README-en.md

genocon2021-docker

A docker image where you can run a judge program (eval.c) and a converter for multiple sequence alignment (decode_cigar.py). This repostiory also provides a sample solver (sample_solver.py).

日本語版 も公開しています。

Requirements

• For Windows
  • Windows Subsystem for Linux 2 (WSL2)
  • Docker Desktop for Windows WSL 2 backend
  • Note: this document expects you run all the commands on terminal of Ubuntu on WSL2.
• For MacOS
  • Docker Desktop for Mac
• For Linux
  • Docker

How to Evaluate Your Output on Docker

For Very Small Sample Data

1. Prepare very small sample data

   cd <your working directory for genocon2021>
   
   mkdir -p data/very-small-sample
   echo "ACACAGCGGCGACC\nACACAGCGG-GACC" > data/very-small-sample/answer.txt
   echo "ACACAGCGGCGACC\nACACAGCGGGACC" > data/very-small-sample/output.txt
   echo "ACACAGCGGCGACC\n> 0 3=1XT10=\n< 0 14=\n< 0 9=1D4=\n< 0 14=\n< 0 14=\n< 0 9=1D4=\n=\n" > data/very-small-sample/testcase.txt
   

2. Confirm the judge program works well with the sample output data

   docker run --rm -v $(pwd)/data:/app/data exkazuu/genocon2021 ./eval data/very-small-sample/answer.txt data/very-small-sample/output.txt
   

   The following result is shown:

   raw_score: 27
   final_score (raw_score / 100): 0
   

3. Run the sample solver with data/very-small-sample/testcase.txt to generate data/very-small-sample/sample-output.txt

   • If you run Python 3 on your local PC

     python3 sample_solver.py data/very-small-sample/testcase.txt > data/very-small-sample/sample-output.txt
     

   • If you run Python 3 on Docker container

     docker run --rm -v $(pwd)/data:/app/data exkazuu/genocon2021 python3 sample_solver.py data/very-small-sample/testcase.txt > data/very-small-sample/sample-output.txt
     

4. Run the judge program with the output data of the sample solver

   docker run --rm -v $(pwd)/data:/app/data exkazuu/genocon2021 ./eval data/very-small-sample/answer.txt data/very-small-sample/sample-output.txt
   

   The following result is shown:

   raw_score: -72
   final_score (raw_score / 100): 0
   

5. Run YOUR solver with data/very-small-sample/testcase.txt to generate data/very-small-sample/your-output.txt

6. Run the judge program with the output data of YOUR solver

   docker run --rm -v $(pwd)/data:/app/data exkazuu/genocon2021 ./eval data/very-small-sample/answer.txt data/very-small-sample/your-output.txt
   

For Sample Data (src_genocon2021.tar.gz)

1. Create data directory

   cd <your working directory for genocon2021>
   
   mkdir -p data
   

2. Download src_genocon2021.tar.gz (Please see the topic on 2021/9/11 in https://atcoder.jp/contests/genocon2021)

3. Extract src_genocon2021.tar.gz (e.g. tar -xvf src_genocon2021.tar.gz)

4. Move src_genocon2021/dat directory into data directory created at the step 1 (e.g. mv src_genocon2021/dat <your working directory for genocon2021>/data/)

5. Confirm the judge program works well with the sample output data

   docker run --rm -v $(pwd)/data:/app/data exkazuu/genocon2021 ./eval data/dat/gen1_small_10.answer.txt data/dat/gen1_small_10.output.txt
   

   The following result is shown:

   raw_score: 59948
   final_score (raw_score / 100): 599
   

6. Run the sample solver with data/dat/gen1_small_10.testcase.txt to generate data/dat/gen1_small_10.output.txt

   • If you run Python 3 on your local PC

     python3 sample_solver.py data/dat/gen1_small_10.testcase.txt > data/dat/sample-output.txt
     

   • If you run Python 3 on Docker container

     docker run --rm -v $(pwd)/data:/app/data exkazuu/genocon2021 python3 sample_solver.py data/dat/gen1_small_10.testcase.txt > data/dat/sample-output.txt
     

7. Run the judge program with the output data of the sample solver

   docker run --rm -v $(pwd)/data:/app/data exkazuu/genocon2021 ./eval data/dat/gen1_small_10.answer.txt data/dat/sample-output.txt
   

   The following result is shown:

   raw_score: 44560
   final_score (raw_score / 100): 445
   

8. Run YOUR program with data/dat/gen1_small_10.testcase.txt to generate data/dat/your-output.txt

9. Run the judge program with YOUR output data

   docker run --rm -v $(pwd)/data:/app/data exkazuu/genocon2021 ./eval data/dat/gen1_small_10.answer.txt data/dat/your-output.txt
   

How to Convert testcase.txt into Multiple Sequence Alignment (MSA)

1. docker run --rm -v $(pwd)/data:/app/data exkazuu/genocon2021 python3 decode_cigar.py data/very-small-sample/testcase.txt > msa.txt

2. Open msa.txt (e.g. less msa.txt)

For Mainteners

Format Code

clang-format -i eval.c && npx prettier -w README*.md

Deploy Docker Image

docker build -t exkazuu/genocon2021 . && docker push exkazuu/genocon2021

LICENSE

BSD 3-Clause License