diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml new file mode 100644 index 0000000000000000000000000000000000000000..d1b762954fb7671639e022880a12aeb64e76b175 --- /dev/null +++ b/.gitlab-ci.yml @@ -0,0 +1,24 @@ +image: centos:centos7 +pages: + script: + - yum install -y epel-release wget + - wget https://centos7.iuscommunity.org/ius-release.rpm + - rpm -Uvh ius-release*.rpm + - yum provides python3.5 + - yum install -y python35u python35u-libs python35u-devel python35u-pip + - pip3.5 install -U pip + - pip3.5 install virtualenv + - virtualenv -p python3.5 venv + - . venv/bin/activate + - pip3 install sphinx + - yum install -y make + - pip3 install sphinx + - pip3 install sphinxcontrib-bibtex + - cd jass_preprocessing/doc + - make html + - mv _build/html/ ../../public + artifacts: + paths: + - public + only: + - master diff --git a/README.md b/README.md index a062d1a52502392f00d44b645e6535bf3fdcefbb..ede72e58294191fee24f47ba4c0e0343ff9cc459 100644 --- a/README.md +++ b/README.md @@ -1,33 +1,7 @@ - # Preprocessing package for cleaning and formating data for JASS This helper package convert heterogeneous GWAS summary statistic format to the IMPG input format. -## Installation - -*Requirement* : - -## Usage - -Once installed the preprocessing can be launch in the following manner: - - - -## reference panel format: - -The user is expected to provide a reference panel with the following -column naming and column types: - -| chr | pos | snp_id | ref | alt | MAF | -|-----|-----|--------|-----|-----|-----| -|1 |13116 |rs62635286 | T| G| 0.0970447| -|1 |13118 |rs200579949 |A |G |0.0970447| -|1 |14604 |rs541940975 |A |G |0.147564| -|1 |14930 |rs75454623 |A |G |0.482228| - -*** - -## Output format -['rsID', 'pos', 'A0', "A1", "Z" ] +The package is documented at http://statistical-genetics.pages.pasteur.fr/JASS_Pre-processing/ \ No newline at end of file