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<p style="margin-top:0;margin-bottom:0">Hi</p>
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<p style="margin-top:0;margin-bottom:0">Thanks. I had suspected this after looking at the fmodel script, but hadn't yet found the maps options. I will change to call those scripts internally.</p>
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<p style="margin-top:0;margin-bottom:0">Thanks <br>
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<p style="margin-top:0;margin-bottom:0">elliot<br>
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>From:</b> cctbxbb-bounces@phenix-online.org <cctbxbb-bounces@phenix-online.org> on behalf of Billy Poon <BKPoon@lbl.gov><br>
<b>Sent:</b> 24 May 2018 19:00:18<br>
<b>To:</b> cctbx mailing list<br>
<b>Subject:</b> Re: [cctbxbb] Automated Travis CI for phenix</font>
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<div dir="ltr">Hi Elliot,
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<div>Also, to run those files from the command-line, you would have something like,</div>
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<div><font face="monospace, monospace">libtbx.python <CCTBX directory>/mmtbx/command_line/fmodel.py <your command-line arguments></font></div>
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<div>The <font face="monospace, monospace">libtbx.python</font> will call python with the proper environment to be cctbx-aware.</div>
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<div>--</div>
<div><span style="font-size:12.8000001907349px">Billy K. Poon</span><br>
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<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>
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<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>
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<div dir="ltr">Hi Elliot,
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<div>phenix.fmodel and phenix.maps scripts are fully available in cctbx: </div>
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<div>cctbx_project/mmtbx/command_line/fmodel.py</div>
<div>cctbx_project/mmtbx/command_line/maps.py<br>
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<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>
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<div>Best regards,</div>
<div>Oleg Sobolev.</div>
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<div class="x_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>
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<p style="margin-top:0; margin-bottom:0">Hi <br>
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<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>
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<p style="margin-top:0; margin-bottom:0">Any suggestions would be greatly appreciated?</p>
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<p style="margin-top:0; margin-bottom:0">Software (with dockerfile): <a href="https://github.com/nelse003/exhaustive_search" class="x_m_6502851118787850595m_-8703486745181727331m_684510683438442452OWAAutoLink" id="x_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="x_m_6502851118787850595m_-8703486745181727331m_684510683438442452OWAAutoLink" id="x_m_6502851118787850595m_-8703486745181727331m_684510683438442452LPlnk568116" target="_blank"></a>Current
docker image: <a href="https://hub.docker.com/r/nelse003/ccp4_phenix_docker/" class="x_m_6502851118787850595m_-8703486745181727331m_684510683438442452OWAAutoLink" id="x_m_6502851118787850595m_-8703486745181727331m_684510683438442452LPlnk586983" target="_blank">
https://hub.docker.com/r/nelse003/ccp4_phenix_docker/</a><br>
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<p style="margin-top:0; margin-bottom:0">Thanks</p>
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<p style="margin-top:0; margin-bottom:0">Elliot<br>
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<div style="font-family:Tahoma; font-size:13px"><span id="x_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="x_m_6502851118787850595m_-8703486745181727331m_684510683438442452currentHitHighlight" id="x_m_6502851118787850595m_-8703486745181727331m_6845106834384424520.8464987595853596" name="x_searchHitInReadingPane">DPhil</span>
<span class="x_m_6502851118787850595m_-8703486745181727331m_684510683438442452highlight" id="x_m_6502851118787850595m_-8703486745181727331m_6845106834384424520.8938159649426187" name="x_searchHitInReadingPane">
Student</span>, <a href="http://www.sabsidc.ox.ac.uk/" rel="noopener noreferrer" id="x_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="x_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="x_m_6502851118787850595m_-8703486745181727331m_684510683438442452LPNoLP" target="_blank">Oxford Protein
Informatics Group</a>, Department of Statistics, University of Oxford</span></font></div>
</span><span id="x_m_6502851118787850595m_-8703486745181727331m_684510683438442452ms-rterangepaste-end"></span><br>
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