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authorJason W. Bacon <jwb@FreeBSD.org>2021-05-15 15:23:08 +0000
committerJason W. Bacon <jwb@FreeBSD.org>2021-05-15 15:23:08 +0000
commit43397d188c684b83c4bff3e9b78862a1f6ab47f7 (patch)
tree8980213ed2126c57fd0a31e1228a5384fe804b33
parent0cfb296d8e06db9f00e75bbcbfab1bae015b1e70 (diff)
downloadports-43397d188c684b83c4bff3e9b78862a1f6ab47f7.tar.gz
ports-43397d188c684b83c4bff3e9b78862a1f6ab47f7.zip
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.
-rw-r--r--biology/ucsc-userapps/Makefile17
-rw-r--r--biology/ucsc-userapps/distinfo6
-rw-r--r--biology/ucsc-userapps/pkg-plist1
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