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</o:shapelayout></xml><![endif]--></head><body lang=EN-US link=blue vlink=purple><div class=WordSection1><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Hi Ralf, <o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p>&nbsp;</o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Thanks for the hint. I got it to work with &#8216;cmd /c phenix.refine&#8217; from the cygwin prompt. Was loathe to change all the .bat files as suggested in the thread, but it pointed me to the solution. Is there an overwhelming reason why .bat files are used as opposed to the old style mini .exe files? Would be really nice to have the old style back or at least the option to recreate them as a post processing step. <o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p>&nbsp;</o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Carsten<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p>&nbsp;</o:p></span></p><div style='border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0in 0in 0in'><p class=MsoNormal><b><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'>From:</span></b><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'> phenixbb-bounces@phenix-online.org [mailto:phenixbb-bounces@phenix-online.org] <b>On Behalf Of </b>Ralf Grosse-Kunstleve<br><b>Sent:</b> Wednesday, January 04, 2012 11:10 PM<br><b>To:</b> PHENIX user mailing list<br><b>Subject:</b> Re: [phenixbb] CCI-Apps - Cygwin incompatibility after upgrade<o:p></o:p></span></p></div><p class=MsoNormal><o:p>&nbsp;</o:p></p><p class=MsoNormal>Hi Carsten,<o:p></o:p></p><div><p class=MsoNormal><o:p>&nbsp;</o:p></p></div><div><p class=MsoNormal>Could you try this?<o:p></o:p></p></div><div><p class=MsoNormal><o:p>&nbsp;</o:p></p></div><div><p class=MsoNormal><a href="http://cygwin.com/ml/cygwin/2001-01/msg00724.html">http://cygwin.com/ml/cygwin/2001-01/msg00724.html</a><o:p></o:p></p></div><div><p class=MsoNormal><o:p>&nbsp;</o:p></p></div><div><p class=MsoNormal style='margin-bottom:12.0pt'>Ralf<o:p></o:p></p><div><p class=MsoNormal>On Wed, Jan 4, 2012 at 6:28 PM, Schubert, Carsten [JRDUS] &lt;<a href="mailto:CSCHUBER@its.jnj.com">CSCHUBER@its.jnj.com</a>&gt; wrote:<o:p></o:p></p><div><p><span style='font-family:"Calibri","sans-serif"'>Hi,</span><o:p></o:p></p><p><span style='font-family:"Calibri","sans-serif"'>After upgrading my cci_apps install on Windows from 1.7-718 to 1.7.3-928 the interoperability with cygwin is</span> <span style='font-family:"Calibri","sans-serif"'>gone.</span> <span style='font-family:"Calibri","sans-serif"'>Calling phenix.refine just gives a</span> <span style='font-family:"Calibri","sans-serif"'>&#8216;Command not found&#8217; error.</span> <span style='font-family:"Calibri","sans-serif"'>Turns out that the</span> <span style='font-family:"Calibri","sans-serif"'>little .exe files for each subprogram were replaced by .bat files. That is fine if one just wants to use the DOS CLI, but</span> <span style='font-family:"Calibri","sans-serif"'>cygwin is not able to call</span> <span style='font-family:"Calibri","sans-serif"'>programs via .bat files as far as I know.</span> <o:p></o:p></p><p><span style='font-family:"Calibri","sans-serif"'>Is there a workaround for this problem besides working in the DOS CLI (yuk)?</span><o:p></o:p></p><p><span style='font-family:"Calibri","sans-serif"'>Thanks </span><o:p></o:p></p><p><span style='font-family:"Calibri","sans-serif";color:#888888'>Carsten</span><span style='color:#888888'><o:p></o:p></span></p></div><p class=MsoNormal style='margin-bottom:12.0pt'><br>_______________________________________________<br>phenixbb mailing list<br><a href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a><br><a href="http://phenix-online.org/mailman/listinfo/phenixbb" target="_blank">http://phenix-online.org/mailman/listinfo/phenixbb</a><o:p></o:p></p></div><p class=MsoNormal><o:p>&nbsp;</o:p></p></div></div></body></html>