svn commit: r522851 - head/biology/abyss
Yuri Victorovich
yuri at FreeBSD.org
Mon Jan 13 04:06:15 UTC 2020
Author: yuri
Date: Mon Jan 13 04:06:14 2020
New Revision: 522851
URL: https://svnweb.freebsd.org/changeset/ports/522851
Log:
biology/abyss: Update 2.1.5 -> 2.2.3
Reported by: portscout
Modified:
head/biology/abyss/Makefile
head/biology/abyss/distinfo
head/biology/abyss/pkg-plist
Modified: head/biology/abyss/Makefile
==============================================================================
--- head/biology/abyss/Makefile Mon Jan 13 03:32:40 2020 (r522850)
+++ head/biology/abyss/Makefile Mon Jan 13 04:06:14 2020 (r522851)
@@ -1,14 +1,9 @@
# $FreeBSD$
PORTNAME= abyss
-DISTVERSION= 2.1.5
-PORTREVISION= 6
+DISTVERSION= 2.2.3
CATEGORIES= biology
-MASTER_SITES= http://www.bcgsc.ca/platform/bioinfo/software/${PORTNAME}/releases/${DISTVERSION}/
-PATCH_SITES= https://github.com/bcgsc/${PORTNAME}/commit/
-PATCHFILES= 25eb9d2a914fb211fdfe04fcda5593f29fd23ff5.patch:-p1
-
MAINTAINER= yuri at FreeBSD.org
COMMENT= Assembly By Short Sequences: parallel, paired-end sequence assembler
@@ -24,11 +19,13 @@ LIB_DEPENDS= libffi.so:devel/libffi \
RUN_DEPENDS= bash:shells/bash \
gmake:devel/gmake
-USES= compiler:c++11-lang gmake iconv:wchar_t localbase:ldflags shebangfix sqlite
-SHEBANG_FILES= bin/${PORTNAME}-*
+USES= autoreconf compiler:c++11-lang gmake iconv:wchar_t localbase:ldflags shebangfix sqlite
+SHEBANG_FILES= bin/${PORTNAME}-* DataBase/abyss-db-txt
SHEBANG_LANG= make
make_OLD_CMD= /usr/bin/make
make_CMD= ${PREFIX}/bin/gmake
+USE_GITHUB= yes
+GH_ACCOUNT= bcgsc
GNU_CONFIGURE= yes
CONFIGURE_ARGS= --without-sparsehash # configure fails to find std::hash, reported to the ML: https://groups.google.com/forum/#!topic/trans-abyss/SZDBKR5bKxs
Modified: head/biology/abyss/distinfo
==============================================================================
--- head/biology/abyss/distinfo Mon Jan 13 03:32:40 2020 (r522850)
+++ head/biology/abyss/distinfo Mon Jan 13 04:06:14 2020 (r522851)
@@ -1,5 +1,3 @@
-TIMESTAMP = 1561103807
-SHA256 (abyss-2.1.5.tar.gz) = 65bfc8241e6ff5adf7601ae4ae93a75e3db86d6bff5d593c75aaff7f0ef41757
-SIZE (abyss-2.1.5.tar.gz) = 1201318
-SHA256 (25eb9d2a914fb211fdfe04fcda5593f29fd23ff5.patch) = 93ad66c42610c4fba8cfbe256a2ab689bf4a76974c3b97a9e1094863614ad934
-SIZE (25eb9d2a914fb211fdfe04fcda5593f29fd23ff5.patch) = 1701
+TIMESTAMP = 1578886491
+SHA256 (bcgsc-abyss-2.2.3_GH0.tar.gz) = c7b93290b2ccffcf2f3ca42262621c636108f6dbc21f5684ebeeb4f682200675
+SIZE (bcgsc-abyss-2.2.3_GH0.tar.gz) = 1203318
Modified: head/biology/abyss/pkg-plist
==============================================================================
--- head/biology/abyss/pkg-plist Mon Jan 13 03:32:40 2020 (r522850)
+++ head/biology/abyss/pkg-plist Mon Jan 13 04:06:14 2020 (r522851)
@@ -45,7 +45,6 @@ bin/abyss-overlap
bin/abyss-paired-dbg
bin/abyss-pe
bin/abyss-samtoafg
-bin/abyss-samtobreak
bin/abyss-scaffold
bin/abyss-sealer
bin/abyss-stack-size
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