Re: [galaxy-dev] Adding categories to Main
Keith, please see the comments inline. thanks M. On Fri, Sep 11, 2015 at 4:54 PM Suderman Keith wrote: > Hi Martin, > > On Sep 11, 2015, at 12:44 PM, Martin Čech wrote: > > Hi Keith, > > how is the NLP category working for you? Do you want it on Main Tool Shed? > > > The NLP category is working great. I am still in the early testing phase > and likely won't need anything in Main for some time yet, but Steve Cassidy > might have a different opinion. > > Also I have noticed you are putting the version of your tools in the > repository names. I would like to discourage that as it will create > confusion once you update your tool (as you will be unable to update the > repo name). The XML wrappers have they own version tracking tag for these > purposes. You can learn about this and more in the Tooldev Best Practices > document: http://galaxy-iuc-standards.readthedocs.org/en/latest/ > > > I was under the impression ( > http://gregvonkuster.org/galaxy-tool-shed-revisiting-best-practices-populating-repository/) > that the best practice for package names was package__ and > for tools it was _. > That is correct for packages and suites but incorrect for tools. Sorry for the confusion. > > There is also some friction (for lack of a better term) between versioning > our web services and versioning the Galaxy wrappers that call our web > services. For example, I might have multiple versions of the Galaxy > wrappers for our stanford_2.0.0 services and multiple versions of the > Galaxy wrappers for our stanford_2.1.0 services. The 2.0.0 services are not > going away just because the 2.1.0 services are available, so I think the > stanford_2.0.0 and stanford_2.1.0 Galaxy wrappers have to be separate > repositories. > In this case the naming kinda makes sense to me (lapps_stanford_2_0_0 and lapps_stanford_2_1_0 that is). However could the remote Standford API version be a parameter of the tool instead? i.e. you would have only 'lapps_stanford' and select the version you want to use from a dropdown and the tool form would adjust (this is technically possible and used) and after execution called the right underlying script? > > Having said that, I am planning to remove all my current repositories and > repopulate as I try to automate things on my end so suggestions for naming > strategies are always welcome. > > "There are only two hard problems in computer science, cache invalidation > and naming things" > - author unknown > > Thank you for using Galaxy. > > > Thank you (all) for making Galaxy! ;-) > > Cheers, > Keith > > > Martin > > On Fri, Aug 7, 2015 at 2:57 PM Martin Čech wrote: > >> No sub-categories yet; we plan on tackling the browsing issue by having >> good search. :) >> >> M. >> >> On Fri, Aug 7, 2015 at 2:43 PM Keith Suderman >> wrote: >> >>> Awesome! >>> >>> One concern we have is lumping all NLP tools into a single category; are >>> sub-categories (and sub-sub-categories) possible? However, we can start >>> with this and see what we need later. >>> >>> Cheers, >>> Keith >>> >>> On Aug 7, 2015, at 12:25 PM, Martin Čech wrote: >>> >>> Dear Keith, >>> >>> I have created 'NLP' category at https://testtoolshed.g2.bx.psu.edu for >>> you to test out the Tool Shed environment. >>> >>> Unless your tools are proprietary I strongly recommend using the Main >>> Tool Shed at https://toolshed.g2.bx.psu.edu for their publishing and >>> distribution. Let me know when you are ready with the tools and I will >>> create the category for you in there. >>> >>> We happily welcome every tool contribution to Galaxy! Thank you for it. >>> >>> Martin, Galaxy Team >>> >>> >>> On Fri, Aug 7, 2015 at 12:56 PM Björn Grüning >>> wrote: >>> Hi Keith, the Galaxy team can add new categories to the Tool Shed very easily and such a mail is exactly the way to go. As soon as the Galaxy teams has added the category you can use tools like planemo to upload all your tools at once. https://github.com/galaxyproject/planemo Looking forward to see NLP tools in Galaxy and the Main TS! Awesome! Bjoern > Dear Galaxy Team, > > A colleague would like to upload some NLP (Natural Language > Processing) tools to the Galaxy Test/Main tools sheds, but we are > unclear what "categories" to use for the tools. I see that the > Main/Test tools sheds have a category for "Text Manipulation", but > that does not seem appropriate for NLP tools. Is it possible to have > new categories added to the tool shed(s)? If so, what is the > process? > > I am just starting to investigate setting up our own local tool shed > and I am coming across mentions of repository capsules and exporting > tool sheds. Would it be preferable to install the NLP tools to a > local tool shed and then export a repository/capsule to be imported > to the Test/Main tools sheds? What happens if our tool shed uses a > disjoint set of categor
Re: [galaxy-dev] Adding categories to Main
Hi Martin, On Sep 11, 2015, at 12:44 PM, Martin Čech wrote: > Hi Keith, > > how is the NLP category working for you? Do you want it on Main Tool Shed? The NLP category is working great. I am still in the early testing phase and likely won't need anything in Main for some time yet, but Steve Cassidy might have a different opinion. > Also I have noticed you are putting the version of your tools in the > repository names. I would like to discourage that as it will create confusion > once you update your tool (as you will be unable to update the repo name). > The XML wrappers have they own version tracking tag for these purposes. You > can learn about this and more in the Tooldev Best Practices document: > http://galaxy-iuc-standards.readthedocs.org/en/latest/ I was under the impression (http://gregvonkuster.org/galaxy-tool-shed-revisiting-best-practices-populating-repository/) that the best practice for package names was package__ and for tools it was _. There is also some friction (for lack of a better term) between versioning our web services and versioning the Galaxy wrappers that call our web services. For example, I might have multiple versions of the Galaxy wrappers for our stanford_2.0.0 services and multiple versions of the Galaxy wrappers for our stanford_2.1.0 services. The 2.0.0 services are not going away just because the 2.1.0 services are available, so I think the stanford_2.0.0 and stanford_2.1.0 Galaxy wrappers have to be separate repositories. Having said that, I am planning to remove all my current repositories and repopulate as I try to automate things on my end so suggestions for naming strategies are always welcome. "There are only two hard problems in computer science, cache invalidation and naming things" - author unknown > Thank you for using Galaxy. Thank you (all) for making Galaxy! ;-) Cheers, Keith > > Martin > > On Fri, Aug 7, 2015 at 2:57 PM Martin Čech wrote: > No sub-categories yet; we plan on tackling the browsing issue by having good > search. :) > > M. > > On Fri, Aug 7, 2015 at 2:43 PM Keith Suderman wrote: > Awesome! > > One concern we have is lumping all NLP tools into a single category; are > sub-categories (and sub-sub-categories) possible? However, we can start with > this and see what we need later. > > Cheers, > Keith > > On Aug 7, 2015, at 12:25 PM, Martin Čech wrote: > >> Dear Keith, >> >> I have created 'NLP' category at https://testtoolshed.g2.bx.psu.edu for you >> to test out the Tool Shed environment. >> >> Unless your tools are proprietary I strongly recommend using the Main Tool >> Shed at https://toolshed.g2.bx.psu.edu for their publishing and >> distribution. Let me know when you are ready with the tools and I will >> create the category for you in there. >> >> We happily welcome every tool contribution to Galaxy! Thank you for it. >> >> Martin, Galaxy Team >> >> >> On Fri, Aug 7, 2015 at 12:56 PM Björn Grüning >> wrote: >> Hi Keith, >> >> the Galaxy team can add new categories to the Tool Shed very easily and >> such a mail is exactly the way to go. As soon as the Galaxy teams has >> added the category you can use tools like planemo to upload all your >> tools at once. >> >> https://github.com/galaxyproject/planemo >> >> Looking forward to see NLP tools in Galaxy and the Main TS! Awesome! >> Bjoern >> >> >> > Dear Galaxy Team, >> > >> > A colleague would like to upload some NLP (Natural Language >> > Processing) tools to the Galaxy Test/Main tools sheds, but we are >> > unclear what "categories" to use for the tools. I see that the >> > Main/Test tools sheds have a category for "Text Manipulation", but >> > that does not seem appropriate for NLP tools. Is it possible to have >> > new categories added to the tool shed(s)? If so, what is the >> > process? >> > >> > I am just starting to investigate setting up our own local tool shed >> > and I am coming across mentions of repository capsules and exporting >> > tool sheds. Would it be preferable to install the NLP tools to a >> > local tool shed and then export a repository/capsule to be imported >> > to the Test/Main tools sheds? What happens if our tool shed uses a >> > disjoint set of categories than Test/Main? >> > >> > Cheers, Keith >> > >> > -- Research Associate Department of >> > Computer Science Vassar College Poughkeepsie, NY >> > >> > >> > ___ 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: https://lists.galaxyproject.org/ >> > >> > To search Galaxy mailing lists use the unified search at: >> > http://galaxyproject.org/search/mailinglists/ >> > > > -- > Research Associate > Department of Computer Science > Vassar College > Poughkeepsie, NY > >
Re: [galaxy-dev] Adding categories to Main
Hi Keith, how is the NLP category working for you? Do you want it on Main Tool Shed? Also I have noticed you are putting the version of your tools in the repository names. I would like to discourage that as it will create confusion once you update your tool (as you will be unable to update the repo name). The XML wrappers have they own version tracking tag for these purposes. You can learn about this and more in the Tooldev Best Practices document: http://galaxy-iuc-standards.readthedocs.org/en/latest/ Thank you for using Galaxy. Martin On Fri, Aug 7, 2015 at 2:57 PM Martin Čech wrote: > No sub-categories yet; we plan on tackling the browsing issue by having > good search. :) > > M. > > On Fri, Aug 7, 2015 at 2:43 PM Keith Suderman > wrote: > >> Awesome! >> >> One concern we have is lumping all NLP tools into a single category; are >> sub-categories (and sub-sub-categories) possible? However, we can start >> with this and see what we need later. >> >> Cheers, >> Keith >> >> On Aug 7, 2015, at 12:25 PM, Martin Čech wrote: >> >> Dear Keith, >> >> I have created 'NLP' category at https://testtoolshed.g2.bx.psu.edu for >> you to test out the Tool Shed environment. >> >> Unless your tools are proprietary I strongly recommend using the Main >> Tool Shed at https://toolshed.g2.bx.psu.edu for their publishing and >> distribution. Let me know when you are ready with the tools and I will >> create the category for you in there. >> >> We happily welcome every tool contribution to Galaxy! Thank you for it. >> >> Martin, Galaxy Team >> >> >> On Fri, Aug 7, 2015 at 12:56 PM Björn Grüning >> wrote: >> >>> Hi Keith, >>> >>> the Galaxy team can add new categories to the Tool Shed very easily and >>> such a mail is exactly the way to go. As soon as the Galaxy teams has >>> added the category you can use tools like planemo to upload all your >>> tools at once. >>> >>> https://github.com/galaxyproject/planemo >>> >>> Looking forward to see NLP tools in Galaxy and the Main TS! Awesome! >>> Bjoern >>> >>> >>> > Dear Galaxy Team, >>> > >>> > A colleague would like to upload some NLP (Natural Language >>> > Processing) tools to the Galaxy Test/Main tools sheds, but we are >>> > unclear what "categories" to use for the tools. I see that the >>> > Main/Test tools sheds have a category for "Text Manipulation", but >>> > that does not seem appropriate for NLP tools. Is it possible to have >>> > new categories added to the tool shed(s)? If so, what is the >>> > process? >>> > >>> > I am just starting to investigate setting up our own local tool shed >>> > and I am coming across mentions of repository capsules and exporting >>> > tool sheds. Would it be preferable to install the NLP tools to a >>> > local tool shed and then export a repository/capsule to be imported >>> > to the Test/Main tools sheds? What happens if our tool shed uses a >>> > disjoint set of categories than Test/Main? >>> > >>> > Cheers, Keith >>> > >>> > -- Research Associate Department of >>> > Computer Science Vassar College Poughkeepsie, NY >>> > >>> > >>> > ___ 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: https://lists.galaxyproject.org/ >>> > >>> > To search Galaxy mailing lists use the unified search at: >>> > http://galaxyproject.org/search/mailinglists/ >>> > >>> >> >> -- >> Research Associate >> Department of Computer Science >> Vassar College >> Poughkeepsie, NY >> >> >> ___ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] custom tool - accessing user's data in bash script
Hi Piotr, I guess you need to work a lot with symlinks. link all your Galaxy inputs to a temp folder, provide the path to the temp folder to KNIME + a path to a second tempfolder with the results and tell Galaxy to collect all files int the result folder. Cheers, Bjoern On 11.09.2015 16:26, Piotr Grabowski wrote: Hello Galaxy Devs and Deployers! I have a rather basic question about how to handle custom tools in Galaxy (I'm fresh to this framework). I am trying to link my local Galaxy with KNIME workflow that we developed in our group. I am trying to link it via a bash script that is running headless KNIME and it seems almost to work, but... In order for this workflow to run I have to specify in the command line things like result folder or where a dynamically generated parameter file is located. This parameter file is generate by the bash script before running KNIME. The paths will be always dynamic, depending on users etc. So I can't simply hard-code the path. Is there a way to make bash aware of where the current Galaxy user's folders and files are upon execution in Galaxy? Below a simplified scheme of what I am doing: User uploads txt file -> Clicks RUN -> bash script builds a parameter file (gawk ... >> param.csv) -> /knime run workflow --set the path to the parameter .csv file + set export folder Any ideas ? Best, Piotr ___ 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: https://lists.galaxyproject.org/ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] custom tool - accessing user's data in bash script
Hello Galaxy Devs and Deployers! I have a rather basic question about how to handle custom tools in Galaxy (I'm fresh to this framework). I am trying to link my local Galaxy with KNIME workflow that we developed in our group. I am trying to link it via a bash script that is running headless KNIME and it seems almost to work, but... In order for this workflow to run I have to specify in the command line things like result folder or where a dynamically generated parameter file is located. This parameter file is generate by the bash script before running KNIME. The paths will be always dynamic, depending on users etc. So I can't simply hard-code the path. Is there a way to make bash aware of where the current Galaxy user's folders and files are upon execution in Galaxy? Below a simplified scheme of what I am doing: User uploads txt file -> Clicks RUN -> bash script builds a parameter file (gawk ... >> param.csv) -> /knime run workflow --set the path to the parameter .csv file + set export folder Any ideas ? Best, Piotr ___ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] FastQC galaxy issue
Hi, are you running fastqc on the compressed tarfile? Or is this file unpacked already when you are running fastqc on it? Thanks, Bjoern On 10.09.2015 09:39, Hakeem Almabrazi wrote: Hi, I have encountered the following issue when I try to use FastQC tool in Galaxy. The fastqc file is validated using the fastqvalidator tool and the same files have been processed by other tools (i.e bwa) without any complaints about the fastqc . Also, if I ran the fastqc from the command line it gets executed without any issue too. I have updated my galaxy repository in case there is new updates and the FastQC version is v0.11.2 Is this something to do with the FastQC wrapper in galaxy? If it helps, the fastq files are in the file system and I link to them into galaxy using the options Link and Fastqqsanger as data type. Any help will be highly appreciated. ……….. Fatal error: Exit code 1 () Failed to process L-20417_S7_L007_R2_001.fastq uk.ac.babraham.FastQC.Sequence.SequenceFormatException: ID line didn't start with '@' at uk.ac.babraham.FastQC.Sequence.FastQFile.readNext(FastQFile.java:158) at uk.ac.babraham.FastQC.Sequence.FastQFile.(FastQFile.java:89) at uk.ac.babraham.FastQC.Sequence.SequenceFactory.getSequenceFile(SequenceFactory.java:104) at uk.ac.babraham.FastQC.Sequence.SequenceFactory.getSequenceFile(SequenceFactory.java:62) at uk.ac.babraham.FastQC.Analysis.OfflineRunner.processFile(OfflineRunner.java:122) at uk.ac.babraham.FastQC.Analysis.OfflineRunner.(OfflineRunner.java:95) at uk.ac.babraham.FastQC.FastQCApplication.main(FastQCApplication.java:308) Traceback (most recent call last): File "/gpfs/home/galaxyadmin/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/fastqc/8c650f7f76e9/fastqc/rgFastQC.py", line 162, in fastqc_runner.run_fastqc() File "/gpfs/home/galaxyadmin/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/fastqc/8c650f7f76e9/fastqc/rgFastQC.py", line 136, in run_fastqc self.copy_output_file_to_dataset() File "/gpfs/home/galaxyadmin/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/fastqc/8c650f7f76e9/fastqc/rgFastQC.py", line 109, in copy_output_file_to_dataset with open(result_file[0], 'rb') as fsrc: IndexError: list index out of range Disclaimer: This email and its attachments may be confidential and are intended solely for the use of the individual to whom it is addressed. If you are not the intended recipient, any reading, printing, storage, disclosure, copying or any other action taken in respect of this e-mail is prohibited and may be unlawful. If you are not the intended recipient, please notify the sender immediately by using the reply function and then permanently delete what you have received. Any views or opinions expressed are solely those of the author and do not necessarily represent those of Sidra Medical and Research Center. ___ 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: https://lists.galaxyproject.org/ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] FastQC galaxy issue
Hi again, After struggling with this issue for few days and exhausted all my options, the only thing that was left was to use the "Copy the file into galaxy" instead of "Link files into Galaxy" in the loading page. It took while to copy but after it was done, I noticed the file was decompressed and it size was (240 GB) instead of the 30GB. I re-ran the FastQC tool and it worked. I am not sure if this is a bug in the copying/linking part or at the FastQC wrapper. Has anyone encountered this issue? Can anyone try to link a fastq file and run the FastQC to confirm what I am seeing? It is very important to us that we link the fastq files instead of copying them into galaxy. I appreciate any feedback. Regards, Hakeem From: galaxy-dev [mailto:galaxy-dev-boun...@lists.galaxyproject.org] On Behalf Of Hakeem Almabrazi Sent: Thursday, September 10, 2015 10:40 AM To: galaxy-dev@lists.galaxyproject.org Subject: [galaxy-dev] FastQC galaxy issue Hi, I have encountered the following issue when I try to use FastQC tool in Galaxy. The fastqc file is validated using the fastqvalidator tool and the same files have been processed by other tools (i.e bwa) without any complaints about the fastqc . Also, if I ran the fastqc from the command line it gets executed without any issue too. I have updated my galaxy repository in case there is new updates and the FastQC version is v0.11.2 Is this something to do with the FastQC wrapper in galaxy? If it helps, the fastq files are in the file system and I link to them into galaxy using the options Link and Fastqqsanger as data type. Any help will be highly appreciated. ... Fatal error: Exit code 1 () Failed to process L-20417_S7_L007_R2_001.fastq uk.ac.babraham.FastQC.Sequence.SequenceFormatException: ID line didn't start with '@' at uk.ac.babraham.FastQC.Sequence.FastQFile.readNext(FastQFile.java:158) at uk.ac.babraham.FastQC.Sequence.FastQFile.(FastQFile.java:89) at uk.ac.babraham.FastQC.Sequence.SequenceFactory.getSequenceFile(SequenceFactory.java:104) at uk.ac.babraham.FastQC.Sequence.SequenceFactory.getSequenceFile(SequenceFactory.java:62) at uk.ac.babraham.FastQC.Analysis.OfflineRunner.processFile(OfflineRunner.java:122) at uk.ac.babraham.FastQC.Analysis.OfflineRunner.(OfflineRunner.java:95) at uk.ac.babraham.FastQC.FastQCApplication.main(FastQCApplication.java:308) Traceback (most recent call last): File "/gpfs/home/galaxyadmin/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/fastqc/8c650f7f76e9/fastqc/rgFastQC.py", line 162, in fastqc_runner.run_fastqc() File "/gpfs/home/galaxyadmin/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/fastqc/8c650f7f76e9/fastqc/rgFastQC.py", line 136, in run_fastqc self.copy_output_file_to_dataset() File "/gpfs/home/galaxyadmin/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/fastqc/8c650f7f76e9/fastqc/rgFastQC.py", line 109, in copy_output_file_to_dataset with open(result_file[0], 'rb') as fsrc: IndexError: list index out of range Disclaimer: This email and its attachments may be confidential and are intended solely for the use of the individual to whom it is addressed. If you are not the intended recipient, any reading, printing, storage, disclosure, copying or any other action taken in respect of this e-mail is prohibited and may be unlawful. If you are not the intended recipient, please notify the sender immediately by using the reply function and then permanently delete what you have received. Any views or opinions expressed are solely those of the author and do not necessarily represent those of Sidra Medical and Research Center. Disclaimer: This email and its attachments may be confidential and are intended solely for the use of the individual to whom it is addressed. If you are not the intended recipient, any reading, printing, storage, disclosure, copying or any other action taken in respect of this e-mail is prohibited and may be unlawful. If you are not the intended recipient, please notify the sender immediately by using the reply function and then permanently delete what you have received. Any views or opinions expressed are solely those of the author and do not necessarily represent those of Sidra Medical and Research Center. ___ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] LDAP and valid username
Hi, I configure authentication with the LDAP (Active Directory) of my compagny. But the username (sAMAccoutName) contains a dot (eg : e.hirchaud). And that was a problem because the dot is not allow in galaxy username and auto-registration fails because of that. For testing I change the regex in "security/validate_user_input.py" and authorize character dot and it's work ! I know its not a good practice to change core code so I want to know if they are known "risks" or sides effects if I keep this change and if you have a best solution ? Thanks! Edouard -- Édouard Hirchaud ANSES Laboratoire de Ploufragan-Plouzané Unité Génétique Virale et Biosécurité 22440 Ploufragan Tel : (33) 02 96 01 62 71 ___ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Tool with multiple outputs.
Hi Bjoern, I'll try to use collections and return soon. I could not find the tag of the documentation [1], has any record in the documentation about it? [1] https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax Thanks for the reply. Att. On Fri, Sep 11, 2015 at 5:42 AM, Bjoern Gruening wrote: > Hi Léo, > > maybe you can use a dataset collection instead. This is a new way to > handle multiple datasets of the same type. > > For an example see this tool: > > https://github.com/bgruening/galaxytools/blob/master/tools/rna_tools/rna_shapes/RNAShapes.xml#L218 > > Cheers, > Bjoern > > On 10.09.2015 23:01, Léo Biscassi wrote: > > Good afternoon people! > I am developing a tool that will have multiple outputs where they have to > be data sets in history. > Read the tutorial [1] and from it developed my [2] [3] tool, however, have > only the .txt output file, the .mol2 files are not showing up in history, > someone can tell me why? > > [1] > https://wiki.galaxyproject.org/Admin/Tools/Multiple%20Output%20Files#Handling_Multiple_Output_Files_in_Galaxy > [2] https://gist.github.com/leobiscassi/8058b6307d388167866a > [3] https://gist.github.com/leobiscassi/bc54a7df261c4ee81aa9 > > Att. > -- > *Léo Biscassi* > Facebook - https://pt-br.facebook.com/lbiscassi > Linkedin - https://br.linkedin.com/in/leobiscassi > Skype - biscassi.leo > Twitter - https://twitter.com/leobiscassi > >- > > > > > ___ > 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: > https://lists.galaxyproject.org/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ > > > -- *Léo Biscassi* Facebook - https://pt-br.facebook.com/lbiscassi Linkedin - https://br.linkedin.com/in/leobiscassi Skype - biscassi.leo Twitter - https://twitter.com/leobiscassi - ___ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Tool with multiple outputs.
Hi Christian, Yes, I remembered to refresh tool panel. Thanks for the reply. Att. On Fri, Sep 11, 2015 at 5:02 AM, Christian Brenninkmeijer < christian.brenninkmei...@manchester.ac.uk> wrote: > Hi, > Did you remember to refresh the history panel after the tool finished? > That caught me out multiple times when testing multiple outputs. > > Christian > -- > *From:* galaxy-dev [galaxy-dev-boun...@lists.galaxyproject.org] on behalf > of Léo Biscassi [leo.bisca...@gmail.com] > *Sent:* Thursday, September 10, 2015 10:01 PM > *To:* galaxy-dev@lists.galaxyproject.org > *Subject:* [galaxy-dev] Tool with multiple outputs. > > Good afternoon people! > I am developing a tool that will have multiple outputs where they have to > be data sets in history. > Read the tutorial [1] and from it developed my [2] [3] tool, however, have > only the .txt output file, the .mol2 files are not showing up in history, > someone can tell me why? > > [1] > https://wiki.galaxyproject.org/Admin/Tools/Multiple%20Output%20Files#Handling_Multiple_Output_Files_in_Galaxy > [2] https://gist.github.com/leobiscassi/8058b6307d388167866a > [3] https://gist.github.com/leobiscassi/bc54a7df261c4ee81aa9 > > Att. > -- > *Léo Biscassi* > Facebook - https://pt-br.facebook.com/lbiscassi > Linkedin - https://br.linkedin.com/in/leobiscassi > Skype - biscassi.leo > Twitter - https://twitter.com/leobiscassi > >- > > > -- *Léo Biscassi* Facebook - https://pt-br.facebook.com/lbiscassi Linkedin - https://br.linkedin.com/in/leobiscassi Skype - biscassi.leo Twitter - https://twitter.com/leobiscassi - ___ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Tool with multiple outputs.
Hi Léo, maybe you can use a dataset collection instead. This is a new way to handle multiple datasets of the same type. For an example see this tool: https://github.com/bgruening/galaxytools/blob/master/tools/rna_tools/rna_shapes/RNAShapes.xml#L218 Cheers, Bjoern On 10.09.2015 23:01, Léo Biscassi wrote: Good afternoon people! I am developing a tool that will have multiple outputs where they have to be data sets in history. Read the tutorial [1] and from it developed my [2] [3] tool, however, have only the .txt output file, the .mol2 files are not showing up in history, someone can tell me why? [1] https://wiki.galaxyproject.org/Admin/Tools/Multiple%20Output%20Files#Handling_Multiple_Output_Files_in_Galaxy [2] https://gist.github.com/leobiscassi/8058b6307d388167866a [3] https://gist.github.com/leobiscassi/bc54a7df261c4ee81aa9 Att. -- *Léo Biscassi* Facebook - https://pt-br.facebook.com/lbiscassi Linkedin - https://br.linkedin.com/in/leobiscassi Skype - biscassi.leo Twitter - https://twitter.com/leobiscassi * ___ 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: https://lists.galaxyproject.org/ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Tool with multiple outputs.
Hi, Did you remember to refresh the history panel after the tool finished? That caught me out multiple times when testing multiple outputs. Christian From: galaxy-dev [galaxy-dev-boun...@lists.galaxyproject.org] on behalf of Léo Biscassi [leo.bisca...@gmail.com] Sent: Thursday, September 10, 2015 10:01 PM To: galaxy-dev@lists.galaxyproject.org Subject: [galaxy-dev] Tool with multiple outputs. Good afternoon people! I am developing a tool that will have multiple outputs where they have to be data sets in history. Read the tutorial [1] and from it developed my [2] [3] tool, however, have only the .txt output file, the .mol2 files are not showing up in history, someone can tell me why? [1] https://wiki.galaxyproject.org/Admin/Tools/Multiple%20Output%20Files#Handling_Multiple_Output_Files_in_Galaxy [2] https://gist.github.com/leobiscassi/8058b6307d388167866a [3] https://gist.github.com/leobiscassi/bc54a7df261c4ee81aa9 Att. -- Léo Biscassi Facebook - https://pt-br.facebook.com/lbiscassi Linkedin - https://br.linkedin.com/in/leobiscassi Skype - biscassi.leo Twitter - https://twitter.com/leobiscassi * ___ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
