Re: [galaxy-dev] stdout in history
Hi All, I think it makes a lot of sense to allow disabling the addition of stderr and/or stdout to dataset.info on a per tool/output dataset basis. I’ve added a Trello card for this here: https://trello.com/c/hC5HABnr. Not sure when anyone might have a chance to look into it, but pull requests are always welcome. Thanks for using Galaxy, Dan On May 31, 2014, at 11:12 AM, Jorrit Boekel wrote: > Hi Neil, > > I had some problems with this before too, so I created an tool config option > a long time ago in my own galaxy fork. Never really bothered with submitting > it, but it lives in these commits: > > https://bitbucket.org/glormph/adapt/commits/4ba256a9b8782642429ecb5472a456584bed86d5 > https://bitbucket.org/glormph/adapt/commits/86ec8b1cfeb737dfa31a1b6faf18d918bea7b4c3 > > I started implementing it in datatypes (first commit), but moved it to tool > config instead. If this is really interesting I guess I can submit a pull > request, but it felt a bit hacky at the time. > > cheers, > — > Jorrit Boekel > Proteomics systems developer > BILS / Lehtiö lab > Scilifelab Stockholm, Sweden > > > > On 30 May 2014, at 14:35, neil.burd...@csiro.au wrote: > >> Hi, >> It seems that the first 4/5 lines that are printed in the source code >> tools appear in the history (when expended) and in stdout link. Is there >> anyway to stop "print" statements appearing in the history panel? >> >> Thanks >> Neil >> ___ >> 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/ ___ 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] stdout in history
Hi Neil, I had some problems with this before too, so I created an tool config option a long time ago in my own galaxy fork. Never really bothered with submitting it, but it lives in these commits: https://bitbucket.org/glormph/adapt/commits/4ba256a9b8782642429ecb5472a456584bed86d5 https://bitbucket.org/glormph/adapt/commits/86ec8b1cfeb737dfa31a1b6faf18d918bea7b4c3 I started implementing it in datatypes (first commit), but moved it to tool config instead. If this is really interesting I guess I can submit a pull request, but it felt a bit hacky at the time. cheers, — Jorrit Boekel Proteomics systems developer BILS / Lehtiö lab Scilifelab Stockholm, Sweden On 30 May 2014, at 14:35, neil.burd...@csiro.au wrote: > Hi, > It seems that the first 4/5 lines that are printed in the source code > tools appear in the history (when expended) and in stdout link. Is there > anyway to stop "print" statements appearing in the history panel? > > Thanks > Neil > ___ > 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] stdout in history
Hi Neil, I've only used this with my own tools, but basically it looks like: whatever_your_tool_has_now > /dev/null where > /dev/null discards the output. Best, Wolfgang On 31.05.2014 01:11, neil.burd...@csiro.au wrote: Yes that would work. Can you supply an example if possible please? Thanks Neil Message: 3 Date: Fri, 30 May 2014 15:04:47 +0200 From: Wolfgang Maier To: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] stdout in history Message-ID: Content-Type: text/plain; charset=UTF-8; format=flowed you could just redirect stdout to /dev/null in the tool's xml line ? Is that an option for you ? Cheers, Wolfgang On 30.05.2014 14:35, neil.burd...@csiro.au wrote: Hi, It seems that the first 4/5 lines that are printed in the source code tools appear in the history (when expended) and in stdout link. Is there anyway to stop "print" statements appearing in the history panel? Thanks Neil ___ 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] stdout in history
Yes that would work. Can you supply an example if possible please? Thanks Neil Message: 3 Date: Fri, 30 May 2014 15:04:47 +0200 From: Wolfgang Maier To: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] stdout in history Message-ID: Content-Type: text/plain; charset=UTF-8; format=flowed you could just redirect stdout to /dev/null in the tool's xml line ? Is that an option for you ? Cheers, Wolfgang On 30.05.2014 14:35, neil.burd...@csiro.au wrote: > Hi, > It seems that the first 4/5 lines that are printed in the source > code tools appear in the history (when expended) and in stdout link. Is > there anyway to stop "print" statements appearing in the history panel? > > Thanks > Neil > > -- ___ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ End of galaxy-dev Digest, Vol 95, Issue 29 ** ___ 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] stdout in history
you could just redirect stdout to /dev/null in the tool's xml line ? Is that an option for you ? Cheers, Wolfgang On 30.05.2014 14:35, neil.burd...@csiro.au wrote: Hi, It seems that the first 4/5 lines that are printed in the source code tools appear in the history (when expended) and in stdout link. Is there anyway to stop "print" statements appearing in the history panel? Thanks Neil ___ 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] stdout in history
Hi, It seems that the first 4/5 lines that are printed in the source code tools appear in the history (when expended) and in stdout link. Is there anyway to stop "print" statements appearing in the history panel? Thanks Neil ___ 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/
