Update ucsc-fatovcf to 472

bioconda · Nov 25, 2024 · 70a6024 · 70a6024
1 parent 4ee97c3
commit 70a6024
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Showing 5 changed files with 58 additions and 42 deletions.
diff --git a/recipes/ucsc-fatovcf/build.sh b/recipes/ucsc-fatovcf/build.sh
@@ -3,18 +3,18 @@
 export INCLUDE_PATH=${PREFIX}/include
 export LIBRARY_PATH=${PREFIX}/lib
 export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib"
-export CFLAGS="${CFLAGS} -I${PREFIX}/include ${LDFLAGS}"
+export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}"
+export CXXFLAGS="${CXXFLAGS} -O3 -I${PREFIX}/include ${LDFLAGS}"
 export USE_HIC=0
 
 mkdir -p "${PREFIX}/bin"
 export MACHTYPE=$(uname -m)
 export BINDIR=$(pwd)/bin
 export L="${LDFLAGS}"
 mkdir -p "${BINDIR}"
-(cd kent/src/lib && make)
-(cd kent/src/htslib && make)
-(cd kent/src/jkOwnLib && make)
-(cd kent/src/hg/lib && make)
-(cd kent/src/hg/utils/faToVcf && make)
-cp bin/faToVcf "${PREFIX}/bin"
-chmod +x "${PREFIX}/bin/faToVcf"
+(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j"${CPU_COUNT}")
+(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j"${CPU_COUNT}")
+(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j"${CPU_COUNT}")
+(cd kent/src/hg/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j"${CPU_COUNT}")
+(cd kent/src/hg/utils/faToVcf && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j"${CPU_COUNT}")
+install -v -m 0755 bin/faToVcf "${PREFIX}/bin"
diff --git a/recipes/ucsc-fatovcf/htmshell.patch b/recipes/ucsc-fatovcf/htmshell.patch
diff --git a/recipes/ucsc-fatovcf/include.macos.patch b/recipes/ucsc-fatovcf/include.macos.patch
@@ -0,0 +1,27 @@
+--- a/kent/src/inc/common.mk	2017-11-07 17:46:00.000000000 -0500
++++ b/kent/src/inc/common.mk	2017-11-13 17:44:51.017090255 -0500
+@@ -17,7 +17,7 @@
+ endif
+
+ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${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-fatovcf/include.patch b/recipes/ucsc-fatovcf/include.patch
@@ -1,5 +1,5 @@
---- kent/src/inc/common.mk	2017-11-07 17:46:00.000000000 -0500
-+++ kent/src/inc/common.mk	2017-11-13 17:44:51.017090255 -0500
+--- 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
 
@@ -9,24 +9,24 @@
 
  # to check for Mac OSX Darwin specifics:
  UNAME_S := $(shell uname -s)
---- kent/src/inc/common.mk	2022-10-25 12:00:00.000000000 +0100
-+++ kent/src/inc/common.mk	2022-10-25 12:00:00.000000000 +0100
+--- a/kent/src/inc/common.mk	2022-10-25 12:00:00.000000000 +0100
++++ b/kent/src/inc/common.mk	2022-10-25 12:00:00.000000000 +0100
 @@ -147,4 +147,4 @@
 -       L+=${PREFIX}/lib/libssl.a ${PREFIX}/lib/libcrypto.a -ldl
 +       L+=${PREFIX}/lib/libssl.so ${PREFIX}/lib/libcrypto.so -ldl
     else
       ifneq ($(wildcard /opt/local/lib/libssl.a),)
           L+=/opt/local/lib/libssl.a
---- kent/src/hg/lib/straw/makefile	2022-10-26 12:00:00.000000000 +0100
-+++ kent/src/hg/lib/straw/makefile	2022-10-26 12:00:00.000000000 +0100
+--- 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
---- kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed	2018-06-06 02:23:56.000000000 +0200
-+++ kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed	2018-06-06 02:23:56.000000000 +0200
+--- 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

diff --git a/recipes/ucsc-fatovcf/meta.yaml b/recipes/ucsc-fatovcf/meta.yaml
@@ -1,7 +1,7 @@
 {% set package = "ucsc-fatovcf" %}
 {% set program = "faToVcf" %}
-{% set version = "448" %}
-{% set sha256 = "90c28f06f3f5b6d79ff141cbf745e6a0c1b289a2ce640bbd1b0a14c826f08a85" %}
+{% set version = "473" %}
+{% set sha256 = "ed929a7141440e0718ed453283e6e7dde103e8e2facf27d2367be7b34e53e597" %}
 
 package:
   name: {{ package }}
@@ -11,12 +11,11 @@ source:
   url: http://hgdownload.cse.ucsc.edu/admin/exe/userApps.archive/userApps.v{{ version }}.src.tgz
   sha256: {{ sha256 }}
   patches:
-    - include.patch
-    - htmshell.patch
+    - include.patch  # [linux]
+    - include.macos.patch  # [osx]
 
 build:
-  number: 1
-  skip: True  # [osx]
+  number: 0
   run_exports:
     - {{ pin_subpackage(package, max_pin=None) }}
 
@@ -25,30 +24,31 @@ requirements:
     - make
     - {{ compiler('c') }}
     - {{ compiler('cxx') }}
-    - binutils # [linux]
   host:
     - libpng
     - libuuid
     - mysql-connector-c
-    - openssl
     - libopenssl-static
+    - clangdev  # [osx]
     - zlib
   run:
     - libpng
     - libuuid
     - mysql-connector-c
-    - openssl
+    - libopenssl-static
 
 test:
   commands:
-    # just check for existence, because the individual packages have no unified behavior
-    - which {{ program }}
+    # just check for existence and exec bit, because the individual packages have no unified behavior
+    - test -x ${PREFIX}/bin/{{ program }}
 
 about:
-  home: "http://hgdownload.cse.ucsc.edu/admin/exe/"
-  license: "varies; see http://genome.ucsc.edu/license"
-  summary: "Extract VCF from a multi-sequence FASTA alignment"
+  home: "https://hgdownload.cse.ucsc.edu/admin/exe"
+  license: "Varies; see https://genome.ucsc.edu/license"
+  summary: "Extract VCF from a multi-sequence FASTA alignment."
+  dev_url: "https://github.com/ucscGenomeBrowser/kent"
+  doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/v{{ version }}_base/README"
 
 extra:
   additional-platforms:
-    - linux-aarch64
+    - linux-aarch64