Error compiling pyrosetta

[Anonymous]

Hi,

I’m running into an issue when trying to compile pyrosetta from source.  I’m following these directions:

http://www.pyrosetta.org/documentation#TOC-Building-PyRosetta-from-source

Those directions worked for me when I was using rosetta3.8.

I recently downloaded rosetta_src_2017.39.59729_bundle and get this issue:

>pwd

/opt/software/rosetta/rosetta_src_2017.39.59729_bundle/main/source/src/python/PyRosetta

>python build.py -j4 –create-package /opt/software/pyrosetta/pyrosetta_curr

Creating PyRosetta in “Release” mode in: /opt/software/rosetta/rosetta_src_2017.39.59729_bundle/main/source/build/PyRosetta/linux/clang/python-2.7/release

Updating Binder and other Git submodules…

cd /opt/software/rosetta/rosetta_src_2017.39.59729_bundle/main/source/.. && git submodule update –init –recursive — source/src/python/PyRosetta/binder

fatal: Not a git repository (or any of the parent directories): .git

Encounter error while executing: cd /opt/software/rosetta/rosetta_src_2017.39.59729_bundle/main/source/.. && git submodule update –init –recursive — source/src/python/PyRosetta/binder

Encounter error while executing: cd /opt/software/rosetta/rosetta_src_2017.39.59729_bundle/main/source/.. && git submodule update –init –recursive — source/src/python/PyRosetta/binder

fatal: Not a git repository (or any of the parent directories): .git

 

Any ideas how to fix this?

[Anonymous]

This looks like an error that i fixed a few release cycles ago. How recent is your Rosetta source? Could you please post its version here (and what package you use and where it was obtained) and then try the same command line with most recent release?

[Anonymous]

Hi Sergey,

This is the most recent version that’s available for download (2017 wk 39)

Branched off:af0fe23c4f7abb07b1e74df46596171cd53e814b

The only version info I can find is in “.release.json”:

{

  “date”: “2017-09-28 07:58:22.502995”, 

  “release”: 154, 

  “source”: {

    “binder”: “0dbb5c08c1ff9208cc94f5875f129e1e147272ee”, 

    “demos”: “f8e337cddb4089603de5ac2e5d88b00033cdb2f1”, 

    “documentation”: “0882942db2f9c0d02fc7f61bde35ecc74297b547”, 

    “main”: “af0fe23c4f7abb07b1e74df46596171cd53e814b”, 

    “tools”: “2a9d2b68a8d46b58e5f6a9be399c8f82deb2019a”

  }, 

  “version”: “rosetta.source.release-154”, 

  “week”: 39, 

  “year”: 2017

}

[Anonymous]

I will look this up. As an immediate workaround you can do the following: in build.py edit code around lines ~664 and change it from 

if not Options.binder:

    execute(‘Updating…

    output = execute(‘Checking if Binder submodule present…’,

    if ‘source/src/python/PyRosetta/binder’ not in output: 

    Options.binder = install_llvm_tool(‘binder’, rosetta_source_path+’/src/python/PyRosetta/binder/source’, rosetta_source_path + ‘/build/prefix’, Options.binder_debug)

 

to 

if not Options.binder:

    Options.binder = install_llvm_tool(‘binder’, rosetta_source_path+’/src/python/PyRosetta/binder/source’, rosetta_source_path + ‘/build/prefix’, Options.binder_debug)

and then try to re-run the build

 

[Anonymous]

Hi Sergey,

I tried that and get a new error:

 >python build.py -j4 –create-package /opt/software/pyrosetta/pyrosetta_curr

Creating PyRosetta in “Release” mode in: /opt/software/rosetta/rosetta_src_2017.39.59729_bundle/main/source/build/PyRosetta/linux/clang/python-2.7/release

fatal: Not a git repository (or any of the parent directories): .git

Encounter error while executing: cd /opt/software/rosetta/rosetta_src_2017.39.59729_bundle/main/source/src/python/PyRosetta/binder/source && git rev-parse HEAD

Encounter error while executing: cd /opt/software/rosetta/rosetta_src_2017.39.59729_bundle/main/source/src/python/PyRosetta/binder/source && git rev-parse HEAD

fatal: Not a git repository (or any of the parent directories): .git

 

[Anonymous]

I’ve gotten PyRosetta to compile (starting from rosetta_src_2017.39 in Ubuntu 16.04).  In addition to commenting out the lines described above, I made the following changes (starting at ~line 133).

Commenting out the line that starts:

binder_head = execute(‘Getting binder HEAD ….

Comment out the next line:

signature = dict(config = “LLVM …”)

replace that signature line with this:

signature = dict(config = ‘LLVM install by install_llvm_tool version: 1.0’, binder = ‘ unknown’)

 

Compiles fine now.  Probably not an ideal way to solve the problem, but just documentating this in case anyone else needs a workaround.

[Anonymous]

Thank you for posting workaround! I am working on fixign this issue so hopefully this will be ready before next weekly release.

[Author]

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