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[pkgsrc/trunk]: pkgsrc/biology/bedtools biology/bedtools: Update to 2.30.0
details: https://anonhg.NetBSD.org/pkgsrc/rev/e98c5ce29ea7
branches: trunk
changeset: 446378:e98c5ce29ea7
user: bacon <bacon%pkgsrc.org@localhost>
date: Mon Feb 08 01:49:25 2021 +0000
description:
biology/bedtools: Update to 2.30.0
Some major performance improvements
Numerous minor bug fixes and enhancements
Added a do-test target to the pkgsrc Makefile
diffstat:
biology/bedtools/Makefile | 12 +--
biology/bedtools/PLIST | 2 +-
biology/bedtools/distinfo | 16 +++--
biology/bedtools/patches/patch-Makefile | 15 ++++-
biology/bedtools/patches/patch-src_utils_BamTools_include_SamHeader.hpp | 27 ++++++++++
biology/bedtools/patches/patch-src_utils_htslib_Makefile | 4 +-
biology/bedtools/patches/patch-test_test.sh | 20 +++++++
7 files changed, 76 insertions(+), 20 deletions(-)
diffs (165 lines):
diff -r 0092de9c2d91 -r e98c5ce29ea7 biology/bedtools/Makefile
--- a/biology/bedtools/Makefile Sun Feb 07 21:06:43 2021 +0000
+++ b/biology/bedtools/Makefile Mon Feb 08 01:49:25 2021 +0000
@@ -1,6 +1,6 @@
-# $NetBSD: Makefile,v 1.1 2021/01/22 17:07:50 bacon Exp $
+# $NetBSD: Makefile,v 1.2 2021/02/08 01:49:25 bacon Exp $
-DISTNAME= bedtools-2.29.2
+DISTNAME= bedtools-2.30.0
CATEGORIES= biology
MASTER_SITES= ${MASTER_SITE_GITHUB:=arq5x/}
GITHUB_PROJECT= bedtools2
@@ -12,7 +12,7 @@
LICENSE= mit
USE_LANGUAGES= c c++
-USE_TOOLS+= gmake
+USE_TOOLS+= bash:test gmake
REPLACE_SH+= scripts/vcfsort.sh
REPLACE_PYTHON= scripts/makeBashScripts.py
@@ -21,10 +21,8 @@
SUBST_SED.pybin= -e 's|python|${PYTHONBIN}|g'
SUBST_FILES.pybin= Makefile
-# Avoid conflict with C++20 <version> by adding .txt suffix
-post-extract:
- ${MV} ${WRKSRC}/src/utils/gzstream/version \
- ${WRKSRC}/src/utils/gzstream/version.txt
+do-test:
+ cd ${WRKSRC}/test && bash test.sh
.include "../../devel/zlib/buildlink3.mk"
.include "../../archivers/bzip2/buildlink3.mk"
diff -r 0092de9c2d91 -r e98c5ce29ea7 biology/bedtools/PLIST
--- a/biology/bedtools/PLIST Sun Feb 07 21:06:43 2021 +0000
+++ b/biology/bedtools/PLIST Mon Feb 08 01:49:25 2021 +0000
@@ -1,4 +1,4 @@
-@comment $NetBSD: PLIST,v 1.1 2021/01/22 17:07:50 bacon Exp $
+@comment $NetBSD: PLIST,v 1.2 2021/02/08 01:49:25 bacon Exp $
bin/annotateBed
bin/bamToBed
bin/bamToFastq
diff -r 0092de9c2d91 -r e98c5ce29ea7 biology/bedtools/distinfo
--- a/biology/bedtools/distinfo Sun Feb 07 21:06:43 2021 +0000
+++ b/biology/bedtools/distinfo Mon Feb 08 01:49:25 2021 +0000
@@ -1,8 +1,10 @@
-$NetBSD: distinfo,v 1.1 2021/01/22 17:07:50 bacon Exp $
+$NetBSD: distinfo,v 1.2 2021/02/08 01:49:25 bacon Exp $
-SHA1 (bedtools-2.29.2.tar.gz) = 51f03e1cac60f99c062d9babb6385800c89c78f6
-RMD160 (bedtools-2.29.2.tar.gz) = 08ea14501ddfc85f2d4a5a756a10512a61ec93f2
-SHA512 (bedtools-2.29.2.tar.gz) = 06b0016674acb08fd85b80fe1a8ff1ebce5c54c0a30ff7f4e52e63fe5b3f3841413f49df3c51088454d79048ca267fde8c23d9ed51f309ee6916d9b49610be41
-Size (bedtools-2.29.2.tar.gz) = 20638840 bytes
-SHA1 (patch-Makefile) = d6a76cb23e623842d6d5c60d67eff928b45b091c
-SHA1 (patch-src_utils_htslib_Makefile) = ba513efa59eed05321c176185fb576f4892ea7a5
+SHA1 (bedtools-2.30.0.tar.gz) = b3bae21434f261818e15875727b4a3c5c7366bc7
+RMD160 (bedtools-2.30.0.tar.gz) = 1cc30e5bc3df12f38d8f1e055ff2f939d7608395
+SHA512 (bedtools-2.30.0.tar.gz) = 3d69d6a53d3e5d15597dfefa26f7895231adbf3c1fe3b16ee4213e497ef01a20698add2f0e6f03d8eb7cd7c70709955f0ebdf897a025a83d31ef17e2c91f9856
+Size (bedtools-2.30.0.tar.gz) = 20639858 bytes
+SHA1 (patch-Makefile) = d21b4a69ce18eac7de59d277a03d0a5f5e2e1cb5
+SHA1 (patch-src_utils_BamTools_include_SamHeader.hpp) = 7ab168b247b5edf7f3eccd9ef7329a5e1605c787
+SHA1 (patch-src_utils_htslib_Makefile) = 8785ff3110f8df26e0cc5b2fdf1e2e02d6cdc836
+SHA1 (patch-test_test.sh) = e3a17815d6a30c17db7134613d25f08c6be3494e
diff -r 0092de9c2d91 -r e98c5ce29ea7 biology/bedtools/patches/patch-Makefile
--- a/biology/bedtools/patches/patch-Makefile Sun Feb 07 21:06:43 2021 +0000
+++ b/biology/bedtools/patches/patch-Makefile Mon Feb 08 01:49:25 2021 +0000
@@ -1,8 +1,8 @@
-$NetBSD: patch-Makefile,v 1.1 2021/01/22 17:07:50 bacon Exp $
+$NetBSD: patch-Makefile,v 1.2 2021/02/08 01:49:25 bacon Exp $
# Respect pkgsrc env, drop bash dep
---- Makefile.orig 2019-12-17 20:12:15.000000000 +0000
+--- Makefile.orig 2021-02-05 21:42:03.926301547 +0000
+++ Makefile
@@ -4,7 +4,7 @@
# (c) 2009 Aaron Quinlan
@@ -31,7 +31,16 @@
SUBDIRS = $(SRC_DIR)/annotateBed \
$(SRC_DIR)/bamToBed \
-@@ -191,9 +191,9 @@ $(BIN_DIR)/intersectBed: | $(BIN_DIR)
+@@ -155,7 +155,7 @@ $(CCPREFIX) $(CC_WRAPPER) $(CXX) $(ALL_C
+ @mv -f $*.Td $*.d
+ endef
+
+-$(OBJ_DIR)/%.d: ;
++$(OBJ_DIR)/%.d: $(OBJ_DIR) ;
+ .PRECIOUS: $(OBJ_DIR)/%.d
+
+ -include $(patsubst %.o,%.d,$(BUILT_OBJECTS))
+@@ -197,9 +197,9 @@ $(BIN_DIR)/intersectBed: | $(BIN_DIR)
.PHONY: all
install: all
diff -r 0092de9c2d91 -r e98c5ce29ea7 biology/bedtools/patches/patch-src_utils_BamTools_include_SamHeader.hpp
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/biology/bedtools/patches/patch-src_utils_BamTools_include_SamHeader.hpp Mon Feb 08 01:49:25 2021 +0000
@@ -0,0 +1,27 @@
+$NetBSD: patch-src_utils_BamTools_include_SamHeader.hpp,v 1.1 2021/02/08 01:49:25 bacon Exp $
+
+# Silence compiler warnings
+
+--- src/utils/BamTools/include/SamHeader.hpp.orig 2021-01-24 16:15:06 UTC
++++ src/utils/BamTools/include/SamHeader.hpp
+@@ -7,6 +7,7 @@
+ #include <string.h>
+ #include <api/BamAux.h>
+ #include <stdlib.h>
++#include <sysexits.h>
+
+
+ #ifdef WITH_HTS_CB_API
+@@ -29,7 +30,11 @@ namespace htslib_future {
+ ops.cb_data = buffer;
+ samFile* fp = hts_open_callback(NULL, &ops, "w");
+
+- sam_hdr_write(fp, hdr);
++ if ( sam_hdr_write(fp, hdr) != 0 )
++ {
++ fputs("sam_hdr_rebuild: Error: sam_hdr_write() failed.\n", stderr);
++ exit(EX_IOERR);
++ }
+
+ hts_close(fp);
+
diff -r 0092de9c2d91 -r e98c5ce29ea7 biology/bedtools/patches/patch-src_utils_htslib_Makefile
--- a/biology/bedtools/patches/patch-src_utils_htslib_Makefile Sun Feb 07 21:06:43 2021 +0000
+++ b/biology/bedtools/patches/patch-src_utils_htslib_Makefile Mon Feb 08 01:49:25 2021 +0000
@@ -1,8 +1,8 @@
-$NetBSD: patch-src_utils_htslib_Makefile,v 1.1 2021/01/22 17:07:50 bacon Exp $
+$NetBSD: patch-src_utils_htslib_Makefile,v 1.2 2021/02/08 01:49:25 bacon Exp $
# Respect pkgsrc env
---- src/utils/htslib/Makefile.orig 2021-01-21 22:49:18.823750624 +0000
+--- src/utils/htslib/Makefile.orig 2021-01-23 19:33:26.000000000 +0000
+++ src/utils/htslib/Makefile
@@ -22,7 +22,7 @@
# FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
diff -r 0092de9c2d91 -r e98c5ce29ea7 biology/bedtools/patches/patch-test_test.sh
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/biology/bedtools/patches/patch-test_test.sh Mon Feb 08 01:49:25 2021 +0000
@@ -0,0 +1,20 @@
+$NetBSD: patch-test_test.sh,v 1.1 2021/02/08 01:49:25 bacon Exp $
+
+# Warning for impending failed tests
+
+--- test/test.sh.orig 2021-02-07 19:54:21.793084552 +0000
++++ test/test.sh
+@@ -1,5 +1,13 @@
+ set -e; # Alert user to any uncaught error
+
++if [ $(uname) = FreeBSD ] || [ $(uname) = NetBSD ]; then
++ if ! df | fgrep -q fdesc; then
++ echo "fdesc FS must be mounted in order to run $0."
++ echo "It uses bash process substitutions, e.g. <(ls)."
++ exit 1
++ fi
++fi
++
+ ulimit -c unlimited
+
+ STARTWD=$(pwd);
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