is brought up. It has serious limitations in terms or workflow running, but it can probably be made to work for individual tool executions. Hmm. Any real life examples of this in use? I guess looking for the magic string $__new_file_path__ in the command tag is the only way to identify this? Hi Peter, I used the current functionality here: http://toolshed.g2.bx.psu.edu/view/cjav/split_by_barcode The code for the underlining tool is available here: https://github.com/cjav/ngs-tools Hope it helps, Carlos ___ 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/ ___ 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/
Re: [galaxy-dev] Tools with multiple input files, and multiple output files
On Feb 19, 2014 10:08 AM, Carlos Borroto carlos.borr...@gmail.com wrote: Hi Peter, I used the current functionality here: http://toolshed.g2.bx.psu.edu/view/cjav/split_by_barcode The code for the underlining tool is available here: https://github.com/cjav/ngs-tools Hope it helps, Carlos Thanks - a non-trivial example to study always helps :) On Wed, Feb 19, 2014 at 3:33 PM, Michael Crusoe michael.cru...@gmail.com wrote: FYI: it is my understanding that such tools cannot be used in a workflow at this time. That would be a problem :( 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] using svg foreignObject tags can circumvent html sanitization
Hello Tobias, Thanks for the heads up. I am not sure what the best way to address this is - but if I still was responsible for a public server I think I would open my datatype_conf.xml file and replace all instances of application/xml and image/svg+xml with text/plain in an effort to get Galaxy not to serve user generated SVG data as plain text. -John On Tue, Feb 18, 2014 at 7:01 PM, Tobias Sargeant tobias.sarge...@gmail.com wrote: In experimenting with how we could embed javascript/unsanitized html in tool output we came across the following method. Given that the current default is to disallow such activities, we thought it might be useful to bring it to your attention. The attached file provides an example, which, when uploaded to a history and viewed produces a popup on the current stable release of galaxy (local install and https://usegalaxy.org). Cheers, Tobias Sargeant. ___ 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/ ___ 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/
Re: [galaxy-dev] Galaxy-LIMS and multiple sample
Hello Davide, yes it does. Also these two modifications of Galaxy might be if an interest to you as they enhanced the sample tracking further: http://bcbio.wordpress.com/2011/01/11/next-generation-sequencing-information-management-and-analysis-system-for-galaxy/ http://bioinformatics.oxfordjournals.org/content/29/9/1233.long Martin On Wed, Feb 19, 2014 at 9:51 AM, Davide Cittaro daweonl...@gmail.comwrote: Dear all, I don't have an instance of galaxy that manages sequencing requests. I would like to, but I would like to know a single thing: Is the interface friendly enough to make me define multiple sample at once in a single request? Thanks d ___ 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/ ___ 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/
Re: [galaxy-dev] Tools with multiple input files, and multiple output files
On Wed, Feb 19, 2014 at 11:04 AM, Peter Cock p.j.a.c...@googlemail.com wrote: On Wed, Feb 19, 2014 at 3:33 PM, Michael Crusoe michael.cru...@gmail.com wrote: FYI: it is my understanding that such tools cannot be used in a workflow at this time. That would be a problem :( Well, I haven't checked but I don't see why it would be a problem if your tool is the last one in the workflow. It cannot be an intermediary step as there is no easy way to link the outputs of a this kind of tool to the next tool. --Carlos ___ 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/
Re: [galaxy-dev] Tools with multiple input files, and multiple output files
I suggested augmenting the tool_conf syntax as part of the DataCollection
development.
To replace the need for the the multiple output determined at runtime,
I suggest being able to declare data collections within the outputs tags, and
being able to use regular expressions in the from_work_dir param to populate
the collections.
In workflows, one would want to be able to hook a data collection output to a
data input.
Mothur Metagenomics tool that has an output per distance label and calculator
method
An example of declaring a list of outputs, which will determined at run time
based on from_work_dir regular expression:
tool id=mothur_classify_otu name=Classify.otu version=1.20.0
force_history_refresh=True
...
outputs
dataset_collection type=list label=${tool.name} on ${on_string} consensus
taxonomies
data format=cons.taxonomy name=splicing_diff label=${tool.name} on ${on_string}:
${file_name} from_work_dir=^\S+?\.(unique|[0-9.]*\.cons\.taxonomy)$ /
/dataset_collection
dataset_collection type=list label={tool.name} on ${on_string} taxomy
summaries
data format=cons.taxonomy name=splicing_diff label=${tool.name} on ${on_string}:
${file_name} from_work_dir=^\S+?\.(unique|[0-9.]*\.cons\.tax\.summary)$ /
/dataset_collection
/outputs
Hey Peter,
Have you seen this solution?
https://wiki.galaxyproject.org/Admin/Tools/Multiple%20Output%20Files#Number_of_Output_datasets_cannot_be_determined_until_tool_run
It always seems to get mentioned when this topic is brought up. It has
serious limitations in terms or workflow running, but it can probably
be made to work for individual tool executions.
Otherwise I would wait for future feature sets, maybe other people
have some good ideas however.
-John
On Wed, Feb 19, 2014 at 7:16 AM, Peter Cockp.j.a.c...@googlemail.com wrote:
Hi all,
I'm looking for examples of tools which take multiple input
files (one or more, determined at run time) and produce
multiple output files (one for each input file). Any
specific suggestions?
I have a number of sequence filtering/renaming tools
where this might be useful - in some cases taking
multiple input files and producing a single output is
fine, but in general I'd like to know how to preserve a
one to one mapping from input files to output files.
I realise this may overlap slightly with the work John is
doing on dataset collections, but for now I'd like to target
the current Galaxy feature set.
In some of the simpler cases, if I have N input datasets
and want N output files, I can just run the tool N times .
This means more steps in the Galaxy GUI, but it isn't
very complicated.
However, for the current problem I need access to all
the inputs at once for setting overall data derived
parameters.
Regards,
Peter
___
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and other Galaxy lists, please use the interface at:
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http://galaxyproject.org/search/mailinglists/
--
James E. Johnson, Minnesota Supercomputing Institute, University of Minnesota
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[galaxy-dev] select with a value preselected
Hello, In my tool UI, I have a select tool as follows: param name=site type=select multiple=true label=Execution Location help=Multi-select list - hold the appropriate key while clicking to select multiple items option value=localhostLocalhost/option option value=midwayMidway/option option value=uc3UC3/option option value=stampedeStampede/option option value=tukeyTukey/option /param How do I tell it to preselect value localhost by default? Currently, user has to explicitly select the a value but if she forgets to do so the tool breaks because nothing is selected by default. Thanks, -- Ketan ___ 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/
Re: [galaxy-dev] select with a value preselected
Hi Ketan, You can specify selected=true[1] [1] https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax#A.3Coption.3E_tag_set On 19 February 2014 20:14, Ketan Maheshwari ketancmaheshw...@gmail.com wrote: Hello, In my tool UI, I have a select tool as follows: param name=site type=select multiple=true label=Execution Location help=Multi-select list - hold the appropriate key while clicking to select multiple items option value=localhostLocalhost/option option value=midwayMidway/option option value=uc3UC3/option option value=stampedeStampede/option option value=tukeyTukey/option /param How do I tell it to preselect value localhost by default? Currently, user has to explicitly select the a value but if she forgets to do so the tool breaks because nothing is selected by default. Thanks, -- Ketan ___ 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/ ___ 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/
Re: [galaxy-dev] select with a value preselected
Great! Thanks. On Wed, Feb 19, 2014 at 2:18 PM, Saket Choudhary sake...@gmail.com wrote: Hi Ketan, You can specify selected=true[1] [1] https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax#A.3Coption.3E_tag_set On 19 February 2014 20:14, Ketan Maheshwari ketancmaheshw...@gmail.com wrote: Hello, In my tool UI, I have a select tool as follows: param name=site type=select multiple=true label=Execution Location help=Multi-select list - hold the appropriate key while clicking to select multiple items option value=localhostLocalhost/option option value=midwayMidway/option option value=uc3UC3/option option value=stampedeStampede/option option value=tukeyTukey/option /param How do I tell it to preselect value localhost by default? Currently, user has to explicitly select the a value but if she forgets to do so the tool breaks because nothing is selected by default. Thanks, -- Ketan ___ 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/ -- Ketan ___ 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/
Re: [galaxy-dev] package_r_xx problem: X11 is not available
hi, The dependencies installed fine, but R itself gave this error: configure: error: unrecognized option: `-I/galaxy/galaxy_tool_binaries/libpng/1.6.7/devteam/package_libpng_1_6_7/a0b0e0281cc4/include' Try `./configure --help' for more information Any idea what might be wrong? Best, Geert On 02/19/2014 12:55 PM, Björn Grüning wrote: Hi Geert, I tried to update the R package to include the libpng dependency, if you like to test it ... http://testtoolshed.g2.bx.psu.edu/view/iuc/package_r_3_0_2 Do you know if cairo is really needed? If I can I would omit to have a dependency on cairo :) Cheers, Bjoern Hi all, I installed to package_r_2.11 and r_3x from the devteam to use as tool dependency. All installation goes fine, but when I run my tool I get the following error: Error in png(file = ../Plots/outname.png, bg = white, width = 480, : X11 is not available The tool uses the installed R : /galaxy/galaxy_tool_binaries/R/2.11.0/devteam/package_r_2_11_0/8d0a55bf7aaf/lib/R/bin/R If I force the tool to use the system installed version of R, it works fine. Are there packages available in the toolsheds that allow the 'png' function to work? I already tried the R-packages from boris, but they gave compilation errors... I also tried to install the R-png package from cran as a galaxy dependency, but that didn't help either. Thanks for the help, Geert -- Geert Vandeweyer, Ph.D. Department of Medical Genetics University of Antwerp Prins Boudewijnlaan 43 2650 Edegem Belgium Tel: +32 (0)3 275 97 56 E-mail: geert.vandewe...@ua.ac.be http://ua.ac.be/cognitivegenetics http://www.linkedin.com/in/geertvandeweyer ___ 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/
Re: [galaxy-dev] Nightly testing status on the (Test) Tool Shed
Hello Peter, Please see below… On Feb 19, 2014, at 4:41 AM, Peter Cock p.j.a.c...@googlemail.com wrote: Hi Greg, Overnight this has gone back to the previously observed missing data problem (e.g. email of 4th Feb) - no test results at all: http://testtoolshed.g2.bx.psu.edu/view/peterjc/mira4_assembler Test runs 2014-02-18 16:15:52 Automated test environment Time tested: 2014-02-18 16:15:52 System: Architecture: Python version: Galaxy revision: Galaxy database version: Tool shed revision: 12485:64e6873c8825 Tool shed database version: 22 Tool shed mercurial version: 2.2.3 Tools missing tests or test data Tool id: mira_4_0_mapping Tool version: 0.0.2 Tool guid: testtoolshed.g2.bx.psu.edu/repos/peterjc/mira4_assembler/mira_4_0_mapping/0.0.2 Missing components: Functional test definitions missing for mira_4_0_mapping. i.e. No test successes or failures reported. Collapsing the sections a bit: Test runs * 2014-02-18 16:15:52 *Automated test environment This was on Firefox (logged in, or logged out of the Tool Shed). Oddly, switching to Safari (not logged into the Tool Shed) on the same machine, or Chrome on a second machine, I also see an older test run's information where there is test output: Test runs * 2014-02-18 16:15:52 *Automated test environment * Tools missing tests or test data * 2014-02-18 03:40:12 * Automated test environment * Tests that failed * Tools missing tests or test data * Successful installation Might some strange cache or Firefox issue be hiding data? Your above email arrived in my inbox at 4:42 AM EST, and it looks like your repository in question was not yet tested. Using Firefox, I see the following resutls for today's test run, the results of which were updated in your Tool Shed repository at 4:50 AM EST. The nightly Install and Test Framework is finishing at about 8:00 AM EST for hte Test Tool Shed. The runs finish for the Main Tool Shed at about 5:00 AM EST. Test runs 2014-02-19 04:50:21 Automated test environment Time tested: 2014-02-19 04:50:21 System: Linux 3.8.0-30-generic Architecture: x86_64 Python version: 2.7.4 Galaxy revision: 12536:c85f8fb5d63e Galaxy database version: 118 Tool shed revision: 12485:64e6873c8825 Tool shed database version: 22 Tool shed mercurial version: 2.2.3 Tests that failed Tool id: mira_4_0_bait Tool version: mira_4_0_bait Test: test_tool_00 (functional.test_toolbox.TestForTool_testtoolshed.g2.bx.psu.edu/repos/peterjc/mira4_assembler/mira_4_0_bait/0.0.1) Stderr: Fatal error: Exit code 1 () Missing mirabait under $MIRA4, '/ToolDepsTest/MIRA/4.0/peterjc/mira4_assembler/133b863a8a40/mirabait' Folder contained: env.sh Traceback: Traceback (most recent call last): File /var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/test/functional/test_toolbox.py, line 106, in test_tool self.do_it( td ) File /var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/test/functional/test_toolbox.py, line 34, in do_it self._verify_outputs( testdef, test_history, shed_tool_id, data_list, galaxy_interactor ) File /var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/test/functional/test_toolbox.py, line 67, in _verify_outputs galaxy_interactor.verify_output( history, output_data, outfile, attributes=attributes, shed_tool_id=shed_tool_id, maxseconds=maxseconds ) File /var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/test/base/interactor.py, line 312, in verify_output self.twill_test_case.verify_dataset_correctness( outfile, hid=hid, attributes=attributes, shed_tool_id=shed_tool_id, maxseconds=maxseconds ) File /var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/test/base/twilltestcase.py, line 827, in verify_dataset_correctness self._assert_dataset_state( elem, 'ok' ) File /var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/test/base/twilltestcase.py, line 641, in _assert_dataset_state raise AssertionError( errmsg ) AssertionError: Expecting dataset state 'ok', but state is 'error'. Dataset blurb: error Tool id: mira_4_0_bait Tool version: mira_4_0_bait Test: test_tool_01 (functional.test_toolbox.TestForTool_testtoolshed.g2.bx.psu.edu/repos/peterjc/mira4_assembler/mira_4_0_bait/0.0.1) Stderr: Fatal error: Exit code 1 () Missing mirabait under $MIRA4, '/ToolDepsTest/MIRA/4.0/peterjc/mira4_assembler/133b863a8a40/mirabait' Folder contained: env.sh Traceback: Traceback (most recent call last): File /var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/test/functional/test_toolbox.py, line 106, in test_tool
Re: [galaxy-dev] Nightly testing status on the (Test) Tool Shed
On Wed, Feb 19, 2014 at 8:42 PM, Greg Von Kuster g...@bx.psu.edu wrote: Hello Peter, Please see below... ... Your above email arrived in my inbox at 4:42 AM EST, and it looks like your repository in question was not yet tested. Ah. That would partly explain things - perhaps coupled with a cache effect it might even explain why different browsers seemed to give me different output Could Galaxy include the time zone (EST) in the Tool Shed test time stamps and/or show GMT/UTC? (You have no easy way of knowing the user's local timezone do you?). Alternatively, Test in progress would be nice :) As to the test failure, it seems $INSTALL_DIR or at least $MIRA4 only contains env.sh (which puzzles me). Thanks, 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Nightly testing status on the (Test) Tool Shed
Hi Peter, Dave B and I just discovered that issue that causes your tests to fail. The problem lies with our current implementation supporting the move_directory_files action tag, which is used in your recipe. This tag ultimately uses Python's os.listdir via shutil.move. It turns out that certain Python versions produce different results from os.listdir - the order is different. This is a problem with MIRA because during the instlllation it is moving a directory of files where the directory includes symlinks to other files in the directory. When the symlinks are moved after the files to which they link, problems occur. Again, this behavior is intermittent depending on the Pyhton version ( and perhaps the os ). In any case, we have a fix for out move_directory_files which Dave is now committing. So your tests should pass with tonight's run - Let's hope! Thanks Peter! Greg Von Kuster On Feb 19, 2014, at 3:49 PM, Peter Cock p.j.a.c...@googlemail.com wrote: On Wed, Feb 19, 2014 at 8:42 PM, Greg Von Kuster g...@bx.psu.edu wrote: Hello Peter, Please see below... ... Your above email arrived in my inbox at 4:42 AM EST, and it looks like your repository in question was not yet tested. Ah. That would partly explain things - perhaps coupled with a cache effect it might even explain why different browsers seemed to give me different output Could Galaxy include the time zone (EST) in the Tool Shed test time stamps and/or show GMT/UTC? (You have no easy way of knowing the user's local timezone do you?). Alternatively, Test in progress would be nice :) As to the test failure, it seems $INSTALL_DIR or at least $MIRA4 only contains env.sh (which puzzles me). Thanks, 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Nightly testing status on the (Test) Tool Shed
On Wed, Feb 19, 2014 at 9:33 PM, Greg Von Kuster g...@bx.psu.edu wrote: Hi Peter, Dave B and I just discovered that issue that causes your tests to fail. The problem lies with our current implementation supporting the move_directory_files action tag, which is used in your recipe. This tag ultimately uses Python's os.listdir via shutil.move. It turns out that certain Python versions produce different results from os.listdir - the order is different. This is a problem with MIRA because during the instlllation it is moving a directory of files where the directory includes symlinks to other files in the directory. When the symlinks are moved after the files to which they link, problems occur. Again, this behavior is intermittent depending on the Pyhton version ( and perhaps the os ). In any case, we have a fix for out move_directory_files which Dave is now committing. So your tests should pass with tonight's run - Let's hope! Thanks Peter! Well done Greg Dave, That explanation makes perfect sense to me - but I can see it took some digging to solve it! There is actually one MIRA binary (mira) and several aliases (e.g. mirabait) which are really symlinks back to mira. Magic. My next query would be: why wasn't the failing action move_directory_files being caught as a failed install? Thanks, 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] package_r_xx problem: X11 is not available
Hi Geert, can you retest please, I had a typo. Unfortunately, I can't test it by myself since my internet connection is to bad here in Slovenia to download that R-tarball. Sorry, Bjoern hi, The dependencies installed fine, but R itself gave this error: configure: error: unrecognized option: `-I/galaxy/galaxy_tool_binaries/libpng/1.6.7/devteam/package_libpng_1_6_7/a0b0e0281cc4/include' Try `./configure --help' for more information Any idea what might be wrong? Best, Geert On 02/19/2014 12:55 PM, Björn Grüning wrote: Hi Geert, I tried to update the R package to include the libpng dependency, if you like to test it ... http://testtoolshed.g2.bx.psu.edu/view/iuc/package_r_3_0_2 Do you know if cairo is really needed? If I can I would omit to have a dependency on cairo :) Cheers, Bjoern Hi all, I installed to package_r_2.11 and r_3x from the devteam to use as tool dependency. All installation goes fine, but when I run my tool I get the following error: Error in png(file = ../Plots/outname.png, bg = white, width = 480, : X11 is not available The tool uses the installed R : /galaxy/galaxy_tool_binaries/R/2.11.0/devteam/package_r_2_11_0/8d0a55bf7aaf/lib/R/bin/R If I force the tool to use the system installed version of R, it works fine. Are there packages available in the toolsheds that allow the 'png' function to work? I already tried the R-packages from boris, but they gave compilation errors... I also tried to install the R-png package from cran as a galaxy dependency, but that didn't help either. Thanks for the help, Geert -- Geert Vandeweyer, Ph.D. Department of Medical Genetics University of Antwerp Prins Boudewijnlaan 43 2650 Edegem Belgium Tel: +32 (0)3 275 97 56 E-mail:geert.vandewe...@ua.ac.be http://ua.ac.be/cognitivegenetics http://www.linkedin.com/in/geertvandeweyer ___ 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/
Re: [galaxy-dev] Nightly testing status on the (Test) Tool Shed
Hi Peter, On Feb 19, 2014, at 6:09 PM, Peter Cock p.j.a.c...@googlemail.com wrote: On Wed, Feb 19, 2014 at 9:33 PM, Greg Von Kuster g...@bx.psu.edu wrote: Hi Peter, Dave B and I just discovered that issue that causes your tests to fail. The problem lies with our current implementation supporting the move_directory_files action tag, which is used in your recipe. This tag ultimately uses Python's os.listdir via shutil.move. It turns out that certain Python versions produce different results from os.listdir - the order is different. This is a problem with MIRA because during the instlllation it is moving a directory of files where the directory includes symlinks to other files in the directory. When the symlinks are moved after the files to which they link, problems occur. Again, this behavior is intermittent depending on the Pyhton version ( and perhaps the os ). In any case, we have a fix for out move_directory_files which Dave is now committing. So your tests should pass with tonight's run - Let's hope! Thanks Peter! Well done Greg Dave, That explanation makes perfect sense to me - but I can see it took some digging to solve it! There is actually one MIRA binary (mira) and several aliases (e.g. mirabait) which are really symlinks back to mira. Magic. My next query would be: why wasn't the failing action move_directory_files being caught as a failed install? Your installation recipe for mira attempts to download a binary and if that fails, it echoes an error, but still performs set_environment actions.. The tool dependency installation process will fall back to attempting the installation using the action tags to handle install from source and compile if downloading a pre-compiled binary fails. However, your recipe does not have include installing from source, so the installation process simply assumed your set_environment tags were all that was necessary. If the recipe for installing from source is not too complex, maybe you could add it to your recipe. It's probabluy not critical though since we now have the fix to the framework. Here is the entire log of the installtion process that helped us uncover the problem - notice that upon failure of the initial binary installation, the process proceeds with install and compile recipe for tool dependency MIRA. tool_shed.galaxy_install.tool_dependencies.fabric_util DEBUG 2014-02-19 04:50:42,285 Successfully downloaded from url: https://downloads.sourceforge.net/project/mira-assembler/MIRA/stable/mira_4.0_linux-gnu_x86_64_static.tar.bz2 tool_shed.galaxy_install.tool_dependencies.install_util ERROR 2014-02-19 04:50:42,318 Error installing tool dependency MIRA version 4.0. Traceback (most recent call last): File /var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py, line 289, in install_and_build_package_via_fabric tool_dependency = fabric_util.install_and_build_package( app, tool_dependency, actions_dict ) File /var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py, line 581, in install_and_build_package destination_dir=os.path.join( action_dict[ 'destination_directory' ] ) ) File /var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/lib/tool_shed/galaxy_install/tool_dependencies/td_common_util.py, line 309, in move_directory_files shutil.move( source_file, destination_file ) File /usr/lib/python2.7/shutil.py, line 301, in move copy2(src, real_dst) File /usr/lib/python2.7/shutil.py, line 130, in copy2 copyfile(src, dst) File /usr/lib/python2.7/shutil.py, line 82, in copyfile with open(src, 'rb') as fsrc: IOError: [Errno 2] No such file or directory: '/var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/test/install_and_test_tool_shed_repositories/repositories_with_tools/tmp/tmpdr4lDp/tmp-toolshed-mtdV8W9PM/mira_4.0_linux-gnu_x86_64_static/bin/mirabait' tool_shed.galaxy_install.tool_dependencies.install_util DEBUG 2014-02-19 04:50:42,541 Error downloading binary for tool dependency MIRA version 4.0: File /var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py, line 289, in install_and_build_package_via_fabric tool_dependency = fabric_util.install_and_build_package( app, tool_dependency, actions_dict ) File /var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py, line 581, in install_and_build_package destination_dir=os.path.join( action_dict[ 'destination_directory' ] ) ) File
