fatal error: 'bifrost/ColoredCDBG.hpp' file not found
Closed this issue · 7 comments
Hi I am trying out BlastFrost and have the error / fatal error: 'bifrost/ColoredCDBG.hpp' file not found/ #include <bifrost/ColoredCDBG.hpp> and the programmed did not install. I have attached a screenshot here. All previous steps up to the final 'make' command seem to have worked fine. I install Bifrost in a similar way without any problems. ho who I resolve this? I'm working on a Mac.
Hello,
it seems that Bifrost is not installed correctly on your system, hence BlastFrost has a problem to find Bifrost. Can you run Bifrost directly without problems (e.g. see the command line interface instructions)? Did you forget to make install Bifrost? Can you check the troubleshooting section in the Bifrost repo if that might cause a problem?
Hi Modupeh,
It seems to me the issue is Blastfrost not finding Bifrost since we know now you have successfully compiled and run Bifrost. At this point, I think its a problem with your environment variables.
When you installed Bifrost, did you do a make install ? If you did, the Bifrost header files (the one ending on .hpp or .tcc) should be located by default in /usr/local/include/bifrost/. Also, could you make sure that your environment variables C_INCLUDE_PATH and CPLUS_INCLUDE_PATH point to /usr/local/include/ ?
Best,
Guillaume
Hi all,
in fact I had exactly same issue as @Modupeh (I'm working as well on Mac, namely macOS 10.14.6). After setting environment variables C_INCLUDE_PATH and CPLUS_INCLUDE_PATH both to /usr/local/include/ I've got following warnings:
Best,
Janusz
Hello Janusz,
It seems to me this is again a new environment variables problem. By setting C_INCLUDE_PATH and CPLUS_INCLUDE_PATH, your OS now knows where are the headers of Bifrost. For some reason, it doesn't know where is the Bifrost library file. For that, you must set LD_LIBRARY_PATH, LIBRARY_PATH and PATH with /usr/local/lib/ (see (Bifrost Troubleshooting)).
The problem here is... Apple. Well, Mac OS technically. All this environment variable thingy is pretty standard on Linux and you (almost) never have to worry about it. Apparently, it is a problem on Mac for a long time now and the solution is to... install Xcode (see weird solution). Or you can use the solution with the export I am providing in the Bifrost Troubleshooting. This solution is only temporary, for the duration of your current session. You can make this permanent by modifying your .bashrc (see permament export).
In general, we will make a bioconda package to ease the install for Mac users. Let me know how it goes and if we can help you further.
Best,
Guillaume
Hi Guillaume,
Thanks for the response. I did the C_INCLUDE_PATH following instructions on Bifrost last week and was able to get it to work. But have now decide to wait until the bioconda package is published. Here is the latest issue I encountered. Blastfrost worked nicely on the test data provided with the download and I was able to get subgraphs which I was able to export and make plots. On my actual data (2 pneumococcal assembled genomes to test), I got a bifrost output of of the 2 expected files but the subgraph command would not work on this using Blastfrost. My feeling is that the bifrost outputs may have been corrupted (speculating) given how quick the analysis completed (~0.9 secs I think). I would have attached the bifrost outputs and the query sequence for your troubleshooting needs but file types are not supported.
Very much looking forward to the condo package.
Hi Modupeh,
great to hear your installation seems to have worked now. I am happy to look into your subgraph issue if you want, just you send me your graph and query (N.Luhmann@warwick.ac.uk).
I will close this issue as the installation problems have been resolved.