Update spaln to 3.0.6 (#47896)

* Update spaln to 3.0.5 * Update spaln to 3.0.6 * edit patches * skip osx for now --------- Co-authored-by: Joshua Zhuang <[email protected]> Co-authored-by: mencian <[email protected]>
bioconda · Sep 3, 2024 · b7f3f0e · b7f3f0e
1 parent e542a72
commit b7f3f0e
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Showing 3 changed files with 18 additions and 23 deletions.
diff --git a/recipes/spaln/makefile.patch b/recipes/spaln/makefile.patch
@@ -1,8 +1,8 @@
 diff --git a/src/Makefile.in b/src/Makefile.in
-index ed5cb96..2d837d0 100644
+index 7e0ab8d..bd09001 100644
 --- a/src/Makefile.in
 +++ b/src/Makefile.in
-@@ -1,19 +1,19 @@
+@@ -1,20 +1,20 @@
  #	Makefile.in for splan/sortgrcd
  #	Copyright(c) Osamu Gotoh <<[email protected]>>
 
@@ -14,9 +14,10 @@ index ed5cb96..2d837d0 100644
 +table_dir = $(PREFIX)/share/spaln/table
 +alndbs_dir = $(PREFIX)/share/spaln/alndbs
 +CXX  = $(CXX)
- #CXX  = clang++
+ # for MACOS uncomment below line
+ #CXX  = clang++ -std=c++11
 -CFLAGS = -O3 -march=native
-+CFLAGS += -O3
++CFLAGS = -O3
  RANLIB = ranlib
 -LD  = g++
 +LD  = $(CXX)

diff --git a/recipes/spaln/meta.yaml b/recipes/spaln/meta.yaml
@@ -1,6 +1,6 @@
 {% set name = "spaln" %}
-{% set version = "3.0.4" %}
-{% set sha256 = "6001a901e2e1ea5dbf19f34ee18b61ebd9afaf3a3c5107f937dd13e9b63ea870" %}
+{% set version = "3.0.6" %}
+{% set sha256 = "0b627609b69e0e1487cbb75ff564cfe3816c24da8552acbaf50bf19bce1c6490" %}
 
 package:
   name: {{ name|lower }}
@@ -16,6 +16,7 @@ source:
 
 build:
   number: 0
+  skip: True  # [osx]
   run_exports:
     - {{ pin_subpackage('spaln', max_pin="x") }}
 
@@ -58,3 +59,5 @@ extra:
     - doi:10.1093/nar/gks708
     - doi:10.1093/bioinformatics/btl067
     - usegalaxy-eu:spaln
+  additional-platforms:
+    - linux-aarch64
diff --git a/recipes/spaln/patch-makefile_ldflags b/recipes/spaln/patch-makefile_ldflags
@@ -1,31 +1,22 @@
+diff --git a/src/Makefile.in b/src/Makefile.in
+index 7e0ab8d..f6c7256 100644
 --- a/src/Makefile.in
 +++ b/src/Makefile.in
-@@ -23,8 +23,9 @@ PROG_F = fitild compild decompild plotild
- PROG = $(PROG_B) $(PROG_A) $(PROG_F)
-
- STDH = stdtype.h
--CLIB = clib.a -lpthread -lm -lz
-+CLIB = clib.a
- SLIB = sblib.a $(CLIB)
-+LLIB = -lpthread -lm -lz
- ULIB = ublib.a $(SLIB)
-
- BINDIR = $(DESTDIR)$(exec_prefix)
-@@ -88,13 +89,13 @@ ls:
+@@ -95,13 +95,13 @@ ls:
  	ls $(SRC) $(HDR)
 
  spaln:	spaln.cc blksrc.o $(SLIB)
--	$(CXX) -o $@ spaln.cc blksrc.o $(SLIB) $(ILIB)
+-	$(CXX) -o $@ spaln.cc blksrc.o $(SLIB) $(LLIB)
 +	$(CXX) $(LDFLAGS) -o $@ spaln.cc blksrc.o $(SLIB) $(LLIB)
  sortgrcd:	sortgrcd.cc $(SLIB)
--	$(CXX) -o $@ sortgrcd.cc $(SLIB) $(ILIB)
+-	$(CXX) -o $@ sortgrcd.cc $(SLIB) $(LLIB)
 +	$(CXX) $(LDFLAGS) -o $@ sortgrcd.cc $(SLIB) $(LLIB)
  makdbs: makdbs.cc dbs.h seq.h bitpat.h $(SLIB)
--	$(CXX) -o $@ makdbs.cc $(SLIB) $(ILIB)
+-	$(CXX) -o $@ makdbs.cc $(SLIB) $(LLIB)
 +	$(CXX) $(LDFLAGS) -o $@ makdbs.cc $(SLIB) $(LLIB)
  makmdm: makmdm.cc mdm.h $(CLIB)
--	$(CXX) -o $@ makmdm.cc $(CLIB) $(ILIB)
+-	$(CXX) -o $@ makmdm.cc $(CLIB) $(LLIB)
 +	$(CXX) $(LDFLAGS) -o $@ makmdm.cc $(CLIB) $(LLIB)
 
  dvn:	dvn.cc autocomp.h $(ULIB)
- 	$(CXX) -o $@ dvn.cc $(ULIB) $(ILIB)
+ 	$(CXX) -o $@ dvn.cc $(ULIB) $(LLIB)