Renamed build to coderbuild. Hopefully I got all references, there were quite a few

Author: jjacobson95

README.md

@@ -36,22 +36,22 @@ please see the [schema description](schema/README.md).
 
 ## Building a local version
 
-The build process can be found in our [build
-directory](build/README.md). Here you can follow the instructions to
+The build process can be found in our [coderbuild
+directory](coderbuild/README.md). Here you can follow the instructions to
 build your own local copy of the data on your machine. 
 
 ## Adding a new dataset
 
-We have standardized the build process so an additional dataset can be
+We have standardized the build (coderbuild) process so an additional dataset can be
 built locally or as part of the next version of coder. Here are the
 steps to follow:
 
-1. First visit the [build
-directory](build/README.md) and ensure you can build a local copy of
+1. First visit the [coderbuild
+directory](coderbuild/README.md) and ensure you can build a local copy of
 CoderData. 
 
 2. Checkout this repository and  create a subdirectory of the
-[build directory](build) with your own build files. 
+[coderbuild directory](coderbuild) with your own build files. 
 
 3. Develop your scripts to build the data files according to our
 [LinkML Schema](schema/coderdata.yaml]). This will require collecting
@@ -66,10 +66,10 @@ validator](https://linkml.io/linkml/data/validating-data) together
 with our schema file. 
 
 You can use the following scripts as part of your build process:
-- [build/utils/fit_curve.py](build/utils/fit_curve.py): This script
+- [coderbuild/utils/fit_curve.py](coderbuild/utils/fit_curve.py): This script
   takes dose-response data and generates the dose-response statistics
   required by CoderData/
-- [build/utils/pubchem_retrieval.py](build/utils/pubchem_retreival.py):
+- [coderbuild/utils/pubchem_retrieval.py](coderbuild/utils/pubchem_retreival.py):
   This script retreives structure and drug synonym information
   required to populate the `Drug` table. 
 
@@ -78,13 +78,13 @@ and arguments:
 
 | shell script     | arguments                | description         |
 |------------------|--------------------------|---------------------|
-| `build_samples.sh` | [latest_samples] | Latest version of samples generated by coderdata build |
+| `build_samples.sh` | [latest_samples] | Latest version of samples generated by coderbuild |
 | `build_omics.sh` | [gene file] [samplefile] | This includes the `genes.csv` that was generated in the original build as well as the sample file generated above. |
 | `build_drugs.sh` | [drugfile1,drugfile2,...]       | This includes a comma-delimited list of all drugs files generated from previous build  |
 | `build_exp.sh`| [samplfile ] [drugfile] | sample file and drug file generated by previous scripts |
 
 5. Put the Docker container file inside the [Docker
-directory](./build/docker) with the name
+directory](./coderbuild/docker) with the name
 `Dockerfile.[datasetname]`. 
 
 6. Run `build_all.py` from the root directory, which should now add in

build/build_test/test_drugs.tsv

@@ -6,7 +6,7 @@ figure below shows a brief description of the process, which is
 designed to be run serially, as new identifiers are generated as data
 are added.
 
-![Build process](coderDataBuild.jpg?raw=true "Build process")
+![CoderBuild process](coderDataBuild.jpg?raw=true "CoderBuild process")
 
 ## build_all.py script
 
@@ -37,13 +37,13 @@ It requires the following authorization tokens to be set in the local environmen
 - Build all datasets and upload to Figshare and GitHub.  
 Required tokens for the following command: `SYNAPSE_AUTH_TOKEN`, `FIGSHARE_TOKEN`, `GITHUB_TOKEN`.  
 ```bash
-python build/build_all.py --all --high_mem --validate --figshare --version 0.1.41 --github-username jjacobson95 --github-email [email protected]
+python coderbuild/build_all.py --all --high_mem --validate --figshare --version 0.1.41 --github-username jjacobson95 --github-email [email protected]
 ```
 
 - Build only the experiment files.  
 **Note**: Preceding steps will not automatically be run. This assumes that docker images, samples, omics, and drugs were all previously built. Ensure all required tokens are set.   
 ```bash
-python build/build_all.py --exp
+python coderbuild/build_all.py --exp
 ```
 
 ## build_dataset.py script
@@ -63,19 +63,19 @@ Example usage:
 
 Build the broad_sanger dataset:
 ```bash
-python build/build_dataset.py --build --dataset broad_sanger
+python coderbuild/build_dataset.py --build --dataset broad_sanger
 ```
 Build the mpnst dataset continuing from broad_sanger sample and drug IDs:
 ```bash
-python build/build_dataset.py --build --dataset mpnst --use_prev_dataset broad_sanger
+python coderbuild/build_dataset.py --build --dataset mpnst --use_prev_dataset broad_sanger
 ```
 Build run schema validation on hcmi dataset:
 ```bash
-python build/build_dataset.py --dataset hcmi --validate
+python coderbuild/build_dataset.py --dataset hcmi --validate
 ```
 Build the broad_sanger dataset but skip previously built files in "local" directory:
 ```bash
-python build/build_dataset.py --dataset broad_sanger --continue
+python coderbuild/build_dataset.py --dataset broad_sanger --continue
 ```
 
 

build/docker/Dockerfile.beataml

@@ -4,7 +4,7 @@ This directory builds the data for the BeatAML samples. To build and
 test this module, run the following commands from the root directory.
 
 ## Build with test data
-Build commands should be similar to every other coderdata build
+Build commands should be similar to every other coderbuild
 module.
 
 
@@ -13,7 +13,7 @@ First we need to build the gene table
 
 1. Build genes docker
 ```
-   docker build -f build/docker/Dockerfile.genes -t genes . --build-arg HTTPS_PROXY=$HTTPS_PROXY 
+   docker build -f coderbuild/docker/Dockerfile.genes -t genes . --build-arg HTTPS_PROXY=$HTTPS_PROXY 
 ```
 
 2. Build gene file
@@ -24,7 +24,7 @@ First we need to build the gene table
 ### Build AML data
 1. Build the Docker image:
    ```
-   docker build -f build/docker/Dockerfile.beataml -t beataml . --build-arg HTTPS_PROXY=$HTTPS_PROXY 
+   docker build -f coderbuild/docker/Dockerfile.beataml -t beataml . --build-arg HTTPS_PROXY=$HTTPS_PROXY 
    ```
 
 2. Generate new identifiers for these samples to create a