From 4cb106f4765836ac5e903657895781e83e971363 Mon Sep 17 00:00:00 2001
From: bluenote-1577 <jimshawster@gmail.com>
Date: Sun, 13 Oct 2024 11:44:03 -0700
Subject: [PATCH] Added the devider recipe (rename of dbghaplo recipe)

---
 recipes/devider/build.sh  | 10 +++++++++
 recipes/devider/meta.yaml | 47 +++++++++++++++++++++++++++++++++++++++
 2 files changed, 57 insertions(+)
 create mode 100644 recipes/devider/build.sh
 create mode 100644 recipes/devider/meta.yaml

diff --git a/recipes/devider/build.sh b/recipes/devider/build.sh
new file mode 100644
index 0000000000000..17d5db214e9a0
--- /dev/null
+++ b/recipes/devider/build.sh
@@ -0,0 +1,10 @@
+#!/bin/bash -euo
+
+# Add workaround for SSH-based Git connections from Rust/cargo.  See https://github.com/rust-lang/cargo/issues/2078 for details.
+# We set CARGO_HOME because we don't pass on HOME to conda-build, thus rendering the default "${HOME}/.cargo" defunct.
+export CARGO_NET_GIT_FETCH_WITH_CLI=true CARGO_HOME="$(pwd)/.cargo"
+
+# build statically linked binary with Rust
+cargo-bundle-licenses --format yaml --output THIRDPARTY.yml
+RUST_BACKTRACE=1 cargo install --verbose --locked --no-track --root $PREFIX --path .
+cp scripts/* $PREFIX/bin
diff --git a/recipes/devider/meta.yaml b/recipes/devider/meta.yaml
new file mode 100644
index 0000000000000..b9ea2b34e8c0d
--- /dev/null
+++ b/recipes/devider/meta.yaml
@@ -0,0 +1,47 @@
+{% set version="0.0.1" %}
+
+package:
+  name: devider
+  version: {{ version }}
+
+source:
+  url: https://github.com/bluenote-1577/devider/archive/v{{ version }}.tar.gz
+  sha256: e2c5e4a2faa51dbfd0ad4cb867d0dc25ea4012e83ec8fea27c1624592fce7dce
+
+build:
+  number: 0
+  run_exports:
+    - {{ pin_subpackage('devider', max_pin="x.x") }}
+
+requirements:
+  build:
+    - {{ compiler("cxx") }}
+    - {{ compiler('rust') }} 
+    - cargo-bundle-licenses
+    - make
+    - cmake >=3.12
+  run:
+    - python 
+    - samtools
+    - minimap2
+    - lofreq >=2.1.5
+    - tabix
+    - pysam >=0.16
+
+test:
+  commands:
+    - devider -h
+    - run_devider_pipeline -h
+    - haplotag_bam -h
+
+about:
+  home: https://github.com/bluenote-1577/devider
+  license: MIT
+  license_file:
+    - LICENSE
+    - THIRDPARTY.yml 
+  summary: Haplotyping small sequences from heterogeneous long-read sequencing samples with a SNP-encoded positional de Bruijn graphs.
+
+extra:
+  recipe-maintainers:
+    - bluenote-1577