[galaxy-dev] Citing Galaxy + Toolshed in an app note of a small tool
Hello Galaxy People! (it's been a while since I've last been here... a pleasure to be back). I intend to publish a small command-line utility, which will also be available through Galaxy Toolshed. It'll be a small application note, so not a lot of space for many citations. The relevant sentence would read something like: The tool is also available for the Galaxy Bioinformatics Platform [Cite1], with automatic installation provided though the Galaxy Tool Shed [Cite2]. What should I use for [cite1 (galaxy) and [cite2 (toolshed)], out of this impressive long list of publications: https://wiki.galaxyproject.org/CitingGalaxy Thanks! -gordon ___ 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] Errors loading data into IGV from Galaxy
Dear John and the Galaxy team, Thank you for your prompt response however, I am still getting the same error that I reported previously. I attempted to load the data again at 9:45am Central Time on Wednesday March 26th, and received the following error Errors were encountered loading the session: https://main.g2.bx.psu.edu/display_application/b35f82886ba2954e/igv_bam/web_link_main/99234cff5c86008d/data/galaxy_b35f82886ba2954e.bam nbs;p org.broad.igv.exceptions.DataLoadException: HTTP access error (status code 500) https://main.g2.bx.psu.edu/display_application/70deaaa1fc17635d/igv_bam/web_link_main/39ca6e346e73f08a/data/galaxy_70deaaa1fc17635d.bam nbs;p org.broad.igv.exceptions.DataLoadException: HTTP access error (status code 500) As I previously stated this IGV session has properly loaded previously but hasn't done so successfully for about week. Please let me know of any additional information that you may need to help trouble shoot this problem, or if I am not addressing this problem in the proper forum or manner. Thank you again for your help, Sincerely, -Paul Hillman- From: John Chilton [jmchil...@gmail.com] Sent: Wednesday, March 26, 2014 9:36 AM To: Hillman, Paul R. Cc: galaxy-...@bx.psu.edu Subject: Re: [galaxy-dev] Errors loading data into IGV from Galaxy I think usegalaxy.org (which main.g2.bx.psu.edu still aliases) was experiencing many issues and was mostly down over the time period you described due to disk and network issues in the data center at TACC. Those specific links no longer seem to produce 500 status code errors and usegalaxy.org has been up and fine for a couple days - so things should work again I guess. Please let the list know if this is not the case. -John On Tue, Mar 25, 2014 at 10:15 AM, Hillman, Paul R. phill...@medicine.tamhsc.edu wrote: Dear Galaxy Team, I have already contacted IgV about this issue and they say that I needed to contact you. I have had and instance of IgV shared with me for some time and it has worked as recently as last week. However, even last week the data was only loading approximately 25% of the time and now will not load at all. Could you please explain the error that I am getting below and what can be done to correct them. Unfortunately the individual who created and shared these files is no longer in the lab so I do not have direct access to the data. Any help would be greatly appreciated. Sincerely, -Paul Hillman- Errors were encountered loading the session: https://main.g2.bx.psu.edu/display_application/b35f82886ba2954e/igv_bam/web_link_main/99234cff5c86008d/data/galaxy_b35f82886ba2954e.bam nbs;p org.broad.igv.exceptions.DataLoadException: HTTP access error (status code 500) https://main.g2.bx.psu.edu/display_application/70deaaa1fc17635d/igv_bam/web_link_main/39ca6e346e73f08a/data/galaxy_70deaaa1fc17635d.bam nbs;p org.broad.igv.exceptions.DataLoadException: HTTP access error (status code 500) ___ 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] adding E.coli K-12 genome for mapping
Hi Guys, is it possible to add E.coli K12 genome for mapping with Bowtie on Andromeda-NCBI portal? thanks, timur ___ 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] trackster is not working on the vrelease_2014.02.10--2--29ce93a13ac7
Hi Jeremy, I cleaned the catche on both safari and firefox, but it doesn't work. It still shows the same error messages. Thank you very much for the help!! Best, Shu-Yi On Mar 26, 2014, at 2:00 PM, Jeremy Goecks wrote: This sounds like a cache issue. Both of these scripts have been removed from the distribution, so they should be absent from the distribution. Can you try clearing your cache and see if that fixes the issue? Thanks, J. -- Jeremy Goecks Assistant Professor of Computational Biology George Washington University On Mar 26, 2014, at 4:39 AM, Charles Girardot charles.girar...@embl.de wrote: Hi Jeremy, After checking, the two js scripts are absent from the release: backbone-relational.js ( static/scripts/packed/libs/backbone/ ) galaxy.utils.js ( static/scripts/packed/utils/ ) bw C On 25 Mar 2014, at 16:16, Shu-Yi Su wrote: Hi Jeremy, Thank you very much for the reply. Yes, we are running on galaxy-dist, and manually pulled to update our installation. The release version is vrelease_2014.02.10--2--29ce93a13ac7. I have tried safari and firefox. Both are not working. Here is the error massage from console: [Error] Failed to load resource: the server responded with a status of 404 (Not Found) (backbone-relational.js, line 0) [Error] Failed to load resource: the server responded with a status of 404 (Not Found) (galaxy.utils.js, line 0) [Error] Error: Script error for: libs/backbone/backbone-relational http://requirejs.org/docs/errors.html#scripterror defaultOnError (require.js, line 1) onError (require.js, line 1) onScriptError (require.js, line 1) [Error] Error: Script error for: utils/galaxy.utils http://requirejs.org/docs/errors.html#scripterror defaultOnError (require.js, line 1) onError (require.js, line 1) onScriptError (require.js, line 1);;; We are also wondering if there is anything we didn't set up probably for our universe_wsgi.ini file. Thank you. Best, Shu-Yi On Mar 25, 2014, at 4:05 PM, Jeremy Goecks wrote: Providing some additional information will help diagnose the problem: *are you running galaxy-dist? If so, have you manually pulled and applied commits from galaxy-central? If so, which ones? *which Web browser are you using? *can you please open the JavaScript console in your browser and provide any errors that you see? Thanks, J. -- Jeremy Goecks Assistant Professor of Computational Biology George Washington University On Mar 24, 2014, at 11:38 AM, Shu-Yi Su shu-yi...@embl.de wrote: Hi all, We have recently updated our local Galaxy installation to vrelease_2014.02.10--2--29ce93a13ac7 (database version is 118). I found that the Trackster is not working. I have checked the latest commits related to Trackster bugs. So i have updated theses files: ./static/scripts/viz/trackster.js (commits date: 2014-02-28) ./static/scripts/viz/trackster_ui.js (commits date: 2014-02-28) ./static/scripts/viz/trackster/tracks.js (commits date: 2014-03-16) ./static/scripts/utils/utils.js (commits date: 2014-03-19) ./static/scripts/utils/config.js (commits date: 2014-03-15) But, it is still not working. I have tried different format…bam, bed, sam….all are not working. I looked into all possible files I can think about that might cause the problems but still don't have any clues. I also looked into the log, and there is no error, but i noticed that there is difference from the log where the trackster was working in previous installation. The log where the trackster is not working: 1. GET /galaxy-dev/visualization/trackster?dataset_id=f04ecb1d3d259245hda_ldda=hda The log where the trackster is working (from the old installation): 1. GET /galaxy/visualization/trackster?dataset_id=5d38b380cba2f4a6hda_ldda=hda…… 2. GET /galaxy/api/datasets/5d38b380cba2f4a6?hda_ldda=hdadata_type=converted_datasets_state…. 3. GET /galaxy/api/datasets/5d38b380cba2f4a6?data_type=datachrom=chr2L….. It looks like that the trackster in new version of Galaxy does not execute the second and the third steps. Here is the screen shot when i clicked View in new visualization (there is nothing shown up---blank) Any ideas or suggestions are appreciated. Thank you very much. Best, Shu-Yi PastedGraphic-1.tiff ___ 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/
Re: [galaxy-dev] Galaxy startup takes very long. Normal?
I'm using galxy-dist. That's why I don't have the setting. Thanks for the information, I'll wait for the next stable release and update the settings then. Geert On 03/26/2014 01:59 PM, Greg Von Kuster wrote: The changeset that made this a configurable setting was committed to the stable branch ind270d3c, which was committed on 2014-02-19 https://bitbucket.org/galaxy/galaxy-central/commits/d270d3cf7627a42b6fac2aa69701deadb89c8ffc If you are tracking the stable branch in the galaxy central repo (which it looks like you are doing), then you should be able to pull it from there. Greg Von Kuster On Mar 26, 2014, at 8:04 AM, Geert Vandeweyer geert.vandewey...@uantwerpen.be mailto:geert.vandewey...@uantwerpen.be wrote: Hi Greg, The setting was not in my universe_sample file. I added it, set log_info to DEBUG and restarted galaxy. The startup time remained the same, and there were many entries in the log file indicating that the lag is indeed the creation of the dependency system: tool_shed.galaxy_install.installed_repository_manager DEBUG 2014-03-26 13:01:01,176 Adding an entry for version 0.1.18 of package samtools to runtime_tool_dependencies_of_installed_tool_dependencies. tool_shed.galaxy_install.installed_repository_manager DEBUG 2014-03-26 13:01:02,645 Adding an entry for version 0.1.18 of package samtools to installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies. tool_shed.galaxy_install.installed_repository_manager DEBUG 2014-03-26 13:01:03,874 Adding an entry for version 0.1.18 of package samtools to runtime_tool_dependencies_of_installed_tool_dependencies. tool_shed.galaxy_install.installed_repository_manager DEBUG 2014-03-26 13:01:05,383 Adding an entry for version 0.1.18 of package samtools to installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies. tool_shed.galaxy_install.installed_repository_manager DEBUG 2014-03-26 13:01:06,533 Adding an entry for version 2.11.0 of package R to runtime_tool_dependencies_of_installed_tool_dependencies. tool_shed.galaxy_install.installed_repository_manager DEBUG 2014-03-26 13:01:08,054 Adding an entry for version 2.11.0 of package R to installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies. tool_shed.galaxy_install.installed_repository_manager DEBUG 2014-03-26 13:01:09,126 Adding an entry for version 2.11.0 of package R to runtime_tool_dependencies_of_installed_tool_dependencies. tool_shed.galaxy_install.installed_repository_manager DEBUG 2014-03-26 13:01:10,596 Adding an entry for version 2.11.0 of package R to installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies. tool_shed.galaxy_install.installed_repository_manager DEBUG 2014-03-26 13:01:11,803 Adding an entry for version 1.02.00 of package lastz to runtime_tool_dependencies_of_installed_tool_dependencies. tool_shed.galaxy_install.installed_repository_manager DEBUG 2014-03-26 13:01:13,332 Adding an entry for version 1.02.00 of package lastz to installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies. tool_shed.galaxy_install.installed_repository_manager DEBUG 2014-03-26 13:01:14,552 Adding an entry for version 3.0.1 of package R_3_0_1 to runtime_tool_dependencies_of_installed_tool_dependencies. tool_shed.galaxy_install.installed_repository_manager DEBUG 2014-03-26 13:01:15,943 Adding an entry for version 3.0.1 of package R_3_0_1 to installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies. tool_shed.galaxy_install.installed_repository_manager DEBUG 2014-03-26 13:01:17,162 Adding an entry for version 0.1.18 of package samtools to runtime_tool_dependencies_of_installed_tool_dependencies. tool_shed.galaxy_install.installed_repository_manager DEBUG 2014-03-26 13:01:18,594 Adding an entry for version 0.1.18 of package samtools to installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies. etc... I also note many double entries in the log files. Do I need a specific changeset for the parameter setting to take effect? Universe_wsgi.ini setting: # Enable use of an in-memory registry with bi-directional relationships between repositories manage_dependency_relationships = False Best, Geert On 03/26/2014 11:53 AM, Greg Von Kuster wrote: Hi Geert, The setting should be in your universe_wsgi.ini.sample, and you woud have to manually edit your universe_wsgi.ini to add it. I would say that 125 installed packages is probably what is causing the slow starts. This feature is not currently useful, so it can be set to not function with no problems. In the future I'll introduce additional benefits for this feature, and I'll look at ways to improve the startup speed. Greg Von Kuster On Mar 26, 2014, at 3:43 AM, Geert Vandeweyer geert.vandewey...@uantwerpen.be mailto:geert.vandewey...@uantwerpen.be wrote: hi Greg, I don't have that setting in my universe. Should I just add it? The output of hg
[galaxy-dev] How to write test cases for custom tool
Hi, I have implemented a custom tool which will parse a given string in to expected format. Installed this custom tool into galaxy and was able to run successfully. I would like to add test cases to this tool, can you please provide me resources to write test cases for this custom tool. Is this tool need functional, unit, integration test cases ? I am not sure about which test cases needed for this tool. Thanks, JanakiRam ___ 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] How to write test cases for custom tool
Hi, I found below resources: - Running testhttps://wiki.galaxyproject.org/Admin/RunningTests?action=showredirect=Admin%2FRunning+Tests - Writing Functional testshttps://wiki.galaxyproject.org/Admin/Tools/Writing%20Tests Thanks, JanakiRam On Thu, Mar 27, 2014 at 2:53 PM, Janaki Rama Rao Gollapudi janakiram.gollap...@india.semanticbits.com wrote: Hi, I have implemented a custom tool which will parse a given string in to expected format. Installed this custom tool into galaxy and was able to run successfully. I would like to add test cases to this tool, can you please provide me resources to write test cases for this custom tool. Is this tool need functional, unit, integration test cases ? I am not sure about which test cases needed for this tool. Thanks, JanakiRam ___ 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] ERROR executing tool
Hi, I tried to GROOMER my fastq data in fastq data, and galaxy did not allowed
me:Error executing tool: objectstore, __call_method failed: get_filename on ,
kwargs: {}could you please help me?Thank you
viR
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Re: [galaxy-dev] How to write test cases for custom tool
Hi, I have added tests to tool dependency xml, but how should I run these tests, can you please help me to run test cases. . tests test param name=input1 value=some string/ param name=input2 value=expected format/ output name=output file=output.txt/ /test /tests .. Thanks, G.JanakiRam On Thu, Mar 27, 2014 at 3:27 PM, Janaki Rama Rao Gollapudi janakiram.gollap...@india.semanticbits.com wrote: Hi, I found below resources: - Running testhttps://wiki.galaxyproject.org/Admin/RunningTests?action=showredirect=Admin%2FRunning+Tests - Writing Functional testshttps://wiki.galaxyproject.org/Admin/Tools/Writing%20Tests Thanks, JanakiRam On Thu, Mar 27, 2014 at 2:53 PM, Janaki Rama Rao Gollapudi janakiram.gollap...@india.semanticbits.com wrote: Hi, I have implemented a custom tool which will parse a given string in to expected format. Installed this custom tool into galaxy and was able to run successfully. I would like to add test cases to this tool, can you please provide me resources to write test cases for this custom tool. Is this tool need functional, unit, integration test cases ? I am not sure about which test cases needed for this tool. Thanks, JanakiRam ___ 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] How to write test cases for custom tool
As Janaki replied below, see: http://wiki.galaxyproject.org/Admin/RunningTests?action=showredirect=Admin%2FRunning+Tests On Mar 27, 2014, at 7:15 AM, Janaki Rama Rao Gollapudi janakiram.gollap...@india.semanticbits.com wrote: Hi, I have added tests to tool dependency xml, but how should I run these tests, can you please help me to run test cases. . tests test param name=input1 value=some string/ param name=input2 value=expected format/ output name=output file=output.txt/ /test /tests .. Thanks, G.JanakiRam On Thu, Mar 27, 2014 at 3:27 PM, Janaki Rama Rao Gollapudi janakiram.gollap...@india.semanticbits.com wrote: Hi, I found below resources: Running test Writing Functional tests Thanks, JanakiRam On Thu, Mar 27, 2014 at 2:53 PM, Janaki Rama Rao Gollapudi janakiram.gollap...@india.semanticbits.com wrote: Hi, I have implemented a custom tool which will parse a given string in to expected format. Installed this custom tool into galaxy and was able to run successfully. I would like to add test cases to this tool, can you please provide me resources to write test cases for this custom tool. Is this tool need functional, unit, integration test cases ? I am not sure about which test cases needed for this tool. Thanks, JanakiRam ___ 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] How to write test cases for custom tool
Hi, Thanks for reply. I composed a details email for better clarity. when run grep command in galaxy home folder ( ./run_functional_tests.sh -list | grep barcode-parse), I got no results. What I did was: - Implemented a custom tool (It has one python script and tool definition file. These files are located in ../tools/Mytools/customToolName/) - Then run the ToolShed in my local which is running on port 9009 (I have) - Created a new repository in the ToolShed (which is running on 9009) and uploaded .py and .xml files in to it - Now I run the galaxy (running on port 8080) and browse the my custom tool from my local galaxy and install the custom tool successfully - And shed_tool_conf.xml file updated with new section: - - section id=mTools name=MyTools version= - tool file=xxx.xx.x.xx/repos/janakiram-t1/barcode_parse_1/b6a60d02b1a2/barcode_parse_1/barcode- parse.xml guid=xxx.xx.x.xx:9009/repos/janakiram-t1/barcode_parse_1/barcode-parse/1.0.0 - tool_shedxxx.xxx.x.xx:9009/tool_shed - repository_namebarcode_parse_1/repository_name - repository_ownerjanakiram-t1/repository_owner - installed_changeset_revisionb6a60d02b1a2/installed_changeset_revision - idxxx.xxx.x.xx:9009/repos/janakiram-t1/barcode_parse_1/barcode-parse/1.0.0/id - version1.0.0/version - /tool - /section - My tool definition file look likes below: - - tool id=barcode-parse name=Barcode parse - descriptionsome description/description - command interpreter=pythonbarcode-parse.py $input1 $input2 $output/command - inputs - param format=input name=input1 type=text size=50 label=barcode help=Enter barcode - validator type=empty_field message=please enter barcode/ - /param - param format=input name=input2 type=text size=50 label=Expected format help=Enter format to parse barcode - validator type=empty_field message=please enter expected format barcode/ - /param - /inputs - outputs - data format=txt name=output / - /outputs - tests -test - param name=input1 value=test-01-sample-test-02-sampl1-test-03-sample3/ - param name=input2 value=name-id/ - output name=output file=barcode-parse.txt/ -/test - /tests - help -Parse the barcode into expected format - /help - /tool - As galaxy using tool_conf.xml.sample, this file has no section for my custom tool. I have added a section manually like below: section name=MyTools id=mTools tool file=myTools/barcode-parse/barcode-parse.xml / /section Then my tool id found when I run the grep command. After that Then I run the below command to run the test cases: sh run_functional_tests.sh -id barcode-parse But I got below out put (from the run_functional_tests.html) AttributeError: 'module' object has no attribute 'test_toolbox:TestForTool_barcode-parse' Am I doing anything wrong. Thanks, JanakiRam On Thu, Mar 27, 2014 at 6:16 PM, Greg Von Kuster g...@bx.psu.edu wrote: As Janaki replied below, see: http://wiki.galaxyproject.org/Admin/RunningTests?action=showredirect=Admin%2FRunning+Tests On Mar 27, 2014, at 7:15 AM, Janaki Rama Rao Gollapudi janakiram.gollap...@india.semanticbits.com wrote: Hi, I have added tests to tool dependency xml, but how should I run these tests, can you please help me to run test cases. . tests test param name=input1 value=some string/ param name=input2 value=expected format/ output name=output file=output.txt/ /test /tests .. Thanks, G.JanakiRam On Thu, Mar 27, 2014 at 3:27 PM, Janaki Rama Rao Gollapudi janakiram.gollap...@india.semanticbits.com wrote: Hi, I found below resources: - Running testhttps://wiki.galaxyproject.org/Admin/RunningTests?action=showredirect=Admin%2FRunning+Tests - Writing Functional testshttps://wiki.galaxyproject.org/Admin/Tools/Writing%20Tests Thanks, JanakiRam On Thu, Mar 27, 2014 at 2:53 PM, Janaki Rama Rao Gollapudi janakiram.gollap...@india.semanticbits.com wrote: Hi, I have implemented a custom tool which will parse a given string in to expected format. Installed this custom tool into galaxy and was able to run successfully. I would like to add test cases to this tool, can you please provide me resources to write test cases for this custom tool. Is this tool need functional, unit, integration test cases ? I am not sure about which test cases needed for this tool. Thanks, JanakiRam ___ Please keep all replies on the list by using reply all in your mail client.
Re: [galaxy-dev] How to write test cases for custom tool
Hello Janaki, Thanks for clarifying that you have installed your tools from a Tool Shed. In this case, functional tests do not use Galaxy's tool_conf.xml.sample, so changing it will make no difference. For information about running functional tests on tools installed from the Tool Shed, see: https://wiki.galaxyproject.org/TestingInstalledTools Basically, you'll be doing the following. The functional test framework is not currently set up to test a specific installed tool using a -id flag. You'll have to use just the -installed flagg which will end up testing all installed tools. export GALAXY_TOOL_DEPENDENCY_DIR=tool_dependencies; sh run_functional_tests.sh -installed Greg Von Kuster On Mar 27, 2014, at 8:58 AM, Janaki Rama Rao Gollapudi janakiram.gollap...@india.semanticbits.com wrote: Hi, Thanks for reply. I composed a details email for better clarity. when run grep command in galaxy home folder ( ./run_functional_tests.sh -list | grep barcode-parse), I got no results. What I did was: Implemented a custom tool (It has one python script and tool definition file. These files are located in ../tools/Mytools/customToolName/) Then run the ToolShed in my local which is running on port 9009 (I have) Created a new repository in the ToolShed (which is running on 9009) and uploaded .py and .xml files in to it Now I run the galaxy (running on port 8080) and browse the my custom tool from my local galaxy and install the custom tool successfully And shed_tool_conf.xml file updated with new section: section id=mTools name=MyTools version= tool file=xxx.xx.x.xx/repos/janakiram-t1/barcode_parse_1/b6a60d02b1a2/barcode_parse_1/barcode- parse.xml guid=xxx.xx.x.xx:9009/repos/janakiram-t1/barcode_parse_1/barcode-parse/1.0.0 tool_shedxxx.xxx.x.xx:9009/tool_shed repository_namebarcode_parse_1/repository_name repository_ownerjanakiram-t1/repository_owner installed_changeset_revisionb6a60d02b1a2/installed_changeset_revision idxxx.xxx.x.xx:9009/repos/janakiram-t1/barcode_parse_1/barcode-parse/1.0.0/id version1.0.0/version /tool /section My tool definition file look likes below: tool id=barcode-parse name=Barcode parse descriptionsome description/description command interpreter=pythonbarcode-parse.py $input1 $input2 $output/command inputs param format=input name=input1 type=text size=50 label=barcode help=Enter barcode validator type=empty_field message=please enter barcode/ /param param format=input name=input2 type=text size=50 label=Expected format help=Enter format to parse barcode validator type=empty_field message=please enter expected format barcode/ /param /inputs outputs data format=txt name=output / /outputs tests test param name=input1 value=test-01-sample-test-02-sampl1-test-03-sample3/ param name=input2 value=name-id/ output name=output file=barcode-parse.txt/ /test /tests help Parse the barcode into expected format /help /tool As galaxy using tool_conf.xml.sample, this file has no section for my custom tool. I have added a section manually like below: section name=MyTools id=mTools tool file=myTools/barcode-parse/barcode-parse.xml / /section Then my tool id found when I run the grep command. After that Then I run the below command to run the test cases: sh run_functional_tests.sh -id barcode-parse But I got below out put (from the run_functional_tests.html) AttributeError: 'module' object has no attribute 'test_toolbox:TestForTool_barcode-parse' Am I doing anything wrong. Thanks, JanakiRam On Thu, Mar 27, 2014 at 6:16 PM, Greg Von Kuster g...@bx.psu.edu wrote: As Janaki replied below, see: http://wiki.galaxyproject.org/Admin/RunningTests?action=showredirect=Admin%2FRunning+Tests On Mar 27, 2014, at 7:15 AM, Janaki Rama Rao Gollapudi janakiram.gollap...@india.semanticbits.com wrote: Hi, I have added tests to tool dependency xml, but how should I run these tests, can you please help me to run test cases. . tests test param name=input1 value=some string/ param name=input2 value=expected format/ output name=output file=output.txt/ /test /tests .. Thanks, G.JanakiRam On Thu, Mar 27, 2014 at 3:27 PM, Janaki Rama Rao Gollapudi janakiram.gollap...@india.semanticbits.com wrote: Hi, I found below resources: Running test Writing Functional tests Thanks, JanakiRam On Thu, Mar 27, 2014 at 2:53 PM, Janaki Rama Rao Gollapudi janakiram.gollap...@india.semanticbits.com wrote: Hi, I have implemented a custom tool which will parse a given string in to expected format.
Re: [galaxy-dev] How to write test cases for custom tool
Thank you, I will go through the resources and will reply my results to this email chain. Thanks, JanakiRam On Thu, Mar 27, 2014 at 6:39 PM, Greg Von Kuster g...@bx.psu.edu wrote: Hello Janaki, Thanks for clarifying that you have installed your tools from a Tool Shed. In this case, functional tests do not use Galaxy's tool_conf.xml.sample, so changing it will make no difference. For information about running functional tests on tools installed from the Tool Shed, see: https://wiki.galaxyproject.org/TestingInstalledTools Basically, you'll be doing the following. The functional test framework is not currently set up to test a specific installed tool using a -id flag. You'll have to use just the -installed flagg which will end up testing all installed tools. export GALAXY_TOOL_DEPENDENCY_DIR=tool_dependencies; sh run_functional_tests.sh -installed Greg Von Kuster On Mar 27, 2014, at 8:58 AM, Janaki Rama Rao Gollapudi janakiram.gollap...@india.semanticbits.com wrote: Hi, Thanks for reply. I composed a details email for better clarity. when run grep command in galaxy home folder ( ./run_functional_tests.sh -list | grep barcode-parse), I got no results. What I did was: - Implemented a custom tool (It has one python script and tool definition file. These files are located in ../tools/Mytools/customToolName/) - Then run the ToolShed in my local which is running on port 9009 (I have) - Created a new repository in the ToolShed (which is running on 9009) and uploaded .py and .xml files in to it - Now I run the galaxy (running on port 8080) and browse the my custom tool from my local galaxy and install the custom tool successfully - And shed_tool_conf.xml file updated with new section: - - section id=mTools name=MyTools version= - tool file=xxx.xx.x.xx/repos/janakiram-t1/barcode_parse_1/b6a60d02b1a2/barcode_parse_1/barcode- parse.xml guid=xxx.xx.x.xx:9009/repos/janakiram-t1/barcode_parse_1/barcode-parse/1.0.0 - tool_shedxxx.xxx.x.xx:9009/tool_shed - repository_namebarcode_parse_1/repository_name - repository_ownerjanakiram-t1/repository_owner - installed_changeset_revisionb6a60d02b1a2/installed_changeset_revision - idxxx.xxx.x.xx:9009/repos/janakiram-t1/barcode_parse_1/barcode-parse/1.0.0/id - version1.0.0/version - /tool - /section - My tool definition file look likes below: - - tool id=barcode-parse name=Barcode parse - descriptionsome description/description - command interpreter=pythonbarcode-parse.py $input1 $input2 $output/command - inputs - param format=input name=input1 type=text size=50 label=barcode help=Enter barcode - validator type=empty_field message=please enter barcode/ - /param - param format=input name=input2 type=text size=50 label=Expected format help=Enter format to parse barcode - validator type=empty_field message=please enter expected format barcode/ - /param - /inputs - outputs - data format=txt name=output / - /outputs - tests -test - param name=input1 value=test-01-sample-test-02-sampl1-test-03-sample3/ - param name=input2 value=name-id/ - output name=output file=barcode-parse.txt/ -/test - /tests - help -Parse the barcode into expected format - /help - /tool - As galaxy using tool_conf.xml.sample, this file has no section for my custom tool. I have added a section manually like below: section name=MyTools id=mTools tool file=myTools/barcode-parse/barcode-parse.xml / /section Then my tool id found when I run the grep command. After that Then I run the below command to run the test cases: sh run_functional_tests.sh -id barcode-parse But I got below out put (from the run_functional_tests.html) AttributeError: 'module' object has no attribute 'test_toolbox:TestForTool_barcode-parse' Am I doing anything wrong. Thanks, JanakiRam On Thu, Mar 27, 2014 at 6:16 PM, Greg Von Kuster g...@bx.psu.edu wrote: As Janaki replied below, see: http://wiki.galaxyproject.org/Admin/RunningTests?action=showredirect=Admin%2FRunning+Tests On Mar 27, 2014, at 7:15 AM, Janaki Rama Rao Gollapudi janakiram.gollap...@india.semanticbits.com wrote: Hi, I have added tests to tool dependency xml, but how should I run these tests, can you please help me to run test cases. . tests test param name=input1 value=some string/ param name=input2 value=expected format/ output name=output file=output.txt/ /test /tests ..
Re: [galaxy-dev] adding E.coli K-12 genome for mapping
Hi, I added your request to the card where we track these: https://trello.com/c/mJWnAuuQ/1511-to-request-reference-genome-comment-on-this-card Martin Galaxy team On Wed, Mar 26, 2014 at 3:17 PM, t...@caltech.edu wrote: Hi Guys, is it possible to add E.coli K12 genome for mapping with Bowtie on Andromeda-NCBI portal? thanks, timur ___ 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] Citing Galaxy + Toolshed in an app note of a small tool
Hey Assaf, For Cite1 (Galaxy): doi:10.1186/gb-2010-11-8-r86 For Cite2 (ToolShed): doi:10.1186/gb4161 Thanks for asking! -- jt On Tue, Mar 25, 2014 at 1:15 PM, Assaf Gordon agor...@wi.mit.edu wrote: Hello Galaxy People! (it's been a while since I've last been here... a pleasure to be back). I intend to publish a small command-line utility, which will also be available through Galaxy Toolshed. It'll be a small application note, so not a lot of space for many citations. The relevant sentence would read something like: The tool is also available for the Galaxy Bioinformatics Platform [Cite1], with automatic installation provided though the Galaxy Tool Shed [Cite2]. What should I use for [cite1 (galaxy) and [cite2 (toolshed)], out of this impressive long list of publications: https://wiki.galaxyproject.org/CitingGalaxy Thanks! -gordon ___ 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/
