From e76dd9f8da980e011b6ba2a0c05cc5704f9114d5 Mon Sep 17 00:00:00 2001
From: Joshua Zhuang <71105179+mencian@users.noreply.github.com>
Date: Mon, 28 Oct 2024 16:25:08 -0500
Subject: [PATCH] Update ucsc-pslcdnafilter to 472 (#51700)
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* Update ucsc-pslcdnafilter to 472

* add linux-aarch64 build

* revert linux-aarch64

* revert osx

---------

Co-authored-by: Björn Grüning <bjoern@gruenings.eu>
---
 recipes/ucsc-pslcdnafilter/build.sh           |  6 ++---
 .../ucsc-pslcdnafilter/include.macos.patch    | 27 +++++++++++++++++++
 recipes/ucsc-pslcdnafilter/meta.yaml          | 19 +++++++------
 3 files changed, 39 insertions(+), 13 deletions(-)
 create mode 100644 recipes/ucsc-pslcdnafilter/include.macos.patch

diff --git a/recipes/ucsc-pslcdnafilter/build.sh b/recipes/ucsc-pslcdnafilter/build.sh
index 6f9c17e7cba0b..0d01ae296724e 100644
--- a/recipes/ucsc-pslcdnafilter/build.sh
+++ b/recipes/ucsc-pslcdnafilter/build.sh
@@ -8,7 +8,7 @@ export INCLUDE_PATH="${PREFIX}/include"
 export LIBRARY_PATH="${PREFIX}/lib"
 export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib"
 export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}"
-export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}"
+export CXXFLAGS="${CXXFLAGS} -O3 -I${PREFIX}/include ${LDFLAGS}"
 export BINDIR=$(pwd)/bin
 export L="${LDFLAGS}"
 mkdir -p "${BINDIR}"
@@ -18,5 +18,5 @@ mkdir -p "${BINDIR}"
 (cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}")
 (cd kent/src/utils/stringify && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}")
 (cd kent/src/hg/pslCDnaFilter && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}")
-cp bin/pslCDnaFilter "${PREFIX}/bin"
-chmod 0755 "${PREFIX}/bin/pslCDnaFilter"
+chmod 0755 bin/pslCDnaFilter
+mv bin/pslCDnaFilter "${PREFIX}/bin"
diff --git a/recipes/ucsc-pslcdnafilter/include.macos.patch b/recipes/ucsc-pslcdnafilter/include.macos.patch
new file mode 100644
index 0000000000000..979f87005a72e
--- /dev/null
+++ b/recipes/ucsc-pslcdnafilter/include.macos.patch
@@ -0,0 +1,27 @@
+--- a/kent/src/inc/common.mk	2017-11-07 17:46:00.000000000 -0500
++++ b/kent/src/inc/common.mk	2017-11-13 17:44:51.017090255 -0500
+@@ -17,7 +17,7 @@
+ endif
+ 
+ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE}
+-HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib
++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I${PREFIX}/include
+ 
+ # to check for Mac OSX Darwin specifics:
+ UNAME_S := $(shell uname -s)
+--- a/kent/src/hg/lib/straw/makefile	2022-10-26 12:00:00.000000000 +0100
++++ b/kent/src/hg/lib/straw/makefile	2022-10-26 12:00:00.000000000 +0100
+@@ -1,4 +1,4 @@
+-KENT_INC=-I../../../inc
++KENT_INC=-I../../../inc -I${PREFIX}/include
+
+ straw: straw.o cStraw.o
+ 	ld -r -o ../straw.o straw.o cStraw.o
+--- a/kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed	2018-06-06 02:23:56.000000000 +0200
++++ b/kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed	2018-06-06 02:23:56.000000000 +0200
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python2.7
++#!/usr/bin/env python
+ # expMatrixToBarchartBed
+ """
+ Generate a barChart bed6+5 file from a matrix, meta data, and coordinates.
diff --git a/recipes/ucsc-pslcdnafilter/meta.yaml b/recipes/ucsc-pslcdnafilter/meta.yaml
index 58d533a67e4ff..bb1f6757f31f7 100644
--- a/recipes/ucsc-pslcdnafilter/meta.yaml
+++ b/recipes/ucsc-pslcdnafilter/meta.yaml
@@ -1,7 +1,7 @@
 {% set package = "ucsc-pslcdnafilter" %}
 {% set program = "pslCDnaFilter" %}
-{% set version = "469" %}
-{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %}
+{% set version = "472" %}
+{% set sha256 = "26d126c51d0ba3165519b116b6461af8bfd938505f6c0871cb325a7ab82368f2" %}
 
 package:
   name: "{{ package }}"
@@ -11,11 +11,12 @@ source:
   url: "http://hgdownload.cse.ucsc.edu/admin/exe/userApps.archive/userApps.v{{ version }}.src.tgz"
   sha256: "{{ sha256 }}"
   patches:
-    - "include.patch"
+    - include.patch  # [linux]
+    - include.macos.patch  # [osx]
 
 build:
-  skip: True  # [osx]
   number: 0
+  skip: True  # [osx]
   run_exports:
     - {{ pin_subpackage(package, max_pin=None) }}
 
@@ -28,14 +29,13 @@ requirements:
     - libuuid
     - mysql-connector-c
     - libopenssl-static
+    - clangdev  # [osx]
     - zlib
-
   run:
     - libpng
     - libuuid
     - mysql-connector-c
     - libopenssl-static
-    - zlib
 
 test:
   commands:
@@ -43,8 +43,8 @@ test:
     - test -x ${PREFIX}/bin/{{ program }}
 
 about:
-  home: "https://hgdownload.cse.ucsc.edu/admin/exe/"
-  license: "Varies; see http://genome.ucsc.edu/license"
+  home: "https://hgdownload.cse.ucsc.edu/admin/exe"
+  license: "Varies; see https://genome.ucsc.edu/license"
   summary: "
 Filter cDNA alignments in psl format.  Filtering criteria are
 comparative, selecting near best in genome alignments for each given
@@ -52,10 +52,9 @@ cDNA and non-comparative, based only on the quality of an individual
 alignment.
 "
   dev_url: "https://github.com/ucscGenomeBrowser/kent"
-  doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README"
+  doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/v{{ version }}_base/README"
 
 extra:
   identifiers:
     - biotools:UCSC_Genome_Browser_Utilities
     - doi:10.1093/bib/bbs038
-  
\ No newline at end of file