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ucsc-fatotwobit: update macOS build #50369

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merged 2 commits into from
Aug 28, 2024
Merged

ucsc-fatotwobit: update macOS build #50369

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d28d3ff
ucsc-fatotwobit: update macOS build
mencian Aug 28, 2024
80a6b22
try without mariadb
mencian Aug 28, 2024
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29 changes: 21 additions & 8 deletions recipes/ucsc-fatotwobit/build.sh
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Original file line number Diff line number Diff line change
@@ -1,13 +1,26 @@
#!/bin/bash

mkdir -p "$PREFIX/bin"

export MACHTYPE=$(uname -m)
export BINDIR=$(pwd)/bin
export BINDIR="$(pwd)/bin"
export INCLUDE_PATH="${PREFIX}/include"
export LIBRARY_PATH="${PREFIX}/lib"
export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib"
export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}"
export L="${LDFLAGS}"

mkdir -p "$BINDIR"
(cd kent/src/lib && make)
(cd kent/src/htslib && make)
(cd kent/src/jkOwnLib && make)
(cd kent/src/hg/lib && make)
(cd kent/src/utils/faToTwoBit && make)
cp bin/faToTwoBit "$PREFIX/bin"
chmod +x "$PREFIX/bin/faToTwoBit"

if [[ "$(uname)" == Darwin ]]; then
export LDFLAGS="${LDFLAGS} -Wl,-rpath,${PREFIX}/lib"
export CFLAGS="${CFLAGS} -Wno-unused-command-line-argument"
fi

(cd kent/src/lib && make CC="${CC}" CFLAGS="${CFLAGS}" -j ${CPU_COUNT})
(cd kent/src/htslib && make CC="${CC}" CFLAGS="${CFLAGS}" -j ${CPU_COUNT})
(cd kent/src/jkOwnLib && make CC="${CC}" CFLAGS="${CFLAGS}" -j ${CPU_COUNT})
(cd kent/src/hg/lib && make CC="${CC}" CFLAGS="${CFLAGS}" -j ${CPU_COUNT})
(cd kent/src/utils/faToTwoBit && make CC="${CC}" CFLAGS="${CFLAGS}" -j ${CPU_COUNT})
cp -rf bin/faToTwoBit "$PREFIX/bin"
chmod 0755 "$PREFIX/bin/faToTwoBit"
11 changes: 0 additions & 11 deletions recipes/ucsc-fatotwobit/htmshell.patch
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This file was deleted.

27 changes: 27 additions & 0 deletions recipes/ucsc-fatotwobit/include.macos.patch
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Original file line number Diff line number Diff line change
@@ -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.
16 changes: 8 additions & 8 deletions recipes/ucsc-fatotwobit/include.patch
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Original file line number Diff line number Diff line change
@@ -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

Expand All @@ -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
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34 changes: 16 additions & 18 deletions recipes/ucsc-fatotwobit/meta.yaml
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Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
{% set package = "ucsc-fatotwobit" %}
{% set program = "faToTwoBit" %}
{% set version = "455" %}
{% set sha256 = "e458cadad7c4a5c1b8385edafffa1b29380ac725a0c20535bf5a3bab99fe80db" %}
{% set version = "469" %}
{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %}

package:
name: "{{ package }}"
Expand All @@ -11,15 +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:
skip: True # [osx]
number: 2
ignore_run_exports:
- libpng
- libuuid
number: 1
run_exports:
- {{ pin_subpackage("ucsc-fatotwobit", max_pin=None) }}

Expand All @@ -28,29 +24,31 @@ requirements:
- make
- {{ compiler('c') }}
- {{ compiler('cxx') }}
- binutils # [linux]
- binutils # [linux]
host:
- libpng
- libuuid
- mysql-connector-c
- openssl
- libopenssl-static
- zlib >=1.3.1,<2.0a0
- 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: "Convert DNA from fasta to 2bit format"
home: "https://hgdownload.cse.ucsc.edu/admin/exe"
license: "Varies; see http://genome.ucsc.edu/license"
summary: "Convert DNA from fasta to 2bit format."
dev_url: "https://github.com/ucscGenomeBrowser/kent"
doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/v{{ version }}_base/README"

extra:
additional-platforms:
Expand Down