From 5bcc61c9d33110ea300fcd93a5be59a7be781ae9 Mon Sep 17 00:00:00 2001
From: Mariia Zelenskaia <102167492+mariia-zelenskaia@users.noreply.github.com>
Date: Fri, 9 Aug 2024 06:02:43 +0200
Subject: [PATCH] use semantic nomenclature for the TransAnnot versions
 (#49875)

* use semantic nomenclature for the TransAnnot versions

* Use 3.0.0 as a version

Signed-off-by: Martin Tzvetanov Grigorov <mgrigorov@apache.org>

* Use 3-e15e316 for the package url

Signed-off-by: Martin Tzvetanov Grigorov <mgrigorov@apache.org>

* clean up recipe

* clean up recipe

* clean up recipe

---------

Signed-off-by: Martin Tzvetanov Grigorov <mgrigorov@apache.org>
Co-authored-by: Martin Tzvetanov Grigorov <mgrigorov@apache.org>
Co-authored-by: mencian <joshua.zhuang@yahoo.com>
---
 recipes/transannot/build.sh  | 28 ++++++++++++++++++-------
 recipes/transannot/meta.yaml | 40 ++++++++++++++++++------------------
 2 files changed, 41 insertions(+), 27 deletions(-)

diff --git a/recipes/transannot/build.sh b/recipes/transannot/build.sh
index ae429591a47eb..8f7d428ac11e6 100644
--- a/recipes/transannot/build.sh
+++ b/recipes/transannot/build.sh
@@ -1,6 +1,11 @@
-#!/bin/bash -e
+#!/bin/bash -ex
 
-set -xe
+mkdir -p build && pushd build
+
+export INCLUDES="-I${PREFIX}/include"
+export LIBPATH="-L${PREFIX}/lib"
+export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib"
+export CXXFLAGS="${CXXFLAGS} -O3 -I${PREFIX}/include"
 
 case $(uname -m) in
     aarch64)
@@ -11,8 +16,17 @@ case $(uname -m) in
         ;;
 esac
 
-mkdir build
-cd build
-cmake -DCMAKE_INSTALL_PREFIX="${PREFIX}" -DHAVE_TESTS=0 -DHAVE_MPI=0 "${ARCH_OPTS}" -DVERSION_OVERRIDE="${PKG_VERSION}" ..
-make -j${CPU_COUNT} ${VERBOSE_CM}
-make install
+if [ "$(uname)" == "Darwin" ]; then
+        export CMAKE_EXTRA="-DCMAKE_FIND_FRAMEWORK=NEVER -DCMAKE_FIND_APPBUNDLE=NEVER -Wno-dev"
+else
+        export CMAKE_EXTRA="-Wno-dev"
+fi
+
+cmake -S .. -B . -DCMAKE_INSTALL_PREFIX="${PREFIX}" \
+	-DCMAKE_BUILD_TYPE=RELEASE \
+	-DHAVE_TESTS=0 -DHAVE_MPI=0 "${ARCH_OPTS}" \
+	-DVERSION_OVERRIDE="${PKG_VERSION}" \
+	"${CMAKE_EXTRA}"
+
+cmake --build . --target install -j ${CPU_COUNT} -v
+popd
diff --git a/recipes/transannot/meta.yaml b/recipes/transannot/meta.yaml
index 068bb67a93dbe..315da17189512 100644
--- a/recipes/transannot/meta.yaml
+++ b/recipes/transannot/meta.yaml
@@ -1,49 +1,49 @@
-{% set version = "3-70b2a60" %}
-{% set sha256 = "3b1d2f28362004378528755b8b4e0b8dc45b51cc60562816258bdf16d9cda08d" %}
+{% set name = "transannot" %}
+{% set version = "3.0.0" %}
+{% set sha256 = "6835fc3cc77aafd273abc8f2b4d8213b251b199ff7dd5ae9fa7e1dd19579ae41" %}
 
 package:
-  name: transannot
-  version: {{ version|replace("-", ".")  }}
+  name: {{ name }}
+  version: {{ version }}
+
+source:
+  url: https://github.com/soedinglab/{{ name }}/archive/refs/tags/3-e15e316.tar.gz
+  sha256: {{ sha256 }}
 
 build:
-  number: 1
+  number: 0
   run_exports:
     - {{ pin_subpackage('transannot', max_pin="x") }}
 
-source:
-  url: https://github.com/soedinglab/transannot/archive/{{ version }}.tar.gz
-  sha256: {{ sha256 }}
-
 requirements:
   build:
     - {{ compiler('c') }}
     - {{ compiler('cxx') }}
     - cmake
     - make
+  host:
     - llvm-openmp  # [osx]
     - libgomp      # [linux]
-  host:
-    - perl
     - gawk
     - zlib
     - bzip2
   run:
     - aria2
     - wget
-    - gawk
-    - zlib
-    - bzip2
+    - perl
 
 test:
   commands:
-    - transannot > /dev/null
+    - "transannot > /dev/null"
 
 about:
-  home: https://github.com/soedinglab/transannot
-  summary: "TransAnnot: a fast transcriptome annotation pipeline"
-  license: GPL-3.0-or-later
-  license_family: GPL
-  license_file: LICENSE.md 
+  home: "https://github.com/soedinglab/transannot"
+  summary: "TransAnnot: a fast transcriptome annotation pipeline."
+  license: "GPL-3.0-or-later"
+  license_family: GPL3
+  license_file: "LICENSE.md"
+  dev_url: "https://github.com/soedinglab/transannot"
+  doc_url: "https://github.com/soedinglab/transannot/blob/master/README.md"
 
 extra:
   identifiers: