From e02b7498a1ee811359ac0d44802536d005792f5f Mon Sep 17 00:00:00 2001
From: lcoombe <lauren.e.coombe@gmail.com>
Date: Wed, 10 Apr 2024 11:20:37 -0700
Subject: [PATCH] Make ntEdit a dependency

* Because there are no longer any compiled components of ntRoot, remove meson build system
* Limit dependencies to those specific for ntRoot (remove dependencies of ntEdit)
* Update installation instructions
---
 .gitmodules                                   |  3 ---
 README.md                                     | 11 ++--------
 azure-pipelines.yml                           | 22 ++++---------------
 bin/meson.build                               |  5 -----
 meson.build                                   | 12 ----------
 ...Predictor.pl => ntRootAncestryPredictor.pl |  0
 subprojects/ntEdit                            |  1 -
 7 files changed, 6 insertions(+), 48 deletions(-)
 delete mode 100644 bin/meson.build
 delete mode 100644 meson.build
 rename bin/ntRootAncestryPredictor.pl => ntRootAncestryPredictor.pl (100%)
 delete mode 160000 subprojects/ntEdit

diff --git a/.gitmodules b/.gitmodules
index 897f8d9..e69de29 100644
--- a/.gitmodules
+++ b/.gitmodules
@@ -1,3 +0,0 @@
-[submodule "subprojects/ntEdit"]
-	path = subprojects/ntEdit
-	url = https://github.com/bcgsc/ntEdit.git
diff --git a/README.md b/README.md
index eeab4f7..f721644 100644
--- a/README.md
+++ b/README.md
@@ -39,22 +39,15 @@ Installing ntRoot from the source code:
 ```
 git clone --recurse-submodules https://github.com/bcgsc/ntRoot.git
 cd ntRoot
-meson setup build --prefix=/path/to/install/directory
-cd build
-ninja install
 ```
-ntRoot and all required scripts will be installed to: /path/to/install/directory
+No compilation is required for ntRoot (only the dependencies), so simply add the ntRoot repository to your PATH.
 
 ### Dependencies <a name=dependencies></a>
 - python 3.9+
 - perl
-- [meson](https://mesonbuild.com/)
-- [ninja](https://ninja-build.org/)
+- [ntEdit 2.0.0+](https://github.com/bcgsc/ntEdit)
 - [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)
 - [samtools](https://www.htslib.org/)
 
 
diff --git a/azure-pipelines.yml b/azure-pipelines.yml
index 52397df..77b2439 100644
--- a/azure-pipelines.yml
+++ b/azure-pipelines.yml
@@ -19,19 +19,12 @@ jobs:
   - 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
+      mamba install --yes -c conda-forge -c bioconda meson ninja snakemake perl 'ntedit>=2.0.0'
     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:$PATH
+      export PATH=$(pwd):$PATH
       which ntroot
       cd demo
       ./run_ntroot_demo.sh
@@ -55,19 +48,12 @@ jobs:
   - 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
+      mamba install --yes -c conda-forge -c bioconda snakemake perl 'ntedit>=2.0.0'
     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:$PATH
+      export PATH=$(pwd):$PATH
       which ntroot
       cd demo
       ./run_ntroot_demo.sh
diff --git a/bin/meson.build b/bin/meson.build
deleted file mode 100644
index 78d1c55..0000000
--- a/bin/meson.build
+++ /dev/null
@@ -1,5 +0,0 @@
-scripts = [
-    'ntRootAncestryPredictor.pl'
-]
-
-install_data(scripts, install_dir : 'bin')
\ No newline at end of file
diff --git a/meson.build b/meson.build
deleted file mode 100644
index 6bca1ae..0000000
--- a/meson.build
+++ /dev/null
@@ -1,12 +0,0 @@
-project('ntRoot',
-        version : '1.0.0',
-        license : 'GPL-3')
-
-subproject('ntEdit')
-subdir('bin')
-
-scripts = ['ntroot', 'ntroot_run_pipeline.smk']
-
-install_data(scripts, install_dir : 'bin', install_mode : 'rwxr-xr--')
-
-rootpath = meson.source_root()
diff --git a/bin/ntRootAncestryPredictor.pl b/ntRootAncestryPredictor.pl
similarity index 100%
rename from bin/ntRootAncestryPredictor.pl
rename to ntRootAncestryPredictor.pl
diff --git a/subprojects/ntEdit b/subprojects/ntEdit
deleted file mode 160000
index ed506fb..0000000
--- a/subprojects/ntEdit
+++ /dev/null
@@ -1 +0,0 @@
-Subproject commit ed506fb17b731147136b0782a271c3ef562d2cfa