nanoporetech
installing medaka (with pip) on M1
Medaka is a Research Release.
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Please ensure also to provide the information below, not doing so will likely result in a request for the information.
Describe the bug A clear and concise description of what the bug is including the command that you have run.
Logging Please attach any relevant logging messages. (Use ``` before and after code blocks).
Environment (if you do not have a GPU, write No GPU):
- Installation method [from github source, pypi (pip install), conda]
- OS: [e.g. Ubuntu 16.04]
- medaka version (can be found by running
medaka --version) - GPU model
- Nvidia driver version
- CUDA version
- cuDNN version
Additional context Add any other context about the problem here.
Dear,
I'm trying to install medaka (via pip install medaka) on a MacBook pro M1max (32Gb RAM) OS=sonoma 14.5. All dependancies are installed (most via homebrew). But during the configuration phase, the system doesn't seem to find libhts.a (although present in the homebrew/lib directory). I guess it then tries to install is from scratch (from samtools), but not in a way that works for an M1 cpu. Also the version from samtools I have installed in 1.20 (and htslib/1.20)
Is there a way to go around/fix the issue?
best regards
.... Requirement already satisfied: pyasn1<0.6.0,>=0.4.6 in /opt/homebrew/lib/python3.10/site-packages (from pyasn1-modules>=0.2.1->google-auth<3,>=1.6.3->tensorboard<2.11,>=2.10->tensorflow-macos~=2.10.0->medaka) (0.5.0rc2) Requirement already satisfied: oauthlib>=3.0.0 in /opt/homebrew/lib/python3.10/site-packages (from requests-oauthlib>=0.7.0->google-auth-oauthlib<0.5,>=0.4.1->tensorboard<2.11,>=2.10->tensorflow-macos~=2.10.0->medaka) (3.2.2) Using cached cffi-1.15.0-cp310-cp310-macosx_11_0_arm64.whl (173 kB) Using cached h5py-3.10.0-cp310-cp310-macosx_11_0_arm64.whl (2.7 MB) Using cached tensorflow_macos-2.10.0-cp310-cp310-macosx_12_0_arm64.whl (211.5 MB) Using cached gast-0.4.0-py3-none-any.whl (9.8 kB) Using cached keras-2.10.0-py2.py3-none-any.whl (1.7 MB) Using cached Keras_Preprocessing-1.1.2-py2.py3-none-any.whl (42 kB) Using cached protobuf-3.19.6-py2.py3-none-any.whl (162 kB) Using cached tensorboard-2.10.1-py3-none-any.whl (5.9 MB) Using cached tensorflow_estimator-2.10.0-py2.py3-none-any.whl (438 kB) Using cached google_auth_oauthlib-0.4.6-py2.py3-none-any.whl (18 kB) Using cached tensorboard_data_server-0.6.1-py3-none-any.whl (2.4 kB) Building wheels for collected packages: medaka Building wheel for medaka (pyproject.toml) ... error error: subprocess-exited-with-error
× Building wheel for medaka (pyproject.toml) did not run successfully.
│ exit code: 1
╰─> [117 lines of output]
/opt/homebrew/Cellar/[email protected]/3.10.14/Frameworks/Python.framework/Versions/3.10/lib/python3.10/site-packages/cffi/cparser.py:154: UserWarning: String literal found in cdef() or type source. String literals are ignored here, but you should remove them anyway because some character sequences confuse pre-parsing.
warnings.warn("String literal found in cdef() or type source. "
Bundling models: ['r103_fast_g507', 'r103_fast_snp_g507', 'r103_fast_variant_g507', 'r103_hac_g507', 'r103_hac_snp_g507', 'r103_hac_variant_g507', 'r103_min_high_g345', 'r103_min_high_g360', 'r103_prom_high_g360', 'r103_prom_snp_g3210', 'r103_prom_variant_g3210', 'r103_sup_g507', 'r103_sup_snp_g507', 'r103_sup_variant_g507', 'r1041_e82_260bps_fast_g632', 'r1041_e82_260bps_fast_variant_g632', 'r1041_e82_260bps_hac_g632', 'r1041_e82_260bps_hac_v4.0.0', 'r1041_e82_260bps_hac_v4.1.0', 'r1041_e82_260bps_hac_variant_g632', 'r1041_e82_260bps_hac_variant_v4.1.0', 'r1041_e82_260bps_joint_apk_ulk_v5.0.0', 'r1041_e82_260bps_sup_g632', 'r1041_e82_260bps_sup_v4.0.0', 'r1041_e82_260bps_sup_v4.1.0', 'r1041_e82_260bps_sup_variant_g632', 'r1041_e82_260bps_sup_variant_v4.1.0', 'r1041_e82_400bps_fast_g615', 'r1041_e82_400bps_fast_g632', 'r1041_e82_400bps_fast_variant_g615', 'r1041_e82_400bps_fast_variant_g632', 'r1041_e82_400bps_hac_g615', 'r1041_e82_400bps_hac_g632', 'r1041_e82_400bps_hac_v4.0.0', 'r1041_e82_400bps_hac_v4.1.0', 'r1041_e82_400bps_hac_v4.2.0', 'r1041_e82_400bps_hac_v4.3.0', 'r1041_e82_400bps_hac_v5.0.0', 'r1041_e82_400bps_hac_variant_g615', 'r1041_e82_400bps_hac_variant_g632', 'r1041_e82_400bps_hac_variant_v4.1.0', 'r1041_e82_400bps_hac_variant_v4.2.0', 'r1041_e82_400bps_hac_variant_v4.3.0', 'r1041_e82_400bps_hac_variant_v5.0.0', 'r1041_e82_400bps_sup_g615', 'r1041_e82_400bps_sup_v4.0.0', 'r1041_e82_400bps_sup_v4.1.0', 'r1041_e82_400bps_sup_v4.2.0', 'r1041_e82_400bps_sup_v4.3.0', 'r1041_e82_400bps_sup_v5.0.0', 'r1041_e82_400bps_sup_variant_g615', 'r1041_e82_400bps_sup_variant_v4.1.0', 'r1041_e82_400bps_sup_variant_v4.2.0', 'r1041_e82_400bps_sup_variant_v4.3.0', 'r1041_e82_400bps_sup_variant_v5.0.0', 'r104_e81_fast_g5015', 'r104_e81_fast_variant_g5015', 'r104_e81_hac_g5015', 'r104_e81_hac_variant_g5015', 'r104_e81_sup_g5015', 'r104_e81_sup_g610', 'r104_e81_sup_variant_g610', 'r10_min_high_g303', 'r10_min_high_g340', 'r941_e81_fast_g514', 'r941_e81_fast_variant_g514', 'r941_e81_hac_g514', 'r941_e81_hac_variant_g514', 'r941_e81_sup_g514', 'r941_e81_sup_variant_g514', 'r941_min_fast_g303', 'r941_min_fast_g507', 'r941_min_fast_snp_g507', 'r941_min_fast_variant_g507', 'r941_min_hac_g507', 'r941_min_hac_snp_g507', 'r941_min_hac_variant_g507', 'r941_min_high_g303', 'r941_min_high_g330', 'r941_min_high_g340_rle', 'r941_min_high_g344', 'r941_min_high_g351', 'r941_min_high_g360', 'r941_min_sup_g507', 'r941_min_sup_snp_g507', 'r941_min_sup_variant_g507', 'r941_prom_fast_g303', 'r941_prom_fast_g507', 'r941_prom_fast_snp_g507', 'r941_prom_fast_variant_g507', 'r941_prom_hac_g507', 'r941_prom_hac_snp_g507', 'r941_prom_hac_variant_g507', 'r941_prom_high_g303', 'r941_prom_high_g330', 'r941_prom_high_g344', 'r941_prom_high_g360', 'r941_prom_high_g4011', 'r941_prom_snp_g303', 'r941_prom_snp_g322', 'r941_prom_snp_g360', 'r941_prom_sup_g507', 'r941_prom_sup_snp_g507', 'r941_prom_sup_variant_g507', 'r941_prom_variant_g303', 'r941_prom_variant_g322', 'r941_prom_variant_g360', 'r941_sup_plant_g610', 'r941_sup_plant_variant_g610']
running bdist_wheel
running build
running build_py
creating build
creating build/lib.macosx-14-arm64-cpython-310
creating build/lib.macosx-14-arm64-cpython-310/medaka
copying medaka/tandem.py -> build/lib.macosx-14-arm64-cpython-310/medaka
copying medaka/options.py -> build/lib.macosx-14-arm64-cpython-310/medaka
copying medaka/vcf.py -> build/lib.macosx-14-arm64-cpython-310/medaka
copying medaka/labels.py -> build/lib.macosx-14-arm64-cpython-310/medaka
copying medaka/align.py -> build/lib.macosx-14-arm64-cpython-310/medaka
copying medaka/models.py -> build/lib.macosx-14-arm64-cpython-310/medaka
copying medaka/init.py -> build/lib.macosx-14-arm64-cpython-310/medaka
copying medaka/features.py -> build/lib.macosx-14-arm64-cpython-310/medaka
copying medaka/prediction.py -> build/lib.macosx-14-arm64-cpython-310/medaka
copying medaka/rle.py -> build/lib.macosx-14-arm64-cpython-310/medaka
copying medaka/medaka.py -> build/lib.macosx-14-arm64-cpython-310/medaka
copying medaka/common.py -> build/lib.macosx-14-arm64-cpython-310/medaka
copying medaka/wrappers.py -> build/lib.macosx-14-arm64-cpython-310/medaka
copying medaka/stitch.py -> build/lib.macosx-14-arm64-cpython-310/medaka
copying medaka/keras_ext.py -> build/lib.macosx-14-arm64-cpython-310/medaka
copying medaka/smolecule.py -> build/lib.macosx-14-arm64-cpython-310/medaka
copying medaka/variant.py -> build/lib.macosx-14-arm64-cpython-310/medaka
copying medaka/datastore.py -> build/lib.macosx-14-arm64-cpython-310/medaka
copying medaka/training.py -> build/lib.macosx-14-arm64-cpython-310/medaka
copying medaka/executor.py -> build/lib.macosx-14-arm64-cpython-310/medaka
copying medaka/medaka_counts.py -> build/lib.macosx-14-arm64-cpython-310/medaka
creating build/lib.macosx-14-arm64-cpython-310/medaka/data
copying medaka/data/r1041_e82_400bps_hac_v5.0.0_model.tar.gz -> build/lib.macosx-14-arm64-cpython-310/medaka/data
copying medaka/data/r1041_e82_400bps_hac_variant_v5.0.0_model.tar.gz -> build/lib.macosx-14-arm64-cpython-310/medaka/data
copying medaka/data/r1041_e82_400bps_sup_v5.0.0_model.tar.gz -> build/lib.macosx-14-arm64-cpython-310/medaka/data
copying medaka/data/r1041_e82_400bps_sup_variant_v5.0.0_model.tar.gz -> build/lib.macosx-14-arm64-cpython-310/medaka/data
running build_ext
generating cffi module 'build/temp.macosx-14-arm64-cpython-310/libmedaka.c'
creating build/temp.macosx-14-arm64-cpython-310
Compiling htslib using Makefile
cd submodules;
curl -L -o samtools-1.14.tar.bz2 https://github.com/samtools/samtools/releases/download/1.14/samtools-1.14.tar.bz2;
tar -xjf samtools-1.14.tar.bz2;
rm samtools-1.14.tar.bz2
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
51 7563k 51 3871k 0 0 3926k 0 0:00:01 --:--:-- 0:00:01 3926k
100 7563k 100 7563k 0 0 6768k 0 0:00:01 0:00:01 --:--:-- 27.5M
# this is required only to add in -fpic so we can build python module
Making libhts.a
cd submodules/samtools-1.14/htslib-1.14/ \
&& CFLAGS="-fpic -O3 -std=c99 " ./configure \
&& make -j 4
checking for gcc... /opt/homebrew/bin/clang
checking whether the C compiler works... no
configure: error: in `/private/var/folders/8b/g7kmwclj051fq1xjkjtrtls00000gn/T/pip-install-5s7oaa1j/medaka_c632ed6f0c3a414d88cbc09d1d86ad22/submodules/samtools-1.14/htslib-1.14':
configure: error: C compiler cannot create executables
See `config.log' for more details
make: *** [libhts.a] Error 77
Traceback (most recent call last):
File "/opt/homebrew/lib/python3.10/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 353, in <module>
main()
File "/opt/homebrew/lib/python3.10/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 335, in main
json_out['return_val'] = hook(**hook_input['kwargs'])
File "/opt/homebrew/lib/python3.10/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 251, in build_wheel
// ...... // raise CalledProcessError(retcode, cmd) subprocess.CalledProcessError: Command '['make', 'libhts.a']' returned non-zero exit status 2. [end of output]
note: This error originates from a subprocess, and is likely not a problem with pip. ERROR: Failed building wheel for medaka Failed to build medaka ERROR: Could not build wheels for medaka, which is required to install pyproject.toml-based projects
This thread may be helpful to you:
https://github.com/nanoporetech/medaka/issues/456#issuecomment-1711947247
