Compilation problems

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    • September 9, 2020 at 8:30 pm #3571
      Anonymous

        Hi. I have had some problems installing Rosetta 3.12, I have downloaded the source version, the zlib1g-dev package, gcc 9.3.0 and python 3.8.2, my operating system is Ubuntu 20.04.1 LTS. The problem is when I compile rosetta:

        if I type: ./scons.py -j 2 mode = release bin … this is the output from the terminal:

        ~ / rosetta / main / source $ ./scons.py -j 2 mode = release bin

        / usr / bin / env: “python”: The file or directory does not exist.

         

        If I type: python3 scons.py -j 2 bin mode = release … this is the output from the terminal:

        / rosetta / main / source $ python3 scons.py -j 2 bin mode = release

        scons: Reading SConscript files …

        Running versioning script … Release package detected, using rosetta / main / .release.json to acquire version information …

        Donate. (0.0 seconds)

        ./update_options.sh: line 8: python: command not found

        Traceback (most recent call last):

        File “/ home / soler / rosetta / main / source / SConstruct”, line 162, in main

        SConscript (“SConscript”, “build”)

        File “/home/soler/rosetta/main/source/external/scons-local/scons-local-3.0.4/SCons/Script/SConscript.py”, line 667, in __call__

        return method (* args, ** kw)

        File “/home/soler/rosetta/main/source/external/scons-local/scons-local-3.0.4/SCons/Script/SConscript.py”, line 604, in SConscript

        return _SConscript (self.fs, * files, ** subst_kw)

        File “/home/soler/rosetta/main/source/external/scons-local/scons-local-3.0.4/SCons/Script/SConscript.py”, line 284, in _SConscript

        exec (compile (_file_.read (), _file_.name, ‘exec’),

        File “/ home / soler / rosetta / main / source / SConscript”, line 32, in <module>

        subprocess.check_call ([“./ update_options.sh”])

        File “/usr/lib/python3.8/subprocess.py”, line 364, in check_call

        raise CalledProcessError (retcode, cmd)

        subprocess.CalledProcessError: Command ” returned non-zero exit status 127.

        scons: done reading SConscript files.

        scons: Building targets …

        scons: *** Do not know how to make File target `bin ‘(/ home / soler / rosetta / main / source / bin). Stop.

        scons: building terminated because of errors.

        I would greatly appreciate your help. Thanks in advance.

         

         

         

         

         

         

      • September 9, 2020 at 10:31 pm #15482
        Anonymous

          The issue you’re running into is that Ubuntu 20.04 comes with Python3, but does not come with Python2 by default. Additionally, as historically the `python` command has been Python2, they made the decision not to alias the plain `python` command to Python3 by default, and just not provide it. This means that anything that calls for just `python` won’t work in an off-the-shelf version of Ubuntu 20.04.

          There are two packages which will change this: python-is-python3 and python-is-python2 which will cause the plain `python` command to be either Python3 or Python2, respectively.

          Either one will likely work, but keep in mind that (as of writing in early Sep 2020) we have not yet converted all of the Python scripts in Rosetta to be runnable with Python3. While there are a fair number of scripts which have been converted, and many which are runnable with either version, there are still quite a few which are Python2.7 only. As such, while you can chance installing python-is-python3, you may be safer with python-is-python2.

          • September 10, 2020 at 2:24 am #15484
            Anonymous

              Thank you very much for your help, but how can I install the python-is-python2 package?

               

               
               

            • September 10, 2020 at 12:47 pm #15489
              Anonymous

                On Ubuntu, the command would be `sudo apt install python-is-python2` — this would need to be done by an account with administration rights to the machine.

              • September 13, 2020 at 4:16 am #15497
                Anonymous

                  First of all, thank you very much, I already compiled everything, without errors, the bin directory is full, with the protocols. My goal is to use pepspec, for the design of peptides with a target protein, of course. One question I have is about the flags, do I have to create it myself? or just copy it into some text editor? I’ve been going through the protocol, which I’m not sure if that’s what I saw. Again, thank you very much for your help.

                • September 13, 2020 at 6:35 pm #15498
                  Anonymous

                    You can certainly just create the options file yourself with a text editor. Copying an existing options file and making edits with a text editor is also a valid stratagy. It’s just a plain-text formatted file, so as long as your text editor doesn’t insert spurious characters, you should be good.

                  • September 18, 2020 at 5:06 am #15502
                    Anonymous

                      Good evening, I would like to ask for your help because I am trying to run the pepspec anchor dock protocol, so I am using the following options as flags, which come in the tutorial:

                      -database / home / soler / rosetta / main / database

                      -in: file: s ./KARS.pdb

                      -ex1 – increase the chi1 resolution of the rotamer library

                      -ex2 – increase the chi2 resolution of the rotamer library

                      -extrachi_cutoff 0 – increase rotamer sampling at exposed positions

                      -pepspec: ref_pdb_list KARS.pdb A 5

                      -pepspec: n_peptides 5

                      -pepspec: anchor_type PRO

                      -pepspec: no_prepack_prot false

                      For this, I am executing the protocol on the desktop, in it I have the input structure and the previous flags file.

                       Desktop $ /home/soler/rosetta/main/source/bin/pepspec_anchor_dock.default.linuxgccrelease @flags

                      When I run this in the terminal, it automatically gives me an internal error, this appears when I open rosetta_crash.log:

                      [FILE]: src / utility / options / OptionCollection.cc

                      [LINE]: 1430

                      [START_MESSAGE]

                      Option matching -database not found in indented @file context –

                      [END_MESSAGE]

                      [END_CRASH_REPORT]

                      Can you help me? Thanks in advance

                    • February 9, 2021 at 4:36 pm #15720
                      Anonymous

                        (First off, it’s best to open this new issue as a different post.)

                        The issue here is likley to be the formatting of your options file. Indentation matters. Generally speaking, you want to place the options at the leftmost edge of the file, unless you’re explicitly taking advantage of the options nesting approach. (Which is often unneeded.)

                        The other thing to check is that you wrote the option file with a text editor and not a word processor. In particular, you want to make sure that the ‘-‘ in the option is an ASCII hyphen and not a en-dash or an em-dash. A plain text editor will do an ASCII hyphen when you type ‘-‘, but a word processor might helpfully “fix” it for you.

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