spond
commented
1 year ago Dear @hayleyjaywilson,
I think the source of confusion here is that you pre-msa is a part of a separate HyPhy analysis directory. Once you have installed HyPhy as shown above you should do the following to install HyPhy analyses from hyphy-analysess
$cd /home/hjw58/rds/hpc-work/dn_ds/
$git clone https://github.com/veg/hyphy-analyses.git hyphy-analyse
$cd hyphy-develop
$./hyphy /home/hjw58/rds/hpc-work/dn_ds/hyphy-analyses/codon-msa/pre-msa.bf --helpIn other words, once you have installed an analysis (.bf file), you can ask HyPhy to run it by providing a file path to the analysis file.
Best, Sergei
github-actions[bot]
Same issue as Issue with hyphy-analyses install
1293 but the advice is not solving the problem.
Hello, I have been trying to get Hyphy slac to work with my dataset for a while now. I converted to proteins and then back to a codon alignment using goalign codonalign but have the error saying the alignment is not divisible by 3. So I am trying to use the pre-msa.bf script instead. I follow the instructions here:
git clone https://github.com/veg/hyphy.git hyphy-develop cd hyphy-develop git checkout develop cmake ./ make -j MP ./HYPHYMP analysis-file --help
and get the error:
./HYPHYMP analysis-file --help Error: Could not read batch file '/rds/user/hjw58/hpc-work/dn_ds/hyphy-develop/analysis-file'. Path stack: /rds/user/hjw58/hpc-work/dn_ds/hyphy-develop/res/ /rds/user/hjw58/hpc-work/dn_ds/hyphy-develop/
Which was suggested to be solved by adding a target directory to the end of the command
git clone https://github.com/veg/hyphy.git hyphy-develop
However when I try that:
git clone https://github.com/veg/hyphy.git hyphy-develop /home/hjw58/rds/hpc-work/dn_ds
I get this error: fatal: Too many arguments.
followed by the useage guidelines.
Just doing this:
git clone https://github.com/veg/hyphy.git hyphy-develop cd hyphy-develop git checkout develop cmake ./ make -j MP
Completes but in the process I see that one aspect is failing:
git clone https://github.com/veg/hyphy.git hyphy-develop Cloning into 'hyphy-develop'... remote: Enumerating objects: 32824, done. remote: Counting objects: 100% (1432/1432), done. remote: Compressing objects: 100% (411/411), done. remote: Total 32824 (delta 1019), reused 1327 (delta 979), pack-reused 31392 Receiving objects: 100% (32824/32824), 57.17 MiB | 20.33 MiB/s, done. Resolving deltas: 100% (24279/24279), done. Updating files: 100% (917/917), done. (hpc_cam) [hjw58@login-q-2 dn_ds]$ cd hyphy-develop (hpc_cam) [hjw58@login-q-2 hyphy-develop]$ git checkout develop Branch 'develop' set up to track remote branch 'develop' from 'origin'. Switched to a new branch 'develop' (hpc_cam) [hjw58@login-q-2 hyphy-develop]$ cmake ./ -- The C compiler identification is GNU 8.5.0 -- The CXX compiler identification is GNU 8.5.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Performing Test HAVE_AVX_EXTENSIONS -- Performing Test HAVE_AVX_EXTENSIONS - Success -- Performing Test HAVE_FMA3 -- Performing Test HAVE_FMA3 - Success -- Performing Test HAVE_NEON_EXTENSIONS -- Performing Test HAVE_NEON_EXTENSIONS - Failed Set default compiler flags to -fsigned-char -O3 -std=c++14 -march=native -mtune=native -mavx -mfma -- Found OpenMP_C: -fopenmp (found version "4.5") -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") -- Found CURL: /usr/lib64/libcurl.so (found version "7.61.1") /usr/lib64/libcurl.so -- Found ZLIB: /usr/lib64/libz.so (found suitable version "1.2.11", minimum required is "1.2.9") -- Found MPI_C: /usr/local/software/spack/spack-views/._rocky8-icelake-20220710/ckngsmwknsbdd57po22aw663ckmnmqf4/intel-oneapi-mpi-2021.6.0/intel-2021.6.0/guxuvcpmykplbrr2e3af2yd7njqhau5e/mpi/2021.6.0/lib/release/libmpi.so (found version "3.1") -- Found MPI_CXX: /usr/local/software/spack/spack-views/._rocky8-icelake-20220710/ckngsmwknsbdd57po22aw663ckmnmqf4/intel-oneapi-mpi-2021.6.0/intel-2021.6.0/guxuvcpmykplbrr2e3af2yd7njqhau5e/mpi/2021.6.0/lib/libmpicxx.so (found version "3.1") -- Found MPI: TRUE (found version "3.1") -fsigned-char -O3 -std=c++14 -march=native -mtune=native -mavx -mfma -Xlinker --enable-new-dtags -Xlinker -rpath -Xlinker "/usr/local/software/spack/spack-views/rocky8-icelake-20220710/intel-oneapi-mpi-2021.6.0/intel-2021.6.0/guxuvcpmykplbrr2e3af2yd7njqhau5e/mpi/2021.6.0/lib/release" -Xlinker -rpath -Xlinker "/usr/local/software/spack/spack-views/rocky8-icelake-20220710/intel-oneapi-mpi-2021.6.0/intel-2021.6.0/guxuvcpmykplbrr2e3af2yd7nj qhau5e/mpi/2021.6.0/lib" -Xlinker --enable-new-dtags -fopenmp -- Configuring done -- Generating done -- Build files have been written to: /home/hjw58/rds/hpc-work/dn_ds/hyphy-develop
I cannot use ./HYPHYMP analysis-file --help and change analysis-file to anything else as there are only the following files in the hyphy-develop directory
Therefore I cannot see any of the files such as pre-msa.bf Please could someone advise?