From cbd4c6659c3725eb2b41414d20667023fac59d5d Mon Sep 17 00:00:00 2001
From: Yangyang Li <yangyang.li@northwestern.edu>
Date: Tue, 29 Oct 2024 12:14:21 -0500
Subject: [PATCH 1/4] Create meta.yaml

---
 recipes/deepchopper-cli/meta.yaml | 56 +++++++++++++++++++++++++++++++
 1 file changed, 56 insertions(+)
 create mode 100644 recipes/deepchopper-cli/meta.yaml

diff --git a/recipes/deepchopper-cli/meta.yaml b/recipes/deepchopper-cli/meta.yaml
new file mode 100644
index 0000000000000..ee4fc94a8dc4b
--- /dev/null
+++ b/recipes/deepchopper-cli/meta.yaml
@@ -0,0 +1,56 @@
+{% set name = "deepchopper-cli" %}
+{% set version = "1.2.5" %}
+{% set sha256 = "fc5ceaf204f82eeae1b82488ee44d020c66b0df13d27a86658ed86a7b1774dbb" %}
+
+package:
+  name: {{ name|lower }}
+  version: {{ version }}
+
+source:
+  url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/deepchopper-cli-{{ version }}.tar.gz
+  sha256: {{ sha256 }}
+
+build:
+  number: 0
+  skip: True  # [py < 310]
+  run_exports:
+    - {{ pin_subpackage("deepchopper-cli", max_pin="x") }}
+
+requirements:
+  build:
+    - {{ compiler('rust') }}
+    - {{ compiler('c') }}
+    - make
+    - cmake
+  host:
+    - python
+    - pip
+    - maturin >=1.2.1,<2
+    - setuptools-rust
+    - setuptools
+  run:
+    - python
+
+
+test:
+  commands:
+    - deepchopper-chop -h
+    
+about:
+  home: https://github.com/ylab-hi/DeepChopper
+  license: Apache-2.0
+  license_family: Apache
+  license_file: LICENSE
+  summary: 'A CLI for Genomic Language Model for Chimera Artifact Detection in Nanopore Direct RNA Sequencing.'
+  description: |
+    DeepChopper is a genomic language model designed to identify artificial sequences.
+    It provides functionality for encoding FASTQ files, making predictions, and chopping sequences.
+  doc_url: https://github.com/ylab-hi/DeepChopper
+  dev_url: https://github.com/ylab-hi/DeepChopper
+
+extra:
+  additional-platforms:
+    - linux-aarch64
+    - osx-arm64
+  recipe-maintainers:
+    - yangyangli

From 9e83db04c082656269ab1b59e1588cd993193b13 Mon Sep 17 00:00:00 2001
From: Yangyang Li <yangyang.li@northwestern.edu>
Date: Tue, 29 Oct 2024 12:16:37 -0500
Subject: [PATCH 2/4] Create build.sh

---
 recipes/deepchopper-cli/build.sh | 19 +++++++++++++++++++
 1 file changed, 19 insertions(+)
 create mode 100644 recipes/deepchopper-cli/build.sh

diff --git a/recipes/deepchopper-cli/build.sh b/recipes/deepchopper-cli/build.sh
new file mode 100644
index 0000000000000..ef7692e8e5821
--- /dev/null
+++ b/recipes/deepchopper-cli/build.sh
@@ -0,0 +1,19 @@
+#!/bin/bash
+
+# -e = exit on first error
+# -x = print every executed command
+set -ex
+
+# if [ `uname` == Darwin ]; then
+#   export HOME=`mktemp -d`
+# fi
+
+curl https://sh.rustup.rs -sSf | sh -s -- --default-toolchain nightly --profile=minimal -y
+
+export PATH="$HOME/.cargo/bin:$PATH"
+
+cd py_cli
+
+maturin build --interpreter python --release -b bin
+
+$PYTHON -m pip install target/wheels/*.whl --no-deps --ignore-installed -vv

From e97cb7902d8d0854ea9d35fae082c4cfe1287212 Mon Sep 17 00:00:00 2001
From: Yangyang Li <yangyang.li@northwestern.edu>
Date: Tue, 29 Oct 2024 12:30:17 -0500
Subject: [PATCH 3/4] Update meta.yaml

---
 recipes/deepchopper-cli/meta.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/recipes/deepchopper-cli/meta.yaml b/recipes/deepchopper-cli/meta.yaml
index ee4fc94a8dc4b..d14e1b8fb0005 100644
--- a/recipes/deepchopper-cli/meta.yaml
+++ b/recipes/deepchopper-cli/meta.yaml
@@ -7,7 +7,7 @@ package:
   version: {{ version }}
 
 source:
-  url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/deepchopper-cli-{{ version }}.tar.gz
+  url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/deepchopper_cli-{{ version }}.tar.gz
   sha256: {{ sha256 }}
 
 build:

From 26149b43a14cf931cc5788cb0ecf4935282e238e Mon Sep 17 00:00:00 2001
From: Yangyang Li <yangyang.li@northwestern.edu>
Date: Tue, 29 Oct 2024 13:13:56 -0500
Subject: [PATCH 4/4] Update build.sh

---
 recipes/deepchopper-cli/build.sh | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/recipes/deepchopper-cli/build.sh b/recipes/deepchopper-cli/build.sh
index ef7692e8e5821..191874d4ab76a 100644
--- a/recipes/deepchopper-cli/build.sh
+++ b/recipes/deepchopper-cli/build.sh
@@ -14,6 +14,6 @@ export PATH="$HOME/.cargo/bin:$PATH"
 
 cd py_cli
 
-maturin build --interpreter python --release -b bin
+maturin build --interpreter python --release -b bin --out dist
 
-$PYTHON -m pip install target/wheels/*.whl --no-deps --ignore-installed -vv
+$PYTHON -m pip install dist/*.whl --no-deps --ignore-installed -vv