From nobody Wed Oct 09 22:23:16 2024 X-Original-To: dev-commits-ports-main@mlmmj.nyi.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2610:1c1:1:606c::19:1]) by mlmmj.nyi.freebsd.org (Postfix) with ESMTP id 4XP6pr3vK4z5Z4Dh; Wed, 09 Oct 2024 22:23:16 +0000 (UTC) (envelope-from git@FreeBSD.org) Received: from mxrelay.nyi.freebsd.org (mxrelay.nyi.freebsd.org [IPv6:2610:1c1:1:606c::19:3]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange X25519 server-signature RSA-PSS (4096 bits) server-digest SHA256 client-signature RSA-PSS (4096 bits) client-digest SHA256) (Client CN "mxrelay.nyi.freebsd.org", Issuer "R11" (verified OK)) by mx1.freebsd.org (Postfix) with ESMTPS id 4XP6pr1JB0z4dqZ; Wed, 9 Oct 2024 22:23:16 +0000 (UTC) (envelope-from git@FreeBSD.org) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1728512596; h=from:from:reply-to:subject:subject:date:date:message-id:message-id: to:to:cc:mime-version:mime-version:content-type:content-type: content-transfer-encoding:content-transfer-encoding; bh=p7fM5DIt0cRZe9hgEgZkQIIALN8gnSyssZ2pOGwHfS4=; b=dPA7n10BRffjVIRX+m+RmNSttr2+GHjyRHPM36ISy5D8UUsgXq2zjpyk+mHPelFjL35zXj Dsbu2hOWYE/8UihyCPFoN9YDvJgVeWiW9L6E+bFztmipVLvH0t/orFI7FjeyibR1Qo0ypw ZHONJ9sZxcec6GB3d3565suW29hBkfuhdPvZRUpm+VpxNQ8ocUMscm6R9Xkvkxc7g00pK6 HliRuXU0SXregjfQqe4QUNew40P93sOKMPWhXb5zSyw4iq0UM6G/Ou59/ZM1T5wshdHS72 Nk4w5DxIsQ+123y4TCpYmWyMAD8s94XncNITW1mgOlTPlzcQTqtYS7r27CWiow== ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1728512596; h=from:from:reply-to:subject:subject:date:date:message-id:message-id: to:to:cc:mime-version:mime-version:content-type:content-type: content-transfer-encoding:content-transfer-encoding; bh=p7fM5DIt0cRZe9hgEgZkQIIALN8gnSyssZ2pOGwHfS4=; b=SVSu9nG9fuDGHOESjHemmUu1JB5FJXqXWdew5zgFI+vWnhHwdz/czaFBEhxH7ujdML6qWW Sgnx/26u1jz4Fc4OkdA/NTnGBuIdNrpbRdbuF8Gb8Hf142r/NzU1Xl6VhwcssIN6eN830E B47Krxgk4zMz1oyPozharHHw0YjJtMs3RoQ0SMOoKdI0leLzbHEv35wjFKeb6msdf61piJ 2QATuP3S7xqhdvOPJq63p8Tu0TB8gd0gZ+9Ei2TQrkrADqiXlmM9gXO04IUXV8bXIsfPlA MvEeV5M/jUswfOKG/1Tu7fUO1fTWrL2X9z4O8CC4PYrKXliduVvcD0vlEyrnDw== ARC-Authentication-Results: i=1; mx1.freebsd.org; none ARC-Seal: i=1; s=dkim; d=freebsd.org; t=1728512596; a=rsa-sha256; cv=none; b=qpH7I311Eh6Q6MiaO5lh012nkVL5qLnDd+SHHUbGQSgBT5tQP5NsH/N7jqXzyNtHO7o39G 0/tWbqhsk4o57c2ZmL2ctEOxJx6rLWKo+bl0hj/cySDC1LzriV/Gr2llngRK/t3+S3ynYD GzUp9ealILsTiyZrnsxoGbKjXvV+FfHWHUVJqD/e6qFHg2aeQZzH/zHRbO6wH5sH28jGUn 5eo+c0DnSI90TacZ5LZpa4S+w2xlBikgqH26yG4CTHsINIxl63+Atzat60LBw+1hXPM5vq 7StxcSeQTw/DGRx+8xM3+yNeTBXAmMKjekrYPRbdvChqYJPtuA2XT4oGTtrA+A== Received: from gitrepo.freebsd.org (gitrepo.freebsd.org [IPv6:2610:1c1:1:6068::e6a:5]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange X25519 server-signature RSA-PSS (4096 bits) server-digest SHA256) (Client did not present a certificate) by mxrelay.nyi.freebsd.org (Postfix) with ESMTPS id 4XP6pr0wG6zXfK; Wed, 9 Oct 2024 22:23:16 +0000 (UTC) (envelope-from git@FreeBSD.org) Received: from gitrepo.freebsd.org ([127.0.1.44]) by gitrepo.freebsd.org (8.18.1/8.18.1) with ESMTP id 499MNG6J059871; Wed, 9 Oct 2024 22:23:16 GMT (envelope-from git@gitrepo.freebsd.org) Received: (from git@localhost) by gitrepo.freebsd.org (8.18.1/8.18.1/Submit) id 499MNGnI059868; Wed, 9 Oct 2024 22:23:16 GMT (envelope-from git) Date: Wed, 9 Oct 2024 22:23:16 GMT Message-Id: <202410092223.499MNGnI059868@gitrepo.freebsd.org> To: ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-main@FreeBSD.org From: "Jason W. Bacon" Subject: git: f3b6d6f5f45c - main - biology/bio-mocha: Update to 1.20 List-Id: Commits to the main branch of the FreeBSD ports repository List-Archive: https://lists.freebsd.org/archives/dev-commits-ports-main List-Help: List-Post: List-Subscribe: List-Unsubscribe: X-BeenThere: dev-commits-ports-main@freebsd.org Sender: owner-dev-commits-ports-main@FreeBSD.org MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: 8bit X-Git-Committer: jwb X-Git-Repository: ports X-Git-Refname: refs/heads/main X-Git-Reftype: branch X-Git-Commit: f3b6d6f5f45c96c43580169b1cfc37897625c602 Auto-Submitted: auto-generated The branch main has been updated by jwb: URL: https://cgit.FreeBSD.org/ports/commit/?id=f3b6d6f5f45c96c43580169b1cfc37897625c602 commit f3b6d6f5f45c96c43580169b1cfc37897625c602 Author: Jason W. Bacon AuthorDate: 2024-10-09 22:22:39 +0000 Commit: Jason W. Bacon CommitDate: 2024-10-09 22:23:10 +0000 biology/bio-mocha: Update to 1.20 Numerous bug fixes and enhancements since 1.16 Reported by: portscout --- biology/bio-mocha/Makefile | 11 +++++------ biology/bio-mocha/distinfo | 10 +++++----- biology/bio-mocha/files/patch-Makefile | 28 ++++++++++++++-------------- biology/bio-mocha/pkg-plist | 1 - 4 files changed, 24 insertions(+), 26 deletions(-) diff --git a/biology/bio-mocha/Makefile b/biology/bio-mocha/Makefile index 33147346e72d..a9228be3a30e 100644 --- a/biology/bio-mocha/Makefile +++ b/biology/bio-mocha/Makefile @@ -1,8 +1,9 @@ PORTNAME= bio-mocha -DISTVERSION= 1.16 +DISTVERSION= 1.20 CATEGORIES= biology MASTER_SITES= https://software.broadinstitute.org/software/mocha/ -DISTFILES+= ${PORTNAME}_${DISTVERSION}-20221221.tar.gz +# Get this right, or ports will download bcftools in it's place via tuple +DISTFILES+= ${PORTNAME}_${DISTVERSION}-20240505.tar.gz MAINTAINER= jwb@FreeBSD.org COMMENT= Bcftools plugin for mosaic chromosomal alteration analysis @@ -10,8 +11,8 @@ WWW= https://software.broadinstitute.org/software/mocha/ LICENSE= MIT +BUILD_DEPENDS= bash:shells/bash htslib>=1.21:biology/htslib LIB_DEPENDS= libhts.so:biology/htslib -BUILD_DEPENDS= bash:shells/bash RUN_DEPENDS= bcftools>=${PORTVERSION}:biology/bcftools USES= autoreconf gmake localbase perl5 python:env shebangfix @@ -20,7 +21,7 @@ USE_PERL5= test GH_ACCOUNT= samtools GH_PROJECT= bcftools -GH_TAGNAME= 1.16 +GH_TAGNAME= 1.21 GNU_CONFIGURE= yes SHEBANG_FILES= misc/* test/test.pl @@ -42,8 +43,6 @@ do-install: ${STAGEDIR}${PREFIX}/libexec/bcftools ${INSTALL_PROGRAM} ${WRKSRC}/plugins/mochatools.so \ ${STAGEDIR}${PREFIX}/libexec/bcftools - ${INSTALL_PROGRAM} ${WRKSRC}/plugins/trio-phase.so \ - ${STAGEDIR}${PREFIX}/libexec/bcftools (cd ${WRKSRC}/MoCha && ${COPYTREE_SHARE} . ${STAGEDIR}${DATADIR}) .include diff --git a/biology/bio-mocha/distinfo b/biology/bio-mocha/distinfo index c5a05127a3d6..6f2f8b800396 100644 --- a/biology/bio-mocha/distinfo +++ b/biology/bio-mocha/distinfo @@ -1,5 +1,5 @@ -TIMESTAMP = 1672095342 -SHA256 (bio-mocha_1.16-20221221.tar.gz) = 576cbdda53760f353fc8fd989751716b1d4f8c5e1921f838c263476282cced86 -SIZE (bio-mocha_1.16-20221221.tar.gz) = 68625 -SHA256 (samtools-bcftools-1.16_GH0.tar.gz) = c44c85a04e058e1f1eceeb712106031100bbd700b8ff3f623f7ff872469a4ba3 -SIZE (samtools-bcftools-1.16_GH0.tar.gz) = 3432435 +TIMESTAMP = 1727475837 +SHA256 (bio-mocha_1.20-20240505.tar.gz) = 3beeb7f046b491fed162dfedd83a29b3eebb165fb1f2a25f44df7fa2f063793b +SIZE (bio-mocha_1.20-20240505.tar.gz) = 66752 +SHA256 (samtools-bcftools-1.20-1.21_GH0.tar.gz) = 7484695c5d833fb1a89c2b886ec302db0514ba3c8e5ef7397b9302fa8bd37f8d +SIZE (samtools-bcftools-1.20-1.21_GH0.tar.gz) = 3665160 diff --git a/biology/bio-mocha/files/patch-Makefile b/biology/bio-mocha/files/patch-Makefile index 3299954ae45b..55d6f64d426d 100644 --- a/biology/bio-mocha/files/patch-Makefile +++ b/biology/bio-mocha/files/patch-Makefile @@ -1,6 +1,6 @@ ---- Makefile.orig 2021-03-17 09:16:18 UTC +--- Makefile.orig 2024-09-12 15:06:36 UTC +++ Makefile -@@ -58,13 +58,14 @@ pluginpath = $(plugindir) +@@ -59,13 +59,14 @@ misc_bindir = $(bindir) # Installation location for $(MISC_PROGRAMS) and $(MISC_SCRIPTS) misc_bindir = $(bindir) @@ -12,22 +12,22 @@ -INSTALL_PROGRAM = $(INSTALL) -INSTALL_SCRIPT = $(INSTALL_PROGRAM) +# Use BSD_INSTALL_PROGRAM to strip when WITH_DEBUG not set -+MKDIR_P = mkdir -p -+INSTALL = install -p -+INSTALL_DATA = ${BSD_INSTALL_DATA} -+INSTALL_DIR = $(MKDIR_P) -+INSTALL_MAN = ${BSD_INSTALL_MAN} -+INSTALL_PROGRAM = ${BSD_INSTALL_PROGRAM} -+INSTALL_SCRIPT = ${BSD_INSTALL_SCRIPT} ++MKDIR_P = mkdir -p ++INSTALL = install -p ++INSTALL_DATA = ${BSD_INSTALL_DATA} ++INSTALL_DIR = $(MKDIR_P) ++INSTALL_MAN = ${BSD_INSTALL_MAN} ++INSTALL_PROGRAM = ${BSD_INSTALL_PROGRAM} ++INSTALL_SCRIPT = ${BSD_INSTALL_SCRIPT} PROGRAMS = bcftools MISC_SCRIPTS = \ -@@ -142,7 +143,7 @@ print-version: - ifdef USE_GPL +@@ -144,7 +145,7 @@ ifdef USE_GPL main.o : EXTRA_CPPFLAGS += -DUSE_GPL OBJS += polysomy.o peakfit.o -- GSL_LIBS ?= -lgsl -lcblas -+ GSL_LIBS ?= -lgslcblas + ifndef GSL_LIBS +- GSL_LIBS += -lgsl -lcblas ++ GSL_LIBS += -lgslcblas + endif endif - print-%: diff --git a/biology/bio-mocha/pkg-plist b/biology/bio-mocha/pkg-plist index a56018707fc6..e6767d770f0f 100644 --- a/biology/bio-mocha/pkg-plist +++ b/biology/bio-mocha/pkg-plist @@ -1,7 +1,6 @@ libexec/bcftools/extendFMT.so libexec/bcftools/mocha.so libexec/bcftools/mochatools.so -libexec/bcftools/trio-phase.so %%DATADIR%%/mocha_plot.R %%DATADIR%%/pileup_plot.R %%DATADIR%%/summary_plot.R