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
[](https://github.com/rickyota/genoboost/actions/workflows/genoboost.yml)
[](https://github.com/rickyota/genoboost/actions/workflows/publish.yml)
[](https://github.com/rickyota/genoboost/actions/workflows/build.yml)
-[](https://doi.org/10.5281/zenodo.10205397)
+[](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 \