Closed davidmadariaga closed 4 months ago
Hi @davidmadariaga,
Is there a reason you are trying to compile he code from source rather than installing from one of he packages as in the instructions in the README?
hi, yes!, because none of the other methods worked :(, but i will try again using pip, thanks for answering!!
Hi, hope you are doing great. Im a noob at this, could you please help me?, i would be really grateful. I tried to install lfs following the instructions but it seems that i did it wrong. these are the commands i used and the message i got. Please answer if you have time, dont bother if you cant. Cheers from Chile.
commands:
(. /etc/lsb-release &&
sudo apt-get install git-lfs
and then i wrote this:
ubuntu@atenea:~/medaka$ make install . ./venv/bin/activate && python -c "from setup import check_model_lfs; check_model_lfs()" Cannot import pyabpoa, some features may not be available. Cannot import wurlitzer, some features may not be available. 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_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_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_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_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', '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']
Model files appear to be git lfs stubs. Please refer to README.md for instructions regarding git lfs. If you obtained medaka through a method other than cloning the repository from github, please raise an issue on github.com/nanoporetech/medaka. Makefile:158: recipe for target 'check_lfs' failed make: *** [check_lfs] Error 1