Date: Sat, 15 May 2021 15:25:28 GMT From: "Jason W. Bacon" <jwb@FreeBSD.org> To: ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-main@FreeBSD.org Subject: git: 43397d188c68 - main - biology/ucsc-userapps: Update to v414 Message-ID: <202105151525.14FFPSf6050355@gitrepo.freebsd.org>
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The branch main has been updated by jwb: URL: https://cgit.FreeBSD.org/ports/commit/?id=43397d188c684b83c4bff3e9b78862a1f6ab47f7 commit 43397d188c684b83c4bff3e9b78862a1f6ab47f7 Author: Jason W. Bacon <jwb@FreeBSD.org> AuthorDate: 2021-05-15 15:23:08 +0000 Commit: Jason W. Bacon <jwb@FreeBSD.org> CommitDate: 2021-05-15 15:23:08 +0000 biology/ucsc-userapps: Update to v414 Update license message. Confirmed via conversation with UCSC that some proprietary code is used in the "free" tools build. UCSC is working on it. --- biology/ucsc-userapps/Makefile | 17 +++++++++-------- biology/ucsc-userapps/distinfo | 6 +++--- biology/ucsc-userapps/pkg-plist | 1 + 3 files changed, 13 insertions(+), 11 deletions(-) diff --git a/biology/ucsc-userapps/Makefile b/biology/ucsc-userapps/Makefile index 00c5fcf8e33a..c7e44cc879ed 100644 --- a/biology/ucsc-userapps/Makefile +++ b/biology/ucsc-userapps/Makefile @@ -1,7 +1,7 @@ # Created by: J. Bacon <jwb@FreeBSD.org> PORTNAME= ucsc-userapps -DISTVERSION= 413 +DISTVERSION= 414 CATEGORIES= biology perl5 python MASTER_SITES= http://hgdownload.cse.ucsc.edu/admin/exe/userApps.archive/ DISTNAME= userApps.v${PORTVERSION}.src @@ -11,12 +11,9 @@ COMMENT= Command line tools from the UCSC Genome Browser project LICENSE= UCSC-GB LICENSE_NAME= UCSC Genome Browser License -LICENSE_TEXT= To the best of our knowledge, all of the tools installed by\ - this port are freely available. However, a license is\ - required for commercial download and installation of some\ - binaries and source code in the UCSC Genome Browser\ - distribution.\n\nContact UCSC directly if you are using these\ - tools for commercial purposes.\n\nSee\ +LICENSE_TEXT= Some tools installed by this port require a license for\ + commercial use.\n\nContact UCSC directly if you are using\ + these tools for commercial purposes.\n\nSee\ https://genome.ucsc.edu/license/ for full terms. LICENSE_PERMS= no-dist-mirror no-dist-sell no-pkg-mirror no-pkg-sell @@ -31,6 +28,8 @@ RUN_DEPENDS= bash:shells/bash USES= gmake localbase:ldflags shebangfix perl5 python:3.6+ ssl tar:tgz +RESTRICTED= Redistribution is limited, see license + SHEBANG_FILES= kent/src/checkUmask.sh \ kent/src/utils/bigHeat \ kent/src/utils/chromToUcsc/chromToUcsc \ @@ -47,7 +46,9 @@ MAKE_ENV= BINDIR=${WRKSRC}/bin SUB_FILES= ucsc-shell -# Build only non-commercial tools +# Build mostly non-commercial tools. There is some leakage of proprietary +# code from the libraries per conversation with UCSC. Work to resolve this +# is ongoing. do-build: @${MV} ${WRKSRC}/kent/src/inc/uuid.h ${WRKSRC}/kent/src/inc/my_uuid.h @${MKDIR} ${WRKSRC}/bin diff --git a/biology/ucsc-userapps/distinfo b/biology/ucsc-userapps/distinfo index a75f1d9a21b0..cc2c9ed9a4e7 100644 --- a/biology/ucsc-userapps/distinfo +++ b/biology/ucsc-userapps/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1619366655 -SHA256 (userApps.v413.src.tgz) = 91c51fec26bc61ea0dd9c4d0d13c76ce26e1c7d7f7dddbd3067c70beaec0af19 -SIZE (userApps.v413.src.tgz) = 19186621 +TIMESTAMP = 1621027743 +SHA256 (userApps.v414.src.tgz) = 36910b5c84ea613d4eb6ccb9572f3b34d929c5571578b1d91013391895638ab0 +SIZE (userApps.v414.src.tgz) = 19195157 diff --git a/biology/ucsc-userapps/pkg-plist b/biology/ucsc-userapps/pkg-plist index 3766142e1e8b..e8304be64af2 100644 --- a/biology/ucsc-userapps/pkg-plist +++ b/biology/ucsc-userapps/pkg-plist @@ -55,6 +55,7 @@ userapps/bin/faOneRecord userapps/bin/faPolyASizes userapps/bin/faRandomize userapps/bin/faRc +userapps/bin/faRenameRecords userapps/bin/faSimplify userapps/bin/faSize userapps/bin/faSomeRecords
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