Re: [galaxy-dev] Hidden output files
Hi Frank, This should be resolved as of changeset 7057:08fbfeaaf3e1. Thanks! -Dannon On Mar 27, 2012, at 4:37 AM, Frank Sørensen wrote: Hi Dannon, Unfortunately our server is (still) behind a firewall, so I can't share anything, but I hope you can reproduce the error from the following description. If I make a vanilla test workflow say: Input Dataset - Map with BWA for Illumina (single end) - SAM-to-BAM - flagstat and save it. Then all outputs will show if I run it, even if none of the snowflakes are checked which is not logical. It would be better if the output visibility was checked by default, and the user should actively de-select the outputs that should be hidden, but that's another matter. If I edit the workflow that I just created, and select the output from flagstat to be visible, then the two other (BWA and SAM-to-BAM) will be hidden when I run it, which they should be. So far so good... If I edit the workflow again and select the remaining outputs (BWA and SAM-to-BAM) to be visible and save the workflow, then only BWA will be visible after run, thats a problem, SAM-to-BAM should also be visible since that's what I selected. If I want the output from SAM-to-BAM to be visible, I have to edit the workflow again, and de-select visibility of the output from SAM-to-BAM, save the workflow, and re-edit the workflow and select visibility of the output from SAM-to-BAM and save the workflow. It seems that selection/de-selection of output visibility only works under some circumstances and not others. I can conclude the state of the output visibility on the existing or missing post-hide-action, which is apparent if I select run workflow, and press expand all on the Running workflow screen, so I don't actually have to run the workflow, which is a great help. By tweaking my workflows using this editing / re-editing method, it is actually possible to get the visibility of all outputs into the state that I desire, but it is quite cumbersome on larger workflows. Regards - Frank ___ 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] Hidden output files
Thanks. I have set up Mercurial to fetch updates from galaxy-dist, and it seems that my version of galaxy is up to date. - Should I pull from galaxy-central to get this update (7057:08fbfeaaf3e1)? - If so, could you please tell me how I do that? - Do you know how I permanently change repository from galaxy-dist to galaxy central, without loosing my tools and modifications? Kind Regards - Frank Den 18-04-2012 14:09, Dannon Baker skrev: Hi Frank, This should be resolved as of changeset 7057:08fbfeaaf3e1. Thanks! -Dannon On Mar 27, 2012, at 4:37 AM, Frank Sørensen wrote: Hi Dannon, Unfortunately our server is (still) behind a firewall, so I can't share anything, but I hope you can reproduce the error from the following description. If I make a vanilla test workflow say: Input Dataset - Map with BWA for Illumina (single end) - SAM-to-BAM - flagstat and save it. Then all outputs will show if I run it, even if none of the snowflakes are checked which is not logical. It would be better if the output visibility was checked by default, and the user should actively de-select the outputs that should be hidden, but that's another matter. If I edit the workflow that I just created, and select the output from flagstat to be visible, then the two other (BWA and SAM-to-BAM) will be hidden when I run it, which they should be. So far so good... If I edit the workflow again and select the remaining outputs (BWA and SAM-to-BAM) to be visible and save the workflow, then only BWA will be visible after run, thats a problem, SAM-to-BAM should also be visible since that's what I selected. If I want the output from SAM-to-BAM to be visible, I have to edit the workflow again, and de-select visibility of the output from SAM-to-BAM, save the workflow, and re-edit the workflow and select visibility of the output from SAM-to-BAM and save the workflow. It seems that selection/de-selection of output visibility only works under some circumstances and not others. I can conclude the state of the output visibility on the existing or missing post-hide-action, which is apparent if I select run workflow, and press expand all on the Running workflow screen, so I don't actually have to run the workflow, which is a great help. By tweaking my workflows using this editing / re-editing method, it is actually possible to get the visibility of all outputs into the state that I desire, but it is quite cumbersome on larger workflows. Regards - Frank -- Frank Sørensen, B.Sc., Programmer Molecular Diagnostic Laboratory (MDL) Molekylær Medicinsk Afdeling (MOMA) Århus Universitetshospital Skejby, Brendstrupgårdsvej, 8200 Århus N Tlf. +45 7845 5363 ___ 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] Hidden output files
On Apr 18, 2012, at 8:44 AM, Frank Sørensen wrote: - Should I pull from galaxy-central to get this update (7057:08fbfeaaf3e1)? - If so, could you please tell me how I do that? Sure, you can pull from galaxy-central by issuing a manual pull with source from your galaxy-dist directory: hg pull -u https://bitbucket.org/galaxy/galaxy-central - Do you know how I permanently change repository from galaxy-dist to galaxy central, without loosing my tools and modifications? If you want to permanently change to galaxy-central, you'll need to manually edit the file galaxydirectory/.hg/hgrc. It should look something like this: [paths] default = https://bitbucket.org/galaxy/galaxy-dist Just change galaxy-dist to galaxy-central, save it, and you're good to go. -Dannon ___ 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] Hidden output files
Hi Dannon, Unfortunately our server is (still) behind a firewall, so I can't share anything, but I hope you can reproduce the error from the following description. If I make a vanilla test workflow say: Input Dataset - Map with BWA for Illumina (single end) - SAM-to-BAM - flagstat and save it. Then all outputs will show if I run it, even if none of the snowflakes are checked which is not logical. It would be better if the output visibility was checked by default, and the user should actively de-select the outputs that should be hidden, but that's another matter. If I edit the workflow that I just created, and select the output from flagstat to be visible, then the two other (BWA and SAM-to-BAM) will be hidden when I run it, which they should be. So far so good... If I edit the workflow again and select the remaining outputs (BWA and SAM-to-BAM) to be visible and save the workflow, then only BWA will be visible after run, thats a problem, SAM-to-BAM should also be visible since that's what I selected. If I want the output from SAM-to-BAM to be visible, I have to edit the workflow again, and de-select visibility of the output from SAM-to-BAM, save the workflow, and re-edit the workflow and select visibility of the output from SAM-to-BAM and save the workflow. It seems that selection/de-selection of output visibility only works under some circumstances and not others. I can conclude the state of the output visibility on the existing or missing post-hide-action, which is apparent if I select run workflow, and press expand all on the Running workflow screen, so I don't actually have to run the workflow, which is a great help. By tweaking my workflows using this editing / re-editing method, it is actually possible to get the visibility of all outputs into the state that I desire, but it is quite cumbersome on larger workflows. Regards - Frank Den 23-03-2012 12:53, Dannon Baker skrev: Could you share an offending workflow with me? Or is it any workflow? I've not seen this behavior before, but it definitely shouldn't be random. So in your situation the same workflow run multiple times will not consistently hide the same datasets? -Dannon On Mar 23, 2012, at 6:05 AM, Frank Sørensen wrote: Hi, I seem to have some problems with the visibility of tool outputs in my workflows. When I flag any given output as visible, Galaxy sometimes decides to hide it in the resulting history anyway. I can't find any systematic behavior though. It seems to be rather arbitrary weather Galaxy decides that the file should be hidden or not. I would estimate the random hiding to occur on about 50% of my outputs. Has anyone seen this before? Regards - Frank -- Frank Sørensen, B.Sc., Programmer Molecular Diagnostic Laboratory (MDL) Molekylær Medicinsk Afdeling (MOMA) Århus Universitetshospital Skejby, Brendstrupgårdsvej, 8200 Århus N Tlf. +45 7845 5363 ___ 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/ -- Frank Sørensen, B.Sc., Programmer Molecular Diagnostic Laboratory (MDL) Molekylær Medicinsk Afdeling (MOMA) Århus Universitetshospital Skejby, Brendstrupgårdsvej, 8200 Århus N Tlf. +45 7845 5363 ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-dev] Hidden output files
Hi, I seem to have some problems with the visibility of tool outputs in my workflows. When I flag any given output as visible, Galaxy sometimes decides to hide it in the resulting history anyway. I can't find any systematic behavior though. It seems to be rather arbitrary weather Galaxy decides that the file should be hidden or not. I would estimate the random hiding to occur on about 50% of my outputs. Has anyone seen this before? Regards - Frank -- Frank Sørensen, B.Sc., Programmer Molecular Diagnostic Laboratory (MDL) Molekylær Medicinsk Afdeling (MOMA) Århus Universitetshospital Skejby, Brendstrupgårdsvej, 8200 Århus N Tlf. +45 7845 5363 ___ 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] Hidden output files
Could you share an offending workflow with me? Or is it any workflow? I've not seen this behavior before, but it definitely shouldn't be random. So in your situation the same workflow run multiple times will not consistently hide the same datasets? -Dannon On Mar 23, 2012, at 6:05 AM, Frank Sørensen wrote: Hi, I seem to have some problems with the visibility of tool outputs in my workflows. When I flag any given output as visible, Galaxy sometimes decides to hide it in the resulting history anyway. I can't find any systematic behavior though. It seems to be rather arbitrary weather Galaxy decides that the file should be hidden or not. I would estimate the random hiding to occur on about 50% of my outputs. Has anyone seen this before? Regards - Frank -- Frank Sørensen, B.Sc., Programmer Molecular Diagnostic Laboratory (MDL) Molekylær Medicinsk Afdeling (MOMA) Århus Universitetshospital Skejby, Brendstrupgårdsvej, 8200 Århus N Tlf. +45 7845 5363 ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
