Hi James,<span></span><br><br><font><span style="line-height:normal;background-color:rgba(255,255,255,0)">svn checkout svn://<a href="http://svn.code.sf.net/p/cctbx/code/trunk" target="_blank" style="text-decoration:none">svn.code.sf.net/p/cctbx/code/trunk</a> cctbx_project</span></font><div>
<br></div><div><font><span style="line-height:normal">Should do what you need, and then just use that copy of the sources to replace the cctbx_sources from the bundle. I would copy the extra directories that aren't in the svn trunk so they are alongside the cctbx_project directory (but not inside, just to keep them separate). The usual directory structure amongst the phenix developers is something like:</span></font></div>
<div><font><span style="line-height:normal"><br></span></font></div><div><font><span style="line-height:normal">build/</span></font></div><div><font><span style="line-height:normal">sources/</span></font></div><div><font><span style="line-height:normal">sources/cctbx_project/</span></font></div>
<div><font><span style="line-height:normal">sources/boost/</span></font></div><div><font><span style="line-height:normal">sources/scons/</span></font></div><div><font><span style="line-height:normal">Etc.</span></font></div>
<div><br></div><div>Then</div><div><br></div>cd build/<div>python ../sources/cctbx_project/libtbx/configure.py mmtbx (or whatever modules you wish to build)</div><div>source setpaths.sh</div><div>libtbx.scons -j 2 (number of processors)<br>
<div><font><span style="line-height:normal">Luc added the .gitignore because a few of us are using git-svn as our interface to subversion.</span></font></div><div><font><span style="line-height:normal"><br></span></font></div>
<div><font><span style="line-height:normal">Hope that helps,</span></font></div><div><font><span style="line-height:normal"><br></span></font></div><div><font><span style="line-height:normal">Richard<span></span></span></font></div>
<div><font><span style="line-height:normal"><br></span></font></div><div>On Thursday, April 11, 2013, James Stroud wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi Nat,<br>
<br>
I'm not sure of the correct way to update with SVN. I compared cctbx_sources and the SVN trunk (which had a .gitignore, suggesting its a git repository). The cctbx_sources from the bundle had some extra directories. Should I do an "svn co" of the trunk and then add the extra directories from the cctbx_sources and then re-build in place?<br>
<br>
James<br>
<br>
<br>
<br>
On Apr 11, 2013, at 12:44 PM, Nathaniel Echols wrote:<br>
<br>
> Okay, this problem should be fixed in the latest SVN revision - James,<br>
> could you please update and let us know if you're still seeing<br>
> problems?<br>
><br>
> -Nat<br>
><br>
> On Thu, Apr 11, 2013 at 7:49 AM, Nathaniel Echols <<a>nechols@lbl.gov</a>> wrote:<br>
>> On Thu, Apr 11, 2013 at 12:17 AM, James Stroud <<a>xtald00d@gmail.com</a>> wrote:<br>
>>> I downloaded this library, but its failing. Do you know what I'm doing wrong?<br>
>>><br>
>>> File "/usr/local/cctbx/cctbx_sources/mmtbx/monomer_library/server.py", line 226, in __init__<br>
>>> geostd_list_cif_obj = geostd_list_cif()<br>
>>> File "/usr/local/cctbx/cctbx_sources/mmtbx/monomer_library/server.py", line 69, in geostd_list_cif<br>
>>> strict=strict)<br>
>>> File "/usr/local/cctbx/cctbx_sources/mmtbx/monomer_library/server.py", line 56, in __init__<br>
>>> + ", ".join(mon_lib_env_vars))<br>
>>> mmtbx.monomer_library.server.MonomerLibraryServerError: Cannot find CCP4 monomer library. Please define one of these environment variables: MMTBX_CCP4_MONOMER_LIB, CLIBD_MON<br>
>><br>
>><br>
>> Ah, this I think is genuinely our fault - it is requiring that you<br>
>> have a file which is not part of the CCP4 monomer library at all, but<br>
>> rather part of a separate curated library ("geostd") which we<br>
>> distribute. This is clearly a bug; I'll bug the relevant parties. I<br>
>> think you're doing everything else correctly, though. For now, there<br>
>> are a couple of things to try:<br>
>><br>
>> 1) "touch $MMTBX_CCP4_MONOMER_LIB/list/geostd_list.cif" which may or<br>
>> may not work.<br>
>><br>
>> 2) Just pull out the entire chem_data tree from a Phenix installation<br>
>> and dump it in /usr/local/cctbx. Since we want to make this freely<br>
>> redistributable anyway, this will be a viable long-term solution (and<br>
>> since it's actually causing problems that this isn't readily<br>
>> available, I will see if I can push this quickly).<br>
>><br>
>> But we may have a fix for the crash soon - will post a follow-up if<br>
>> and when it's committed to SVN.<br>
>><br>
>> -Nat<br>
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</blockquote>
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