diff --git a/README.md b/README.md index 6c97519..ae3d9fb 100644 --- a/README.md +++ b/README.md @@ -69,17 +69,17 @@ Miniconda is a lightweight distribution of Conda that includes just Conda and it git clone https://github.com/broadinstitute/gnomad-toolbox.git cd gnomad-toolbox pip install -r requirements.txt - ``` + ``` **Note:** Hail 0.2.127+ requires Java 8 or Java 11 and jupyter labs requires Java 11+, and if you have an Apple M1 or M2, you must have arm64 Java installed, you can first check your Java version by running: ```commandline java -version - ``` + ``` and check if you have the arm64 Java by running: ```commandline file $JAVA_HOME/bin/java - ``` + ``` If you don't have the arm64 Java, you can find it [here](https://www.azul.com/downloads/?os=macos&architecture=arm-64-bit&package=jre#zulu) You might encounter errors when installing the dependencies, such as `pg_config @@ -87,24 +87,24 @@ Miniconda is a lightweight distribution of Conda that includes just Conda and it For example, on Ubuntu, you can install the `libpq-dev` package: ```commandline sudo apt-get install libpq-dev - ``` + ``` or on macOS, you can install the `postgresql` package: ```commandline brew install postgresql - ``` + ``` ### Verify the Setup -1. Start a Python shell and test if Hail and gnomad_toolbox are working: -```commandline -import hail as hl -from gnomad_toolbox.analysis.general import get_variant_count_by_freq_bin -hl.init() -print("Hail and gnomad_toolbox setup is complete!") -``` -Or open the notebooks: -```commandline -jupyter lab -``` + Start a Python shell and test if Hail and gnomad_toolbox are working: + ```commandline + import hail as hl + from gnomad_toolbox.analysis.general import get_variant_count_by_freq_bin + hl.init() + print("Hail and gnomad_toolbox setup is complete!") + ``` + Or open the notebooks: + ```commandline + jupyter lab + ``` ## Part2: Accessing gnomAD Data Locally with example notebooks If you already have experience with gcloud and have no problem running these notebooks, @@ -113,8 +113,7 @@ you can skip this section. ### Install Google Cloud SDK (gcloud) The Google Cloud SDK is required to interact with Google Cloud services and access gnomAD public data locally. -1. Follow the official Google Cloud SDK installation [guide](https://cloud.google. - com/sdk/docs/install) for your operating system. +1. Follow the official Google Cloud SDK installation [guide](https://cloud.google.com/sdk/docs/install) for your operating system. 2. After installation, initialize gcloud to log in and set up your default project: ``` gcloud init @@ -130,13 +129,12 @@ The Google Cloud SDK is required to interact with Google Cloud services and acce ### Configure a Service Account You will need to create a service account in gcloud console IAM & Admin or using -gcloud CLI. Then you can create a key for service account and set the GOOGLE_APPLICATION_CREDENTIALS -variable to the path of the key file. - ```commandline - gcloud iam service-accounts keys create hail-local-sa-key.json --iam-account {YOUR_SERVICE_ACCOUNT} +cloud CLI. Then you can create a key for service account and set the key. - export GOOGLE_APPLICATION_CREDENTIALS=./hail-local-sa-key.json + ```commandline + gcloud iam service-accounts keys create hail-local-sa-key.json --iam-account {YOUR_SERVICE_ACCOUNT} + export GOOGLE_APPLICATION_CREDENTIALS=./hail-local-sa-key.json ``` Now, you can access gnomAD data locally using the gnomad_toolbox functions, however, -avoid running queries on the full dataset as it may take a long time and consume a -lot of resources, and most importantly, it may incur costs. +you should avoid running queries on the full dataset as it may take a long time and +consume a lot of resources, and most importantly, it may generate costs.