[galaxy-dev] Extra files saved outside of Galaxy's history?
Hi all, I have a pipeline involving a series of scripts, which creates directories (and many subdirectories), that I'd like to wrap for use in Galaxy. Although the contents of the folders are not the primary output of the pipeline, (and I don't want them as history items), I'd still like them to be accessible for users to double-check the contents if they so desire. However, I'm not sure where a good place to create/persist the folders would be. Although I'm running a local install on my own machine for the moment, the goal will be to move to a cluster in the near future. Does anyone have experience with this kind of thing or have any ideas? Apologies if I've missed something; I haven't found anything related on the mailing list or the wiki, except for this thread that suggests disabling the cleanup method of the JobWrapper for debugging purposes: http://dev.list.galaxyproject.org/persisting-job-working-directory-td413 8922.html. Thanks for your consideration, Ann ___ 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] MrBayes wrapper - set parameters through Galaxy?
Hello all, I've written a MrBayes wrapper that accepts a Nexus file (presumably containing a data block and a command block). In order to make it a bit easier for new users, I was hoping to be able to let users specify some parameters, such as their model, in Galaxy, as opposed to including it in the command block of the Nexus file. Am I correct in thinking this is not possible since MrBayes does not have a way to invoke commands in-line? To clarify for non-MrBayes people, my limited understanding is that you either invoke the interpreter with $ mb and then enter your commands, or directly execute a Nexus file (containing the data and commands) with $ mb nexusfilename. Please correct me if I'm missing something or thinking about this completely wrong. I'd appreciate any input about MrBayes or a similar kind of tool. Cheers, Ann Ann Gomez Agriculture and Agri-Food Canada | Agriculture et Agroalimentaire Canada KW Neatby Bldg | éd. KW Neatby 960 Carling Ave| 960, avenue Carling Ottawa, ON | Ottawa (ON) K1A 0C6 E-mail Address / Adresse courriel: ann.go...@agr.gc.ca mailto:ann.go...@agr.gc.ca Telephone | Téléphone 613-759-6805 Facsimile | Télécopieur 613-759-1701 Government of Canada | Gouvernement du Canada ___ 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] MrBayes wrapper - set parameters through Galaxy?
Brilliant, thanks! I had seen the FAQ, but didn't know about configfiles. Much appreciated! Ann -Original Message- From: ja...@taylorlab.org [mailto:ja...@taylorlab.org] On Behalf Of James Taylor Sent: Monday, October 29, 2012 2:03 PM To: Gomez, Ann Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] MrBayes wrapper - set parameters through Galaxy? Ann, I think you may be able to do this by generating another nexus file using configfiles in the Galaxy tool config which just contains a command block, similar to the example here: http://mrbayes.sourceforge.net/wiki/index.php/FAQ#How_do_I_run_MrBayes_in_batch_mode.3F -- jt On Mon, Oct 29, 2012 at 1:24 PM, Gomez, Ann ann.go...@agr.gc.ca wrote: Hello all, I've written a MrBayes wrapper that accepts a Nexus file (presumably containing a data block and a command block). In order to make it a bit easier for new users, I was hoping to be able to let users specify some parameters, such as their model, in Galaxy, as opposed to including it in the command block of the Nexus file. Am I correct in thinking this is not possible since MrBayes does not have a way to invoke commands in-line? To clarify for non-MrBayes people, my limited understanding is that you either invoke the interpreter with $ mb and then enter your commands, or directly execute a Nexus file (containing the data and commands) with $ mb nexusfilename. Please correct me if I'm missing something or thinking about this completely wrong. I'd appreciate any input about MrBayes or a similar kind of tool. Cheers, Ann Ann Gomez Agriculture and Agri-Food Canada | Agriculture et Agroalimentaire Canada KW Neatby Bldg | éd. KW Neatby 960 Carling Ave| 960, avenue Carling Ottawa, ON | Ottawa (ON) K1A 0C6 E-mail Address / Adresse courriel: ann.go...@agr.gc.ca Telephone | Téléphone 613-759-6805 Facsimile | Télécopieur 613-759-1701 Government of Canada | Gouvernement du Canada ___ 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/
Re: [galaxy-dev] MrBayes wrapper - set parameters through Galaxy?
Hi Alex, Todd; thanks for the info and links! The Garli tool looks a lot more sophisticated than what I have so far, so I'm sure it will be helpful to look at. Ann -Original Message- From: Oleksandr Moskalenko [mailto:o...@hpc.ufl.edu] Sent: Monday, October 29, 2012 4:26 PM To: Gomez, Ann Cc: galaxy-dev@lists.bx.psu.edu List Subject: Re: [galaxy-dev] MrBayes wrapper - set parameters through Galaxy? Hi Ann, Configfiles is the way to go. I have writtent the BEAST (and TreeAnnotator), Garli, and RAxML wrappers that are all available in the Galaxy ToolShed. BEAST uses an input xml file that it can parse to execute the analysis. Garli can take a config file that's generated by the Galaxy from the options a user selects in the interface. RAxML is a more traditional command-line application albeit with very convoluted combinations of inputs and outputs that change on every release, which is why my wrapper only supports RAxML 7.3.2. Galaxy provides a lot of choices for handling the applications inputs. MrBayes in this regard is most similar to Garli, so you can take a look at that wrapper. You can take the options from the Galaxy mrbayes interface and write them to a config file that can be fed to MrBayes as a separate NEXUS file just as the Chapter 5 How do I run MrBayes in batch mode? of the MrBayes manual describes. Regards, Alex On Oct 29, 2012, at 2:03 PM, James Taylor ja...@jamestaylor.org wrote: Ann, I think you may be able to do this by generating another nexus file using configfiles in the Galaxy tool config which just contains a command block, similar to the example here: http://mrbayes.sourceforge.net/wiki/index.php/FAQ#How_do_I_run_MrBayes _in_batch_mode.3F -- jt On Mon, Oct 29, 2012 at 1:24 PM, Gomez, Ann ann.go...@agr.gc.ca wrote: Hello all, I've written a MrBayes wrapper that accepts a Nexus file (presumably containing a data block and a command block). In order to make it a bit easier for new users, I was hoping to be able to let users specify some parameters, such as their model, in Galaxy, as opposed to including it in the command block of the Nexus file. Am I correct in thinking this is not possible since MrBayes does not have a way to invoke commands in-line? To clarify for non-MrBayes people, my limited understanding is that you either invoke the interpreter with $ mb and then enter your commands, or directly execute a Nexus file (containing the data and commands) with $ mb nexusfilename. Please correct me if I'm missing something or thinking about this completely wrong. I'd appreciate any input about MrBayes or a similar kind of tool. Cheers, Ann Ann Gomez Agriculture and Agri-Food Canada | Agriculture et Agroalimentaire Canada KW Neatby Bldg | éd. KW Neatby 960 Carling Ave| 960, avenue Carling Ottawa, ON | Ottawa (ON) K1A 0C6 E-mail Address / Adresse courriel: ann.go...@agr.gc.ca Telephone | Téléphone 613-759-6805 Facsimile | Télécopieur 613-759-1701 Government of Canada | Gouvernement du Canada ___ 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/ ___ 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/
