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include.patch
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include.patch
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--- a/kent/src/inc/common.mk 2024-09-20 12:47:59.873876212 -0400
+++ b/kent/src/inc/common.mk 2024-09-20 12:50:55.946858032 -0400
@@ -21,7 +21,7 @@
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 -I${BUILD_PREFIX}/include
# to check for Mac OSX Darwin specifics:
UNAME_S := $(shell uname -s)
@@ -239,6 +239,8 @@
else
ifeq (${CONDA_BUILD},1)
L+=${PREFIX}/lib/libssl.a ${PREFIX}/lib/libcrypto.a -ldl
+ L+=${PREFIX}/lib/libssl.so ${PREFIX}/lib/libcrypto.so -ldl
+
else
ifneq (${SSLLIB},)
L+=${SSLLIB}
--- a/kent/src/hg/lib/straw/makefile 2024-09-20 12:53:33.463735840 -0400
+++ b/kent/src/hg/lib/straw/makefile 2024-09-20 12:54:03.783904995 -0400
@@ -1,4 +1,4 @@
-KENT_INC=-I../../../inc
+KENT_INC=-I../../../inc -I${PREFIX}/include
straw: straw.o cStraw.o
ld -r -o ../straw.o straw.o cStraw.o
--- a/kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed 2024-09-20 12:56:19.752664666 -0400
+++ b/kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed 2024-09-20 12:56:35.392752021 -0400
@@ -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.