Hi -----Original Message----- From: Markus Plangg [mailto:[email protected]] Sent: 06 March 2014 15:02 To: [email protected] Subject: Re: [Taverna-users] Portability with external tools
Hi Gareth, thanks for the fast answer and sorry for getting back so late. I didn't receive the mailing list digest until now. I just wasn't really aware before that the scripting environment is stored in the workflow but this makes sense when making use of specific features of the scripting language. I saw that importing a workflow with a different environment than is configured in the workbench it is added to the Tool invocation preferences. Changing it there might be an easy way to switch it for simple commands that are written in a portable way. Cheers, Markus Am 2014-03-05 14:41, schrieb [email protected]: > Hi Markus, > > One work around is too invoke the workflow under Windows as a shell command > within a CYGWIN shell. > Then the 'sh' interpreter, '#!' and 'chmod +x' could be available as system > calls used to Taverna. > > Another tactic is to use a cross-platform scripting language like 'perl' or > 'python' to do any scripting call instead of 'sh/bash/ksh'. > I've been using Perl on both Linux and Windows for years. > Most of the POSIX functions in Windows versions of Perl are mapped to the > appropriate Windows systems calls. > > The '#!' is not supported on Windows. > Windows uses things like 'BAT' files or PowerShell for native scripting. > > You organise your scripting calls with a call like 'scripting_host.exe > ./script_file_path' in a Taverna workflow. > Provided that you use a cross-platform scripting host (Perl/Python) and that > the interpreter is in your system's search path, in theory you could make WF > definitions cross-platform. > > I've never tried as all my Taverna stuff needs only to run under Linux. > > Best Regards, > > G. ------------------------------------------------------------------------------ Subversion Kills Productivity. Get off Subversion & Make the Move to Perforce. With Perforce, you get hassle-free workflows. Merge that actually works. Faster operations. Version large binaries. Built-in WAN optimization and the freedom to use Git, Perforce or both. Make the move to Perforce. http://pubads.g.doubleclick.net/gampad/clk?id=122218951&iu=/4140/ostg.clktrk _______________________________________________ taverna-users mailing list [email protected] [email protected] Web site: http://www.taverna.org.uk Mailing lists: http://www.taverna.org.uk/about/contact-us/ ______________________________________________________________________ This email has been scanned by the Symantec Email Security.cloud service. For more information please visit http://www.symanteccloud.com ______________________________________________________________________ This E-Mail is sent in confidence for the addressee only. Unauthorised recipients must preserve this confidentiality and should please advise the sender immediately by telephone (+1 (617) 600- 4300) and return the original E-Mail to the sender without taking a copy. Cyprotex has taken all reasonable precautions to ensure that no viruses are transmitted from Cyprotex to any third party. Cyprotex accepts no responsibility for any loss or damage resulting directly or indirectly from the use of this E-Mail or the contents. This E-Mail is sent in confidence for the addressee only. Unauthorised recipients must preserve this confidentiality and should please advise the sender immediately by telephone (+44 (0)1625 505100) and return the original E-Mail to the sender without taking a copy. Cyprotex has taken all reasonable precautions to ensure that no viruses are transmitted from Cyprotex to any third party. Cyprotex accepts no responsibility for any loss or damage resulting directly or indirectly from the use of this E-Mail or the contents. ------------------------------------------------------------------------------ Subversion Kills Productivity. Get off Subversion & Make the Move to Perforce. With Perforce, you get hassle-free workflows. Merge that actually works. Faster operations. Version large binaries. Built-in WAN optimization and the freedom to use Git, Perforce or both. Make the move to Perforce. http://pubads.g.doubleclick.net/gampad/clk?id=122218951&iu=/4140/ostg.clktrk _______________________________________________ taverna-users mailing list [email protected] [email protected] Web site: http://www.taverna.org.uk Mailing lists: http://www.taverna.org.uk/about/contact-us/
