From e2f320769ab56bed166a279e74b3cec38c55a4e1 Mon Sep 17 00:00:00 2001 From: Michael Boniface <m.j.boniface@soton.ac.uk> Date: Fri, 21 Feb 2025 11:52:10 +0000 Subject: [PATCH] updated usage example to readme --- README.md | 19 +++++++++---------- 1 file changed, 9 insertions(+), 10 deletions(-) diff --git a/README.md b/README.md index 8f006f9..ee6fe35 100644 --- a/README.md +++ b/README.md @@ -136,7 +136,6 @@ Please execute the following process: ```bash acmc omop install -f <path to downloaded OMOP zip file> -v <release version from email> ``` -Here's a well-structured **README.md** example with the series of steps you provided: --- @@ -146,7 +145,7 @@ Follow these steps to initialize and manage a phenotype using `acmc`. In this ex 1. **Initialize a phenotype in the workspace** -Use the followijng acmc command to initialize the phenotype in a local Git repository: + Use the followijng `acmc` command to initialize the phenotype in a local Git repository: ```bash acmc phen init @@ -154,7 +153,7 @@ acmc phen init 2. **Copy example medical code lists to the phenotype codes directory** -From the command prompt, copy medical code lists `/examples/codes`to the phenotype code directory: + From the command prompt, copy medical code lists `/examples/codes`to the phenotype code directory: ```bash cp -r ./examples/codes/* ./workspace/phen/codes @@ -162,7 +161,7 @@ cp -r ./examples/codes/* ./workspace/phen/codes 3. **Copy the example phenotype configuration file to the phenotype directory** -From the command prompt, copy example phenotype configuration files `/examples/config.json` to the phenotype directory: + From the command prompt, copy example phenotype configuration files `/examples/config.json` to the phenotype directory: ```bash cp -r ./examples/config.json ./workspace/phen @@ -170,7 +169,7 @@ cp -r ./examples/config.json ./workspace/phen 4. **Validate the phenotype configuration** -Use the followijng acmc command to validate the phenotype configuration to ensure it's correct: + Use the followijng `acmc` command to validate the phenotype configuration to ensure it's correct: ```bash acmc phen validate @@ -178,7 +177,7 @@ acmc phen validate 5. **Generate phenotype in read2 code format** -Use the followijng acmc command to generate the phenotype in `read2` format: + Use the followijng `acmc` command to generate the phenotype in `read2` format: ```bash acmc phen map -t read2 @@ -186,7 +185,7 @@ acmc phen map -t read2 6. **Publish phenotype at an initial version** -Use the following `acmc` command to publish the phenotype at an initial version: + Use the following `acmc` command to publish the phenotype at an initial version: ```bash acmc phen publish @@ -202,7 +201,7 @@ acmc phen map -t snomed 8. **Get a copy of the previous version from the repo** -Use the following `acmc` command to retrieve a copy of the previous version (`v1.0.3`) from the repository: + Use the following `acmc` command to retrieve a copy of the previous version (`v1.0.3`) from the repository: ```bash acmc phen copy -v v1.0.3 @@ -210,7 +209,7 @@ acmc phen copy -v v1.0.3 9. **Compare the previous version `v1.0.3` with the latest version** -Use the following `acmc` command to compare the previous version (`v1.0.3`) with the latest version in the repository: + Use the following `acmc` command to compare the previous version (`v1.0.3`) with the latest version in the repository: ```bash python acmc.py phen diff -old ./workspace/v1.0.3/ @@ -218,7 +217,7 @@ python acmc.py phen diff -old ./workspace/v1.0.3/ 10. **Publish the phenotype at the next version** -Use the following `acmc` command to publish the phenotype at the next version: + Use the following `acmc` command to publish the phenotype at the next version: ```bash acmc phen publish -- GitLab