diff options
author | bacon <bacon@pkgsrc.org> | 2021-02-08 01:49:25 +0000 |
---|---|---|
committer | bacon <bacon@pkgsrc.org> | 2021-02-08 01:49:25 +0000 |
commit | 01509bc08bb9b60dad98c315721851783662bfd3 (patch) | |
tree | a2edc4084af53e331b28eb518296e4a1cdec9fa6 | |
parent | 880115a4a205eb88cc4d7ecc4ab322cacaf0cd11 (diff) | |
download | pkgsrc-01509bc08bb9b60dad98c315721851783662bfd3.tar.gz |
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
-rw-r--r-- | biology/bedtools/Makefile | 12 | ||||
-rw-r--r-- | biology/bedtools/PLIST | 2 | ||||
-rw-r--r-- | biology/bedtools/distinfo | 16 | ||||
-rw-r--r-- | biology/bedtools/patches/patch-Makefile | 15 | ||||
-rw-r--r-- | biology/bedtools/patches/patch-src_utils_BamTools_include_SamHeader.hpp | 27 | ||||
-rw-r--r-- | biology/bedtools/patches/patch-src_utils_htslib_Makefile | 4 | ||||
-rw-r--r-- | biology/bedtools/patches/patch-test_test.sh | 20 |
7 files changed, 76 insertions, 20 deletions
diff --git a/biology/bedtools/Makefile b/biology/bedtools/Makefile index b8c917dc20d..bee7cc36d8a 100644 --- a/biology/bedtools/Makefile +++ b/biology/bedtools/Makefile @@ -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= ${MASTER_SITE_GITHUB:=arq5x/} GITHUB_PROJECT= bedtools2 @@ -12,7 +12,7 @@ COMMENT= Swiss army knife for genome arithmetic LICENSE= mit USE_LANGUAGES= c c++ -USE_TOOLS+= gmake +USE_TOOLS+= bash:test gmake REPLACE_SH+= scripts/vcfsort.sh REPLACE_PYTHON= scripts/makeBashScripts.py @@ -21,10 +21,8 @@ SUBST_STAGE.pybin= pre-configure SUBST_SED.pybin= -e 's|python|${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 --git a/biology/bedtools/PLIST b/biology/bedtools/PLIST index c7fd8967b11..4e84b3d9760 100644 --- a/biology/bedtools/PLIST +++ b/biology/bedtools/PLIST @@ -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 --git a/biology/bedtools/distinfo b/biology/bedtools/distinfo index de0e24bd048..da22273729e 100644 --- a/biology/bedtools/distinfo +++ b/biology/bedtools/distinfo @@ -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 --git a/biology/bedtools/patches/patch-Makefile b/biology/bedtools/patches/patch-Makefile index 635ff4b1c2e..1ffa9ea7e71 100644 --- a/biology/bedtools/patches/patch-Makefile +++ b/biology/bedtools/patches/patch-Makefile @@ -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 @@ $NetBSD: patch-Makefile,v 1.1 2021/01/22 17:07:50 bacon Exp $ 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: | $(BIN_DIR) .PHONY: all install: all diff --git a/biology/bedtools/patches/patch-src_utils_BamTools_include_SamHeader.hpp b/biology/bedtools/patches/patch-src_utils_BamTools_include_SamHeader.hpp new file mode 100644 index 00000000000..e0e88b2db0f --- /dev/null +++ b/biology/bedtools/patches/patch-src_utils_BamTools_include_SamHeader.hpp @@ -0,0 +1,27 @@ +$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 --git a/biology/bedtools/patches/patch-src_utils_htslib_Makefile b/biology/bedtools/patches/patch-src_utils_htslib_Makefile index 82e9b790b08..88df304e649 100644 --- a/biology/bedtools/patches/patch-src_utils_htslib_Makefile +++ b/biology/bedtools/patches/patch-src_utils_htslib_Makefile @@ -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 --git a/biology/bedtools/patches/patch-test_test.sh b/biology/bedtools/patches/patch-test_test.sh new file mode 100644 index 00000000000..1aea22bc9d5 --- /dev/null +++ b/biology/bedtools/patches/patch-test_test.sh @@ -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); |