Open rickbeeloo opened 3 years ago
Sorry about this, I'd generally focused on conda and forgotten that pip was still supported too. I have just updated the version on PyPI to the current v1.1.0. Let me know if this fixes the issue
Is still not working. Could you fix the issue?
Same error as previously identified in pip install. When building from source
When building from source the following error apears even so I have the SeqAn3
When using through python unitig_caller-runner.py
I would really appreciate if you could suggest anything, Thanks
Hi, I think the pip installation method must have stopped working when we added seqan3 as a dependency rather than as a submodule. I am going to remove it from the install instructions now, as talking with @samhorsfield96 it seems like it's difficult to get CMake to find Seqan3 in general circumstances.
Is there a reason why the conda install doesn't work for you?
As an alternative building from source with python setup.py install
(which I assume is what you're running above) is the way to go. I still prefer to install the dependencies with conda before doing this:
conda install pybind11 zlib bzip2 bifrost seqan3 pthread-stubs cmake python pip
If you are unable to use conda at all, but have seqan3 installed elsewhere, I think you will have to modify these lines in the CMakeLists.txt to something like:
find_path(SEQAN3_CLONE_DIR name bin PATHS "seqan3_install_dir" NO_DEFAULT_PATH)
find_path(SEQAN3_INCLUDE_DIR name seqan PATHS ${SEQAN3_CLONE_DIR}/include NO_DEFAULT_PATH)
find_path(SEQAN3_SUBMODULES_DIR name submodules PATHS ${SEQAN3_INCLUDE_DIR}/seqan3 NO_DEFAULT_PATH)
pip install unitig-caller
:Gives;
So the error seems to be
CMake Error: The source directory "/tmp/pip-install-n2vbq5l2/unitig-caller" does not appear to contain CMakeLists.txt.
The bioconda installation works fine though