From 905828f06340ccf18faaa54d3d5832329f2779b0 Mon Sep 17 00:00:00 2001
From: Brice Letcher <brice.letcher@ens-lyon.fr>
Date: Fri, 22 Dec 2023 12:42:23 +0100
Subject: [PATCH] Add TE-Aid

---
 recipes/te-aid/build.sh  | 12 ++++++++++++
 recipes/te-aid/meta.yaml | 39 +++++++++++++++++++++++++++++++++++++++
 2 files changed, 51 insertions(+)
 create mode 100644 recipes/te-aid/build.sh
 create mode 100644 recipes/te-aid/meta.yaml

diff --git a/recipes/te-aid/build.sh b/recipes/te-aid/build.sh
new file mode 100644
index 0000000000000..951383d078f1f
--- /dev/null
+++ b/recipes/te-aid/build.sh
@@ -0,0 +1,12 @@
+#!/bin/env bash
+
+set -euo
+
+PACKAGE_HOME=${PREFIX}/share/${PKG_NAME}-${PKG_VERSION}-${PKG_BUILDNUM}
+mkdir -p ${PACKAGE_HOME}
+cp -r ./* ${PACKAGE_HOME}
+
+# Make TE-Aid executable available
+mkdir -p ${PREFIX}/bin
+chmod +x ${PACKAGE_HOME}/TE-Aid
+ln -s ${PACKAGE_HOME}/TE-Aid ${PREFIX}/bin
diff --git a/recipes/te-aid/meta.yaml b/recipes/te-aid/meta.yaml
new file mode 100644
index 0000000000000..450aadf37a95d
--- /dev/null
+++ b/recipes/te-aid/meta.yaml
@@ -0,0 +1,39 @@
+{% set name = "TE-Aid" %}
+{% set version = "0.1.0" %}
+{% set sha256 = "2150a8bb7a16ceba29f824063dd7866da9e827e952b1dbf01fb61f0c89b18904" %}
+
+package:
+  name: {{ name|lower }}
+  version: {{ version }}
+
+source:
+  url: https://github.com/bricoletc/TE-Aid/archive/refs/tags/v{{ version }}.tar.gz
+  sha256: {{ sha256 }}
+
+build:
+  noarch: generic
+  number: 0
+
+requirements:
+  run:
+    - blast >=2.15.0
+    - emboss >=6.6.0
+    - r >=4.2
+
+test:
+  commands:
+    - TE-Aid
+
+about:
+  home: https://github.com/clemgoub/TE-Aid
+  dev_url: https://github.com/clemgoub/TE-Aid
+  license: MIT
+  # license_file: TODO
+  summary: "Annotation helper tool for the manual curation of transposable element consensus sequences"
+  description: |
+    TE-Aid is a shell+R program aimed to help the manual curation of transposable 
+    elements (TE). It inputs a TE consensus sequence (fasta format) and requires a 
+    reference genome (in fasta as well). TE-Aid produces 4 figures reporting i) the genomic 
+    hits with divergence to consensus, ii) the genomic coverage of the consensus, 
+    iii) a self dot-plot, and iv) a structure analysis including TIR and LTR suggestions, 
+    open reading frames (ORFs) and TE protein hit annotation.