From 920eccbf07a85ca3561cad113d5fb9464fe069da Mon Sep 17 00:00:00 2001
From: Lucas van Dijk <info@lucasvandijk.nl>
Date: Fri, 11 Oct 2024 17:02:59 -0500
Subject: [PATCH] Update rna-seqc to 2.4.2 (#51342)

* fix: Add python dependencies

* enh: Add run_exports and add python import test

* fix: Place run_exports in correct location

* fix: Remove pip dependencies and reset build num

* enh: Don't include python package installation

Will create a separate recipe for that

* fix: Fix license_file location

* clean up recipe

---------

Co-authored-by: mencian <joshua.zhuang@yahoo.com>
---
 recipes/rna-seqc/build.sh  |  9 +++++----
 recipes/rna-seqc/meta.yaml | 32 +++++++++++++++++++-------------
 2 files changed, 24 insertions(+), 17 deletions(-)

diff --git a/recipes/rna-seqc/build.sh b/recipes/rna-seqc/build.sh
index 7afd75451acd7..926e8a8e5a0bd 100644
--- a/recipes/rna-seqc/build.sh
+++ b/recipes/rna-seqc/build.sh
@@ -1,9 +1,10 @@
 #!/bin/bash
 set -eu -o pipefail
 
-cd ./travis/build/broadinstitute/rnaseqc
-export CFLAGS="${CFLAGS} -fcommon"
+export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib"
+export CFLAGS="${CFLAGS} -O3 -fcommon"
 
+cd rnaseqc
 pushd SeqLib/bwa
 sed -i.bak '/^DFLAGS=/s/$/ $(LDFLAGS)/' Makefile
 make CC="$CC" CFLAGS="$CFLAGS" LDFLAGS="$LDFLAGS"
@@ -19,7 +20,7 @@ popd
 
 make \
     CC="$CXX" \
-    CPPFLAGS="-I$PREFIX/include -fcommon" \
+    CPPFLAGS="${CPPFLAGS} -O3 -I$PREFIX/include -fcommon" \
     SeqLib/lib/libseqlib.a
 
 make \
@@ -28,5 +29,5 @@ make \
     LIBRARY_PATHS="-L$PREFIX/lib -Wl,-rpath $PREFIX/lib"
 
 mkdir -p $PREFIX/bin
+chmod 0755 rnaseqc
 cp rnaseqc $PREFIX/bin
-
diff --git a/recipes/rna-seqc/meta.yaml b/recipes/rna-seqc/meta.yaml
index f81f069b06e8e..cc91a8ea6f068 100644
--- a/recipes/rna-seqc/meta.yaml
+++ b/recipes/rna-seqc/meta.yaml
@@ -1,16 +1,18 @@
-{% set version = "2.3.5" %}
-{% set sha256sum = "44e81f01f2b661a7621f34e3b645f5727bc7143841f1df053723e23ba298d2c6" %}
+{% set version = "2.4.2" %}
+{% set sha256sum = "b214151408696430aead56921b255e2b09efe5f6087a68446deae399227a1303" %}
 
 package:
-  name: rna-seqc
-  version: '{{ version }}'
+  name: "rna-seqc"
+  version: {{ version }}
 
 source:
   url: 'https://github.com/broadinstitute/rnaseqc/releases/download/v{{ version }}/rnaseqc.v{{ version }}.full_source.tar.gz'
-  sha256: '{{ sha256sum }}'
+  sha256: {{ sha256sum }}
 
 build:
-  number: 6
+  number: 0
+  run_exports:
+    - {{ pin_subpackage("rna-seqc", max_pin="x") }}
 
 requirements:
   build:
@@ -25,19 +27,23 @@ requirements:
     - zlib
   run:
     - curl
-    - bzip2
     - boost-cpp
-    - xz
-    - zlib
+
 test:
   commands:
     - rnaseqc --version
 
 about:
-  home: https://github.com/broadinstitute/rnaseqc 
+  home: "https://github.com/broadinstitute/rnaseqc"
   license_url: https://raw.githubusercontent.com/broadinstitute/rnaseqc/master/LICENSE
-  # license_file: LICENSE  # not distributed :-/
-  license: BSD 3-clause
+  license_file: rnaseqc/LICENSE
+  license: "BSD-3-Clause"
   license_family: BSD
-  summary: Fast, efficient RNA-Seq metrics for quality control and process optimization
+  summary: "Fast, efficient RNA-Seq metrics for quality control and process optimization."
+  dev_url: "https://github.com/broadinstitute/rnaseqc"
+  doc_url: "https://github.com/getzlab/rnaseqc/blob/v{{ version }}/README.md"
 
+extra:
+  identifiers:
+    - biotools:rna-seqc
+    - doi:10.1093/bioinformatics/btab135