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theiaprok_ONT request - update dragonflye to latest version #585

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kapsakcj opened this issue Aug 15, 2024 · 1 comment
Open

theiaprok_ONT request - update dragonflye to latest version #585

kapsakcj opened this issue Aug 15, 2024 · 1 comment
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enhancement This issue is a new feature or request

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@kapsakcj
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🆒

📌 Explain the Request

This is an internal (i.e. Curtis) request to update to the latest version of dragonflye. Mainly to get access to more up-to-date medaka models used during long-read polishing w/ medaka.

This will be important for ONT users that are running the latest MinKNOW software with the latest Dorado basecalling models.

Latest docker image from bioconda is quay.io/biocontainers/dragonflye:1.2.1--hdfd78af_0 and the included medaka version is v1.11.3 which includes these models:

$ docker_run -ti quay.io/biocontainers/dragonflye:1.2.1--hdfd78af_0
sh-5.2$ dragonflye --list_models
[dragonflye] Hello stranger
[dragonflye] You ran: /usr/local/bin/dragonflye --list_models
[dragonflye] This is dragonflye 1.2.1
[dragonflye] Written by Robert A Petit III
[dragonflye] Homepage is https://github.com/rpetit3/dragonflye
[dragonflye] Operating system is linux
[dragonflye] Perl version is v5.32.1
[dragonflye] Machine has 4 CPU cores and 15.61 GB RAM
[dragonflye] Generating a list of available Medaka models:
[dragonflye]    Available:
[dragonflye]    r103_fast_g507
[dragonflye]    r103_fast_snp_g507
[dragonflye]    r103_fast_variant_g507
[dragonflye]    r103_hac_g507
[dragonflye]    r103_hac_snp_g507
[dragonflye]    r103_hac_variant_g507
[dragonflye]    r103_min_high_g345
[dragonflye]    r103_min_high_g360
[dragonflye]    r103_prom_high_g360
[dragonflye]    r103_prom_snp_g3210
[dragonflye]    r103_prom_variant_g3210
[dragonflye]    r103_sup_g507
[dragonflye]    r103_sup_snp_g507
[dragonflye]    r103_sup_variant_g507
[dragonflye]    r1041_e82_260bps_fast_g632
[dragonflye]    r1041_e82_260bps_fast_variant_g632
[dragonflye]    r1041_e82_260bps_hac_g632
[dragonflye]    r1041_e82_260bps_hac_v4.0.0
[dragonflye]    r1041_e82_260bps_hac_v4.1.0
[dragonflye]    r1041_e82_260bps_hac_variant_g632
[dragonflye]    r1041_e82_260bps_hac_variant_v4.1.0
[dragonflye]    r1041_e82_260bps_sup_g632
[dragonflye]    r1041_e82_260bps_sup_v4.0.0
[dragonflye]    r1041_e82_260bps_sup_v4.1.0
[dragonflye]    r1041_e82_260bps_sup_variant_g632
[dragonflye]    r1041_e82_260bps_sup_variant_v4.1.0
[dragonflye]    r1041_e82_400bps_fast_g615
[dragonflye]    r1041_e82_400bps_fast_g632
[dragonflye]    r1041_e82_400bps_fast_variant_g615
[dragonflye]    r1041_e82_400bps_fast_variant_g632
[dragonflye]    r1041_e82_400bps_hac_g615
[dragonflye]    r1041_e82_400bps_hac_g632
[dragonflye]    r1041_e82_400bps_hac_v4.0.0
[dragonflye]    r1041_e82_400bps_hac_v4.1.0
[dragonflye]    r1041_e82_400bps_hac_v4.2.0
[dragonflye]    r1041_e82_400bps_hac_v4.3.0
[dragonflye]    r1041_e82_400bps_hac_variant_g615
[dragonflye]    r1041_e82_400bps_hac_variant_g632
[dragonflye]    r1041_e82_400bps_hac_variant_v4.1.0
[dragonflye]    r1041_e82_400bps_hac_variant_v4.2.0
[dragonflye]    r1041_e82_400bps_hac_variant_v4.3.0
[dragonflye]    r1041_e82_400bps_sup_g615
[dragonflye]    r1041_e82_400bps_sup_v4.0.0
[dragonflye]    r1041_e82_400bps_sup_v4.1.0
[dragonflye]    r1041_e82_400bps_sup_v4.2.0
[dragonflye]    r1041_e82_400bps_sup_v4.3.0
[dragonflye]    r1041_e82_400bps_sup_variant_g615
[dragonflye]    r1041_e82_400bps_sup_variant_v4.1.0
[dragonflye]    r1041_e82_400bps_sup_variant_v4.2.0
[dragonflye]    r1041_e82_400bps_sup_variant_v4.3.0
[dragonflye]    r104_e81_fast_g5015
[dragonflye]    r104_e81_fast_variant_g5015
[dragonflye]    r104_e81_hac_g5015
[dragonflye]    r104_e81_hac_variant_g5015
[dragonflye]    r104_e81_sup_g5015
[dragonflye]    r104_e81_sup_g610
[dragonflye]    r104_e81_sup_variant_g610
[dragonflye]    r10_min_high_g303
[dragonflye]    r10_min_high_g340
[dragonflye]    r941_e81_fast_g514
[dragonflye]    r941_e81_fast_variant_g514
[dragonflye]    r941_e81_hac_g514
[dragonflye]    r941_e81_hac_variant_g514
[dragonflye]    r941_e81_sup_g514
[dragonflye]    r941_e81_sup_variant_g514
[dragonflye]    r941_min_fast_g303
[dragonflye]    r941_min_fast_g507
[dragonflye]    r941_min_fast_snp_g507
[dragonflye]    r941_min_fast_variant_g507
[dragonflye]    r941_min_hac_g507
[dragonflye]    r941_min_hac_snp_g507
[dragonflye]    r941_min_hac_variant_g507
[dragonflye]    r941_min_high_g303
[dragonflye]    r941_min_high_g330
[dragonflye]    r941_min_high_g340_rle
[dragonflye]    r941_min_high_g344
[dragonflye]    r941_min_high_g351
[dragonflye]    r941_min_high_g360
[dragonflye]    r941_min_sup_g507
[dragonflye]    r941_min_sup_snp_g507
[dragonflye]    r941_min_sup_variant_g507
[dragonflye]    r941_prom_fast_g303
[dragonflye]    r941_prom_fast_g507
[dragonflye]    r941_prom_fast_snp_g507
[dragonflye]    r941_prom_fast_variant_g507
[dragonflye]    r941_prom_hac_g507
[dragonflye]    r941_prom_hac_snp_g507
[dragonflye]    r941_prom_hac_variant_g507
[dragonflye]    r941_prom_high_g303
[dragonflye]    r941_prom_high_g330
[dragonflye]    r941_prom_high_g344
[dragonflye]    r941_prom_high_g360
[dragonflye]    r941_prom_high_g4011
[dragonflye]    r941_prom_snp_g303
[dragonflye]    r941_prom_snp_g322
[dragonflye]    r941_prom_snp_g360
[dragonflye]    r941_prom_sup_g507
[dragonflye]    r941_prom_sup_snp_g507
[dragonflye]    r941_prom_sup_variant_g507
[dragonflye]    r941_prom_variant_g303
[dragonflye]    r941_prom_variant_g322
[dragonflye]    r941_prom_variant_g360
[dragonflye]    r941_sup_plant_g610
[dragonflye]    r941_sup_plant_variant_g610

The current default docker image is for dragonflye v1.0.14, which includes medaka v1.6.1 and only includes these models:

$ docker_run -ti us-docker.pkg.dev/general-theiagen/biocontainers/dragonflye:1.0.14--hdfd78af_0
sh-5.0$ medaka --version
medaka 1.6.1
sh-5.0$ dragonflye --list_models
[dragonflye] Hello stranger
[dragonflye] You ran: /usr/local/bin/dragonflye --list_models
[dragonflye] This is dragonflye 1.0.14
[dragonflye] Written by Robert A Petit III
[dragonflye] Homepage is https://github.com/rpetit3/dragonflye
[dragonflye] Operating system is linux
[dragonflye] Perl version is v5.32.1
[dragonflye] Machine has 4 CPU cores and 15.61 GB RAM
[dragonflye] Generating a list of available Medaka models:
[dragonflye]    r103_fast_g507
[dragonflye]    r103_hac_g507
[dragonflye]    r103_min_high_g345
[dragonflye]    r103_min_high_g360
[dragonflye]    r103_prom_high_g360
[dragonflye]    r103_sup_g507
[dragonflye]    r1041_e82_400bps_fast_g615
[dragonflye]    r1041_e82_400bps_hac_g615
[dragonflye]    r1041_e82_400bps_sup_g615
[dragonflye]    r104_e81_fast_g5015
[dragonflye]    r104_e81_hac_g5015
[dragonflye]    r104_e81_sup_g5015
[dragonflye]    r104_e81_sup_g610
[dragonflye]    r10_min_high_g303
[dragonflye]    r10_min_high_g340
[dragonflye]    r941_e81_fast_g514
[dragonflye]    r941_e81_hac_g514
[dragonflye]    r941_e81_sup_g514
[dragonflye]    r941_min_fast_g303
[dragonflye]    r941_min_fast_g507
[dragonflye]    r941_min_hac_g507
[dragonflye]    r941_min_high_g303
[dragonflye]    r941_min_high_g330
[dragonflye]    r941_min_high_g340_rle
[dragonflye]    r941_min_high_g344
[dragonflye]    r941_min_high_g351
[dragonflye]    r941_min_high_g360
[dragonflye]    r941_min_sup_g507
[dragonflye]    r941_prom_fast_g303
[dragonflye]    r941_prom_fast_g507
[dragonflye]    r941_prom_hac_g507
[dragonflye]    r941_prom_high_g303
[dragonflye]    r941_prom_high_g330
[dragonflye]    r941_prom_high_g344
[dragonflye]    r941_prom_high_g360
[dragonflye]    r941_prom_high_g4011
[dragonflye]    r941_prom_sup_g507
[dragonflye]    r941_sup_plant_g610
@kapsakcj kapsakcj added the enhancement This issue is a new feature or request label Aug 15, 2024
@sage-wright
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may be resolved in the next release when we move away from dragonflye altogether 🤔

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