Add CI, update README (#7)

* Set up CI with Azure Pipelines

[skip ci]

* Add ntroot --reads test

* Activate conda env for compilation and test run

* Add btllib to CI, dependencies

* Ensure submodules checked out

* Fix to mamba command

* Add compilers to install

* Add boost as dependency

* Add ntCard dependency

* Add ntHits dependency

* Correction to demo script

* Add genome test

* Add genome demo file

* Correction to run_ntroot_demo.sh

* Add macOS tests

* Add demo section to README

Author: lcoombe

README.md

@@ -25,6 +25,10 @@ ntRoot and all required scripts will be installed to: /path/to/install/directory
 - [meson](https://mesonbuild.com/)
 - [ninja](https://ninja-build.org/)
 - [snakemake](https://snakemake.readthedocs.io/en/stable/)
+- [btllib](https://github.com/bcgsc/btllib)
+- [boost](https://www.boost.org/doc/libs/1_61_0/more/getting_started/unix-variants.html)
+- [ntCard](https://github.com/bcgsc/ntCard)
+- [ntHits](https://github.com/bcgsc/ntHits)
 
 ## Usage
 ```
@@ -54,3 +58,11 @@ optional arguments:
 Note: please specify --reads OR --genome (not both)
 If you have any questions about ntRoot, please open an issue at https://github.com/bcgsc/ntRoot
 ```
+
+## ntRoot demo
+To test your installation:
+```
+cd demo
+./run_ntroot_demo.sh
+```
+Ensure that the ntRoot installation is available on your PATH.

azure-pipelines.yml

@@ -0,0 +1,74 @@
+# See https://docs.microsoft.com/azure/devops/pipelines/languages/python
+
+jobs:
+- job:
+  displayName: ubuntu-latest
+  pool:
+    vmImage: 'ubuntu-latest'
+
+  steps:
+  - checkout: self
+    persistCredentials: true
+    submodules: true
+
+  - script: echo "##vso[task.prependpath]$CONDA/bin"
+    displayName: Add conda to PATH
+
+  - script: conda create --yes --quiet --name ntroot_CI
+    displayName: Create Anaconda environment
+  - script: |
+      source activate ntroot_CI
+      conda install --yes --name ntroot_CI -c conda-forge -c bioconda python=3.9 mamba
+      mamba install --yes -c conda-forge -c bioconda meson ninja snakemake perl btllib compilers boost-cpp ntcard nthits
+    displayName: Install Conda packages
+  
+  - script: |
+      source activate ntroot_CI
+      meson setup build --prefix=$(pwd)/test_build
+      cd build
+      ninja install
+    displayName: Compile ntRoot
+  
+  - script: |
+      source activate ntroot_CI
+      export PATH=$(pwd)/test_build/bin:$PATH
+      which ntroot
+      cd demo
+      ./run_ntroot_demo.sh
+    displayName: Run ntRoot test
+
+- job:
+  displayName: macOS-latest
+  pool:
+    vmImage: 'macOS-latest'
+
+  steps:
+  - checkout: self
+    persistCredentials: true
+    submodules: true
+
+  - script: echo "##vso[task.prependpath]$CONDA/bin"
+    displayName: Add conda to PATH
+
+  - script: conda create --yes --quiet --name ntroot_CI
+    displayName: Create Anaconda environment
+  - script: |
+      source activate ntroot_CI
+      conda install --yes --name ntroot_CI -c conda-forge -c bioconda python=3.9 mamba
+      mamba install --yes -c conda-forge -c bioconda meson ninja snakemake perl btllib compilers boost-cpp ntcard nthits
+    displayName: Install Conda packages
+  
+  - script: |
+      source activate ntroot_CI
+      meson setup build --prefix=$(pwd)/test_build
+      cd build
+      ninja install
+    displayName: Compile ntRoot
+  
+  - script: |
+      source activate ntroot_CI
+      export PATH=$(pwd)/test_build/bin:$PATH
+      which ntroot
+      cd demo
+      ./run_ntroot_demo.sh
+    displayName: Run ntRoot test

demo/HuRef.chr21.fa

@@ -0,0 +1,35 @@
+#!/bin/bash
+
+echo "Running ntRoot demo..."
+echo "Please ensure that ntRoot is on your PATH"
+
+set -eux -o pipefail
+
+echo "Running ntRoot reads demo..."
+wget https://www.bcgsc.ca/downloads/btl/ntroot/reads_demo/ERR3239334.chr21_1.fq.gz
+wget https://www.bcgsc.ca/downloads/btl/ntroot/reads_demo/ERR3239334.chr21_2.fq.gz
+
+ntroot --draft chr21.fa --reads ERR3239334.chr21_ -k 55 -l pop-spec-snp_chr21.vcf.gz
+
+prediction=$(cat ERR3239334.chr21__ntedit_k55_variants.vcf_ancestry-predictions_tile5000000.tsv | awk '{print $1}' |head -n 2 |tail -n 1)
+
+if [ ${prediction} == "EUR" ]; then
+	echo "ntRoot reads test successful!"
+else 
+	echo "ntRoot reads test failed.. Please check your installation."
+	exit 1
+fi
+
+echo "Running ntRoot genome demo..."
+
+ntroot --draft chr21.fa --genome HuRef.chr21.fa -k 55 -l pop-spec-snp_chr21.vcf.gz
+
+prediction=$(cat HuRef.chr21_ntedit_k55_variants.vcf_ancestry-predictions_tile5000000.tsv | awk '{print $1}' |head -n 2 |tail -n 1)
+if [ ${prediction} == "EUR" ]; then
+	echo "ntRoot genome test successful!"
+else 
+	echo "ntRoot genome test failed.. Please check your installation."
+	exit 1
+fi
+
+echo "Done ntRoot tests!"