search

ComparativeGenomicsToolkit / hal

Hierarchical Alignment Format
Other
154 stars 40 forks source link

Error building hal #235

Open Zazzyre opened 2 years ago

Zazzyre commented 2 years ago

Hi,

I'm getting an error when I make hal which I'm assuming is to do with dependencies. I followed the instructions to install everything listed, what do I need to modify to get hal working?

Thanks!

cd api && make libs
make[1]: Entering directory `/projects/zazzy@xsede.org/hal/api'
h5c++ -prefix=DIR/hdf5 -MM -MT ../objs/api/impl/halAlignmentInstance.o -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -Ihdf5_impl -Immap_impl -c impl/halAlignmentInstance.cpp >impl/halAlignmentInstance.depend
/curc/sw/anaconda3/2020.11/bin/h5c++: line 304: x86_64-conda_cos6-linux-gnu-c++: command not found
make[1]: *** [../objs/api/impl/halAlignmentInstance.o] Error 127
make[1]: Leaving directory `/projects/zazzy@xsede.org/hal/api'
make: *** [api.libs] Error 2
glennhickey commented 2 years ago

HAL binaries are included in Cactus releases. Perhaps it would be simpler to use those?

https://github.com/ComparativeGenomicsToolkit/cactus/releases

Zazzyre commented 2 years ago

HAL binaries are included in Cactus releases. Perhaps it would be simpler to use those?

https://github.com/ComparativeGenomicsToolkit/cactus/releases

Are they usable through the docker image with singularity? I'm working on a computing cluster so can't use docker directly but can within singularity

nathanweeks commented 1 year ago

It's been a while since I tried, and I only tested a subset of the HAL binaries, but they should be functional in a Singularity image generated from the Docker / OCI image.