diff --git a/.github/workflows/genoboost.yml b/.github/workflows/genoboost.yml index 8c17886..2354482 100644 --- a/.github/workflows/genoboost.yml +++ b/.github/workflows/genoboost.yml @@ -16,14 +16,14 @@ jobs: run: cargo build --manifest-path ./projects_rust/Cargo.toml --verbose - #test_example: - # runs-on: ubuntu-latest - # needs: build - # steps: - # - uses: actions/checkout@v2 - # - name: test - # run: | - # bash ./genoboost.sh + test_example: + runs-on: ubuntu-latest + needs: build + steps: + - uses: actions/checkout@v2 + - name: test + run: | + bash ./genoboost.sh #test_1kg: # runs-on: ubuntu-latest diff --git a/README.md b/README.md index f02ad00..ae12a74 100644 --- a/README.md +++ b/README.md @@ -1,9 +1,9 @@ -# GenoBoost v1.1.0 +# GenoBoost v1.0.8 [![GenoBoost](https://github.com/rickyota/genoboost/actions/workflows/genoboost.yml/badge.svg)](https://github.com/rickyota/genoboost/actions/workflows/genoboost.yml) [![Release](https://github.com/rickyota/genoboost/actions/workflows/publish.yml/badge.svg)](https://github.com/rickyota/genoboost/actions/workflows/publish.yml) [![Build](https://github.com/rickyota/genoboost/actions/workflows/build.yml/badge.svg)](https://github.com/rickyota/genoboost/actions/workflows/build.yml) -[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.10205397.svg)](https://doi.org/10.5281/zenodo.10205397) +[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.10205707.svg)](https://doi.org/10.5281/zenodo.10205707) ## Getting Started @@ -21,7 +21,7 @@ $ genoboost train \ ## Table of Contents -- [GenoBoost v1.0.7](#genoboost-v107) +- [GenoBoost v1.0.8](#genoboost-v108) - [Getting Started](#getting-started) - [Table of Contents](#table-of-contents) - [News](#news) @@ -53,8 +53,9 @@ $ genoboost train \ - [v1.1.0](https://github.com/rickyota/genoboost/releases/tag/v1.1.0) (May 23, 2024) - Clean code. -- [v1.0.7](https://github.com/rickyota/genoboost/releases/tag/v1.0.7) (Nov 25, 2023) +- [v1.0.8](https://github.com/rickyota/genoboost/releases/tag/v1.0.8) (Nov 25, 2023) - Initial version. + - Tested on Rocky Linux 8.9 and MacOS 14.3.1. ## Introduction @@ -78,12 +79,12 @@ For now, the input genotype format is allowed for plink1 or plink2 only. ### Installation -Using arm architecture including Macbook M1, M2 chip will slow down due to unavailability of SIMD. +Using arm architecture, including Macbook M1 and M2 chips, will stop or slow down the software due to the unavailability of SIMD. I plan to deal with it in the future. #### Plink1 Input -If you want to input plink1, download a program for your computer from [here][release]. +If you want to input plink1, download a compiled program for Linux (tested on Rocky Linux<=8.9), macOS (tested on <=14.3.1), and Windows (not tested) from [here][release]. This should take less than 1 minute. #### Plink2 Input @@ -130,9 +131,11 @@ $ ./genoboost train \ --file-phe ./example/genot.cov \ --cov age,sex \ --major-a2-train \ - --seed 51 + --seed 55 ``` +This test code should take less than 2 minutes. + #### Without Validation If you want to treat all samples as a training dataset, use `--train-only` option. GenoBoost produces SNV weights each for learning rate. Use `--iter-snv` or `--iter` to control the maximum number of SNVs or iterations for training. @@ -165,7 +168,7 @@ $ ./genoboost train \ --phe PHENO1 \ --cov age,sex \ --major-a2-train \ - --seed 51 + --seed 55 ``` #### Cross-validation @@ -180,7 +183,7 @@ $ ./genoboost train \ --cov age,sex \ --major-a2-train \ --cross-validation 5 \ - --seed 51 + --seed 55 ``` #### Options for Training diff --git a/genoboost.docker.sh b/genoboost.docker.sh index 3d009d8..02719be 100644 --- a/genoboost.docker.sh +++ b/genoboost.docker.sh @@ -24,7 +24,7 @@ genoboost-docker train \ --file-phe "$file_cov" \ --cov age,sex \ --major-a2-train \ - --seed 51 + --seed 55 # score genoboost-docker score \ diff --git a/test/script/genoboost.cv.sh b/test/script/genoboost.cv.sh index 5e2a5f0..404e053 100644 --- a/test/script/genoboost.cv.sh +++ b/test/script/genoboost.cv.sh @@ -25,7 +25,8 @@ cp ./projects_rust/target/release/genoboost ./genoboost --cov age,sex \ --learning-rates "0.5 0.2" \ --cross-validation 5 \ - --major-a2-train + --major-a2-train \ + --seed 55 # score ./genoboost score \ diff --git a/test/script/genoboost.docker.sh b/test/script/genoboost.docker.sh index 6a60667..75b8b33 100644 --- a/test/script/genoboost.docker.sh +++ b/test/script/genoboost.docker.sh @@ -24,7 +24,7 @@ genoboost-docker train \ --file-phe "$file_cov" \ --cov age,sex \ --major-a2-train \ - --seed 51 + --seed 55 # score genoboost-docker score \ diff --git a/test/script/genoboost.sh b/test/script/genoboost.sh index fbe0168..bec07a0 100644 --- a/test/script/genoboost.sh +++ b/test/script/genoboost.sh @@ -29,7 +29,7 @@ cp ./projects_rust/target/release/genoboost ./genoboost --learning-rates "0.5 0.2" \ --cov age,sex \ --major-a2-train \ - --seed 51 + --seed 55 #--verbose \