Update subread to v2.0.8 and enable arm64 build

recipes/subread/0001-macOS-Makefile.patch

@@ -0,0 +1,13 @@
+diff --git a/src/Makefile.MacOS b/src/Makefile.MacOS
+index 7620450..7b9f74d 100644
+--- a/src/Makefile.MacOS
++++ b/src/Makefile.MacOS
+@@ -3,7 +3,7 @@ include makefile.version
+
+ CCFLAGS = ${MACOS}  -O9 -w -DMAKE_FOR_EXON  -D MAKE_STANDALONE -D SUBREAD_VERSION=\"${SUBREAD_VERSION}\" -D_FILE_OFFSET_BITS=64 ${WARNING_LEVEL}
+ LDFLAGS =  -pthread -lz -lm ${MACOS} -DMAKE_FOR_EXON -D MAKE_STANDALONE # -DREPORT_ALL_THE_BEST
+-CC = gcc ${CCFLAGS} ${STATIC_MAKE} -ggdb -fomit-frame-pointer -O3 -ffast-math -funroll-loops -mmmx -msse -msse2 -msse3 -fmessage-length=0 
++CC = $(C) ${CCFLAGS} ${STATIC_MAKE} -ggdb -fomit-frame-pointer -O3 -ffast-math -funroll-loops -fmessage-length=0 
+
+
+ ALL_LIBS= core core-junction core-indel sambam-file sublog gene-algorithms hashtable input-files sorted-hashtable gene-value-index exon-algorithms HelperFunctions interval_merge core-bigtable seek-zlib input-blc

recipes/subread/0002-longread-Makefile.patch

@@ -0,0 +1,10 @@
+diff --git a/src/longread-one/Makefile b/src/longread-one/Makefile
+index 06ee3e6..2643584 100644
+--- a/src/longread-one/Makefile
++++ b/src/longread-one/Makefile
+@@ -1,4 +1,4 @@
+-CC_EXEC = gcc
++CC_EXEC = $(C)
+ OPT_LEVEL = 3
+
+ include ../makefile.version

recipes/subread/0003-Linux-Makefile.patch

@@ -0,0 +1,13 @@
+diff --git a/src/Makefile.Linux b/src/Makefile.Linux
+index b76172c..f2ebd4b 100644
+--- a/src/Makefile.Linux
++++ b/src/Makefile.Linux
+@@ -1,7 +1,7 @@
+ #MACOS = -D MACOS 
+
+
+-CC_EXEC = gcc
++CC_EXEC = $(C)
+ OPT_LEVEL = 3
+
+ include makefile.version

recipes/subread/0004-macOS-sse.patch

@@ -0,0 +1,13 @@
+diff --git a/src/Makefile.MacOS b/src/Makefile.MacOS
+index 5c96c75..e33aa51 100644
+--- a/src/Makefile.MacOS
++++ b/src/Makefile.MacOS
+@@ -3,7 +3,7 @@ include makefile.version
+
+ CCFLAGS = ${MACOS}  -O9 -w -DMAKE_FOR_EXON  -D MAKE_STANDALONE -D SUBREAD_VERSION=\"${SUBREAD_VERSION}\" -D_FILE_OFFSET_BITS=64 ${WARNING_LEVEL}
+ LDFLAGS =  -pthread -lz -lm ${MACOS} -DMAKE_FOR_EXON -D MAKE_STANDALONE # -DREPORT_ALL_THE_BEST
+-CC = $(C) ${CCFLAGS} ${STATIC_MAKE} -ggdb -fomit-frame-pointer -O3 -ffast-math -funroll-loops -fmessage-length=0 
++CC = $(C) ${CCFLAGS} ${STATIC_MAKE} -ggdb -fomit-frame-pointer -O3 -mmmx -msse -msse2 -msse3 -ffast-math -funroll-loops -fmessage-length=0 
+
+
+ ALL_LIBS= core core-junction core-indel sambam-file sublog gene-algorithms hashtable input-files sorted-hashtable gene-value-index exon-algorithms HelperFunctions interval_merge core-bigtable seek-zlib input-blc

recipes/subread/build.sh

@@ -6,25 +6,36 @@ mkdir -p "${PREFIX}/bin"
 mkdir -p "${PREFIX}/annotation"
 
 cd src
-MAKEFILE=Makefile.Linux
-if [ `uname` = "Darwin" ];
-then
-  MAKEFILE=Makefile.MacOS
+if [[ `uname` = "Darwin" ]]; then
+	MAKEFILE=Makefile.MacOS
+else
+	MAKEFILE=Makefile.Linux
 fi
 
-if [ $(uname -m) == "aarch64" ]; then
-  sed -i.bak 's/-mtune=core2//' ${MAKEFILE}
-  sed -i.bak 's/-mtune=core2//' ./longread-one/Makefile
+if [[ $(uname -m) == "aarch64" ]]; then
+	sed -i.bak 's/-mtune=core2//' ${MAKEFILE}
+	sed -i.bak 's/-mtune=core2//' ./longread-one/Makefile
+	rm -rf ./*.bak
+	rm -rf ./longread-one/*.bak
 fi
 
-export C_INCLUDE_PATH=${PREFIX}/include
-export LIBRARY_PATH=${PREFIX}/lib
-make -f $MAKEFILE CC_EXEC="$CC -L$PREFIX/lib -fcommon" -j ${CPU_COUNT}
+export C_INCLUDE_PATH="${PREFIX}/include"
+export LIBRARY_PATH="${PREFIX}/lib"
+export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib"
+export C="${CC}"
+
+make -f $MAKEFILE CC_EXEC="$C -L$PREFIX/lib -fcommon" -j"${CPU_COUNT}"
+
 cd ..
-cp bin/utilities/* $PREFIX/bin
-rm -r bin/utilities
-cp bin/* $PREFIX/bin
-cp annotation/* $PREFIX/annotation
+install -v -m 0755 bin/utilities/flattenGTF bin/utilities/genRandomReads \
+	bin/utilities/propmapped bin/utilities/qualityScores \
+	bin/utilities/removeDup bin/utilities/repair \
+	bin/utilities/subread-fullscan "${PREFIX}/bin"
+rm -rf bin/utilities
+
+install -v -m 0755 bin/exactSNP bin/featureCounts bin/subindel bin/subjunc \
+	bin/sublong bin/subread-align bin/subread-buildindex "${PREFIX}/bin"
+cp -rf annotation/* $PREFIX/annotation
 
 # add read permissions to LICENSE
-chmod a+r LICENSE
+chmod a+r LICENSE

recipes/subread/meta.yaml

@@ -1,6 +1,6 @@
 {% set name = "subread" %}
-{% set version = "2.0.6" %}
-{% set sha256 = "f0fdda6b98634d2946028948c220253e10a0f27c7fa5f24913b65b3ac6cbb045" %}
+{% set version = "2.0.8" %}
+{% set sha256 = "cb5dadf71c850f128a8347223fe0ce19e1c17e3959e9f3eba90e8090671f8570" %}
 
 package:
   name: {{ name|lower }}
@@ -11,10 +11,15 @@ source:
   sha256: {{ sha256 }}
   patches:
     - unsignedchar.patch
+    - 0001-macOS-Makefile.patch  # [osx]
+    - 0002-longread-Makefile.patch
+    - 0003-Linux-Makefile.patch  # [linux]
+    - 0004-macOS-sse.patch  # [osx and x86_64]
 
 build:
-  number: 2
-  run_exports: '{{ pin_subpackage(name, max_pin="x") }}'
+  number: 0
+  run_exports:
+    - {{ pin_subpackage(name, max_pin="x") }}
 
 requirements:
   build:
@@ -32,20 +37,22 @@ test:
     - subjunc || [[ $? == 1 ]]
     - subindel || [[ $? = 255 ]]
     - repair -h
-    - txUnique || [[ $? == 1 ]]
     - qualityScores
     - subread-fullscan || [[ $? == 255 ]]
 
 about:
-  home: http://subread.sourceforge.net/
-  license: GPL-3.0-only
-  summary: High-performance read alignment, quantification, and mutation discovery
-  license_file:
-    - LICENSE
+  home: "https://subread.sourceforge.net"
+  license: "GPL-3.0-only"
+  license_family: GPL3
+  summary: "High-performance read alignment, quantification, and mutation discovery."
+  doc_url: "https://subread.sourceforge.net/SubreadUsersGuide.pdf"
+  dev_url: "https://sourceforge.net/projects/subread"
+  license_file: LICENSE
 
 extra:
   additional-platforms:
     - linux-aarch64
+    - osx-arm64
   identifiers:
     - biotools:subread
     - usegalaxy-eu:featurecounts