Re: [galaxy-dev] Set a new metadata attribute
Hi Nikos As a 'quick and dirty' work-around, I suggest generating in addition to the output file a 'log' file, which can be read by the subsequent tool. Hans-Rudolf On 09/26/2014 04:54 PM, Peter Cock wrote: On Fri, Sep 26, 2014 at 3:01 PM, Nikos Sidiropoulos nikos.sid...@gmail.com wrote: Hi all, In a tool that I am writting I want to pass an input parameter value (string) into the output file's metadata. Meaning that one of the tool parameters is a barcode signature, 'NNWTGXN' for example. I want that attribute to be stored somehow in the output file in order to be read by a subsequent tool without the user having to set that parameter again. The files I'll be working with are in FASTQ, BAM and tabular format. Is it possible? Bests, Nikos Your code can write the value directly into an output file (e.g. one of the SAM/BAM headers might work), but I don't think there is anything suitable within Galaxy for re-exporting the parameter value as an input parameter for a future tool. However, at the workflow level you can set variables - might that be a way forward? https://wiki.galaxyproject.org/Learn/AdvancedWorkflow/VariablesEdit 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] Question about Terms and Conditions for public galaxy server under development
Hi, We are developing a galaxy server for public usage and we would like to know if we should use the same terms and conditions as you provide for Galaxy main when we publicly launch our server: https://usegalaxy.org/static/terms.html If so, could you let us know if we can use the exact same text or if we need to replace The Pennsylvania State University with our University name? If we can't use the text in the link above, could you provide recommendations? Kind Regards, Audrey Michel ___ 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] bwa and bwa-mem wrappers...
...have been committed to toolshed: https://toolshed.g2.bx.psu.edu/view/devteam/bwa_0_7_10 and github: https://github.com/nekrut/bwa-mem any feedback (especially in the form of github pull requests) is appreciated. One of the main changes is that these tools have no helper python scripts (all magic happens within the tool xml) and they produce BAM output. a. -- Anton Nekrutenko Professor of Biochemistry and Molecular Biology *http://nekrut.bx.psu.edu http://nekrut.bx.psu.edu* (814) 826-3051 ___ 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] Question about Terms and Conditions for public galaxy server under development
Audrey: I do not see why not (but I'm not a lawyer of course). a. On Fri, Sep 26, 2014 at 8:41 AM, audrey michel audreymann...@gmail.com wrote: Hi, We are developing a galaxy server for public usage and we would like to know if we should use the same terms and conditions as you provide for Galaxy main when we publicly launch our server: https://usegalaxy.org/static/terms.html If so, could you let us know if we can use the exact same text or if we need to replace The Pennsylvania State University with our University name? If we can't use the text in the link above, could you provide recommendations? Kind Regards, Audrey Michel ___ 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/ -- Anton Nekrutenko Professor of Biochemistry and Molecular Biology *http://nekrut.bx.psu.edu http://nekrut.bx.psu.edu* (814) 826-3051 ___ 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/
