<div dir="ltr">Hi Elliot,<div><br></div><div>Also, to run those files from the command-line, you would have something like,</div><div><br></div><div><font face="monospace, monospace">libtbx.python <CCTBX directory>/mmtbx/command_line/fmodel.py <your command-line arguments></font></div><div><br></div><div>The <font face="monospace, monospace">libtbx.python</font> will call python with the proper environment to be cctbx-aware.</div><div><br clear="all"><div><div dir="ltr" class="m_6502851118787850595gmail_signature" data-smartmail="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div dir="ltr"><div dir="ltr"><div><div>--</div><div><span style="font-size:12.8000001907349px">Billy K. Poon</span><br></div></div><div>Research Scientist, Molecular Biophysics and Integrated Bioimaging</div><div>Lawrence Berkeley National Laboratory</div><div>1 Cyclotron Road, M/S 33R0345</div><div>Berkeley, CA 94720</div><div>Tel: (510) 486-5709</div><div>Fax: (510) 486-5909</div><div>Web: <a href="https://phenix-online.org" target="_blank">https://phenix-online.org</a></div></div></div></div></div></div></div></div></div></div></div></div></div></div><br></div></div><br><div class="gmail_quote"><div dir="ltr">On Thu, May 24, 2018 at 10:39 AM Oleg Sobolev <<a href="mailto:osobolev@lbl.gov" target="_blank">osobolev@lbl.gov</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Hi Elliot,<div><br></div><div>phenix.fmodel and phenix.maps scripts are fully available in cctbx: </div><div><br></div><div>cctbx_project/mmtbx/command_line/fmodel.py</div><div>cctbx_project/mmtbx/command_line/maps.py<br></div><div><br></div><div>and have zero dependencies from Phenix closed-source repository.</div><div>You can just call them with cctbx-aware python in your software.</div><div><br></div><div>Best regards,</div><div>Oleg Sobolev.</div></div><div class="gmail_extra"><br><div class="gmail_quote">On Thu, May 24, 2018 at 3:37 AM, Elliot Nelson <span dir="ltr"><<a href="mailto:elliot.nelson@dtc.ox.ac.uk" target="_blank">elliot.nelson@dtc.ox.ac.uk</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div dir="ltr">
<div id="m_6502851118787850595m_-8703486745181727331m_684510683438442452divtagdefaultwrapper" style="font-size:12pt;color:rgb(0,0,0);font-family:Calibri,Helvetica,sans-serif,"EmojiFont","Apple Color Emoji","Segoe UI Emoji",NotoColorEmoji,"Segoe UI Symbol","Android Emoji",EmojiSymbols" dir="ltr">
<p style="margin-top:0;margin-bottom:0">Hi <br>
</p>
<p style="margin-top:0;margin-bottom:0"><br>
</p>
<p style="margin-top:0;margin-bottom:0">I'm looking to run automated integration tests for software, which currently runs from CCTBX, but also calls phenix scripts. These are phenix.fmodel and phenix.maps. Currently I have a docker image which sources CCP4
to get access to CCTBX, but this will not allow me to test stuff reliant on the phenix scripts.
<br>
<br>
As Phenix is not downloadable on command line (CCP4 build can be got through wget command), it is not obvious as the best way to setup up such a docker build on travis CI. I wouldn't want to source a local download of the software as i am unsure of the licesining
implications of hosting a copy of the software.</p>
<p style="margin-top:0;margin-bottom:0"><br>
</p>
<p style="margin-top:0;margin-bottom:0">Any suggestions would be greatly appreciated?</p>
<p style="margin-top:0;margin-bottom:0"><br>
</p>
<p style="margin-top:0;margin-bottom:0">Software (with dockerfile): <a href="https://github.com/nelse003/exhaustive_search" class="m_6502851118787850595m_-8703486745181727331m_684510683438442452OWAAutoLink" id="m_6502851118787850595m_-8703486745181727331m_684510683438442452LPlnk568116" target="_blank">
https://github.com/nelse003/exhaustive_search</a></p>
<p style="margin-top:0;margin-bottom:0"><a href="https://github.com/nelse003/exhaustive_search" class="m_6502851118787850595m_-8703486745181727331m_684510683438442452OWAAutoLink" id="m_6502851118787850595m_-8703486745181727331m_684510683438442452LPlnk568116" target="_blank"></a>Current docker image:
<a href="https://hub.docker.com/r/nelse003/ccp4_phenix_docker/" class="m_6502851118787850595m_-8703486745181727331m_684510683438442452OWAAutoLink" id="m_6502851118787850595m_-8703486745181727331m_684510683438442452LPlnk586983" target="_blank">
https://hub.docker.com/r/nelse003/ccp4_phenix_docker/</a><br>
</p>
<p style="margin-top:0;margin-bottom:0"><br>
</p>
<p style="margin-top:0;margin-bottom:0">Thanks</p>
<p style="margin-top:0;margin-bottom:0"><br>
</p>
<p style="margin-top:0;margin-bottom:0">Elliot<br>
</p>
<p style="margin-top:0;margin-bottom:0"><br>
</p>
<div id="m_6502851118787850595m_-8703486745181727331m_684510683438442452Signature">
<div id="m_6502851118787850595m_-8703486745181727331m_684510683438442452divtagdefaultwrapper" dir="ltr" style="font-size:12pt;color:rgb(0,0,0);font-family:Calibri,Helvetica,sans-serif,"EmojiFont","Apple Color Emoji","Segoe UI Emoji",NotoColorEmoji,"Segoe UI Symbol","Android Emoji",EmojiSymbols">
<div style="font-family:Tahoma;font-size:13px"><span id="m_6502851118787850595m_-8703486745181727331m_684510683438442452ms-rterangepaste-start"></span><span lang="en-GB">
<div style="margin:0"><font size="2" face="Calibri,sans-serif"><span style="font-size:11pt"><span class="m_6502851118787850595m_-8703486745181727331m_684510683438442452currentHitHighlight" id="m_6502851118787850595m_-8703486745181727331m_6845106834384424520.8464987595853596" name="searchHitInReadingPane">DPhil</span>
<span class="m_6502851118787850595m_-8703486745181727331m_684510683438442452highlight" id="m_6502851118787850595m_-8703486745181727331m_6845106834384424520.8938159649426187" name="searchHitInReadingPane">Student</span>,
<a href="http://www.sabsidc.ox.ac.uk/" rel="noopener noreferrer" id="m_6502851118787850595m_-8703486745181727331m_684510683438442452LPNoLP" target="_blank">
Systems Approaches to Biomedical Science</a></span></font></div>
<div style="margin:0"><font size="2" face="Calibri,sans-serif"><span style="font-size:11pt"><a href="http://www.thesgc.org/groupprofile/9489" rel="noopener noreferrer" id="m_6502851118787850595m_-8703486745181727331m_684510683438442452LPNoLP" target="_blank">Protein Crystallography</a>, Structural Genomics Consortium,
NDM, University of Oxford</span></font></div>
<div style="margin:0"><font size="2" face="Calibri,sans-serif"><span style="font-size:11pt"><a href="http://opig.stats.ox.ac.uk/" rel="noopener noreferrer" id="m_6502851118787850595m_-8703486745181727331m_684510683438442452LPNoLP" target="_blank">Oxford Protein Informatics Group</a>, Department of Statistics, University
of Oxford</span></font></div>
</span><span id="m_6502851118787850595m_-8703486745181727331m_684510683438442452ms-rterangepaste-end"></span><br>
</div>
</div>
</div>
</div>
</div>
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