| Port details |
- ucsc-userapps Command line tools from the UCSC Genome Browser project
- 414_1 biology
 =0      414_1Version of this port present on the latest quarterly branch.  RESTRICTED: Redistribution is limited, see license
- Maintainer: jwb@FreeBSD.org
- Port Added: 2021-04-25 17:21:12
- Last Update: 2023-12-30 07:16:41
- Commit Hash: 9ee2e86
- Also Listed In: perl5 python
- License: UCSC-GB
- WWW:
- https://hgdownload.cse.ucsc.edu/admin/exe/
- Description:
- These are the command-line bioinformatics utilities associated with the UCSC
genome browser. Care has been taken to install only the freely available
tools. However, the license information at https://genome.ucsc.edu/license/
is not entirely clear and we may add non-free utilities in the future.
Contact UCSC if you are using this port for commercial purposes.
  ¦  ¦  ¦  ¦ 
- Manual pages:
- FreshPorts has no man page information for this port.
- pkg-plist: as obtained via:
make generate-plist - Dependency lines:
-
- ucsc-userapps>0:biology/ucsc-userapps
- To install the port:
- cd /usr/ports/biology/ucsc-userapps/ && make install clean
- We doubt a package is available for this port because we see it marked as as:
- Restricted
- Package not available
Packages are normally not provided for ports that are marked as above.- To add the package, run one of these commands:
- pkg install biology/ucsc-userapps
- pkg install ucsc-userapps
NOTE: If this package has multiple flavors (see below), then use one of them instead of the name specified above.- PKGNAME: there is no package for this port: _LICENSE_RESTRICTED = delete-package delete-distfiles
- Flavors: there is no flavor information for this port.
- ONLY_FOR_ARCHS: amd64
- distinfo:
- TIMESTAMP = 1621027743
SHA256 (userApps.v414.src.tgz) = 36910b5c84ea613d4eb6ccb9572f3b34d929c5571578b1d91013391895638ab0
SIZE (userApps.v414.src.tgz) = 19195157
No package information for this port in our database- Sometimes this happens. Not all ports have packages.
- Dependencies
- NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
- Build dependencies:
-
- bash : shells/bash
- gmake>=4.3 : devel/gmake
- python3.9 : lang/python39
- perl5>=5.36<5.37 : lang/perl5.36
- Test dependencies:
-
- python3.9 : lang/python39
- Runtime dependencies:
-
- bash : shells/bash
- python3.9 : lang/python39
- perl5>=5.36<5.37 : lang/perl5.36
- Library dependencies:
-
- libiconv.so : converters/libiconv
- libpng.so : graphics/png
- libmysqlclient.so.21 : databases/mysql80-client
- There are no ports dependent upon this port
Configuration Options:- No options to configure
- Options name:
- biology_ucsc-userapps
- USES:
- gmake localbase:ldflags mysql shebangfix perl5 python ssl tar:tgz
- pkg-message:
- For install:
-
ucsc-kentutils is installed in it's own directory in order to avoid install
conflicts with other ports. Run "ucsc-shell" to gain access to ucsc-kentutils
commands in your PATH.
This port installs only freely available components of the UCSC userApps
distribution. See http://genome.ucsc.edu/license/ for more information.
- Master Sites:
|
| Commit History - (may be incomplete: for full details, see links to repositories near top of page) |
| Commit | Credits | Log message |
|---|
414_1
30 Dec 2023 07:16:41
 |
Muhammad Moinur Rahman (bofh) |
biology/ucsc-userapps: Replace dependencies
Currently their is a hardcoded dependency on mysql57-client which is
about to be removed. Ports depending on mysql should always use
USES=mysql rather than hardcoded *_DEPENDS. As I do not have a licensed
version of this application for now switch to USES=mysql. This should
not affect the cluster build at all as this is a RESTRICTED ports.
Approved by: portmgr (blanket) |
414_1
27 Jun 2023 19:34:34
|
Rene Ladan (rene) |
all: remove explicit versions in USES=python for "3.x+"
The logic in USES=python will automatically convert this to 3.8+ by
itself.
Adjust two ports that only had Python 3.7 mentioned but build fine
on Python 3.8 too.
finance/quickfix: mark BROKEN with PYTHON
libtool: compile: c++ -DHAVE_CONFIG_H -I. -I../.. -I -I. -I.. -I../.. -I../C++
-DLIBICONV_PLUG -DPYTHON_MAJOR_VERSION=3 -Wno-unused-variable
-Wno-maybe-uninitialized -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong
-fno-strict-aliasing -DLIBICONV_PLUG -Wall -ansi
-Wno-unused-command-line-argument -Wpointer-arith -Wwrite-strings
-Wno-overloaded-virtual -Wno-deprecated-declarations -Wno-deprecated -std=c++0x
-MT _quickfix_la-QuickfixPython.lo -MD -MP -MF
.deps/_quickfix_la-QuickfixPython.Tpo -c QuickfixPython.cpp -fPIC -DPIC -o
.libs/_quickfix_la-QuickfixPython.o
warning: unknown warning option '-Wno-maybe-uninitialized'; did you mean
'-Wno-uninitialized'? [-Wunknown-warning-option]
QuickfixPython.cpp:175:11: fatal error: 'Python.h' file not found
^~~~~~~~~~
1 warning and 1 error generated.
Reviewed by: portmgr, vishwin, yuri
Differential Revision: <https://reviews.freebsd.org/D40568> |
07 Sep 2022 21:58:51
|
Stefan Eßer (se) |
Remove WWW entries moved into port Makefiles
Commit b7f05445c00f has added WWW entries to port Makefiles based on
WWW: lines in pkg-descr files.
This commit removes the WWW: lines of moved-over URLs from these
pkg-descr files.
Approved by: portmgr (tcberner) |
414_1
07 Sep 2022 21:10:59
|
Stefan Eßer (se) |
Add WWW entries to port Makefiles
It has been common practice to have one or more URLs at the end of the
ports' pkg-descr files, one per line and prefixed with "WWW:". These
URLs should point at a project website or other relevant resources.
Access to these URLs required processing of the pkg-descr files, and
they have often become stale over time. If more than one such URL was
present in a pkg-descr file, only the first one was tarnsfered into
the port INDEX, but for many ports only the last line did contain the
port specific URL to further information.
There have been several proposals to make a project URL available as
a macro in the ports' Makefiles, over time.
(Only the first 15 lines of the commit message are shown above  ) |
414_1
20 Jul 2022 14:20:57
|
Tobias C. Berner (tcberner) |
biology: remove 'Created by' lines
A big Thank You to the original contributors of these ports:
* Aaron Dalton <aaron@FreeBSD.org>
* Akinori MUSHA aka knu <knu@idaemons.org>
* Andrey Zakhvatov
* Bob Zimmermann <rpz@cse.wustl.edu>
* Camson Huynh <chuynh@biolateral.com.au>
* Dan Siercks <dsiercks@uwm.edu>
* Fernan Aguero <fernan@iib.unsam.edu.ar>
* Hannes Hauswedell <h2+fbsdports@fsfe.org>
* J. Bacon <jwb@FreeBSD.org>
* Jason Bacon <jwb@FreeBSD.org>
* Jeremy <karlj000@unbc.ca> (Only the first 15 lines of the commit message are shown above ) |
414_1
25 Oct 2021 12:58:29
|
Alexey Dokuchaev (danfe) |
Style: improve ONLY_FOR_ARCHS_REASON (grammar, markup, etc.)
ONLY_FOR_ARCHS_REASON is used as part of the sentence and thus should
start with lower-case letter and not end with a period which is added
by the framework, similar to other knobs like BROKEN, IGNORE, et al.
While here, remove needless quoting, add missing Oxford comma, expand
contractions and jargonisms, use correct spelling for proper names. |
414_1
24 Sep 2021 21:53:30
|
Jason W. Bacon (jwb) |
biology/ucsc-userapps: Add "kent" command in ${PREFIX}/bin
Standard kent userapps commands are installed under ${PREFIX}/userapps
because of multiple conflicts. The kent command turns the standard
commands into subcommands, so no special PATH is needed.
/usr/local/ucsc-userapps/bin/bigWigToBedGraph [args]
can be run as
kent bigWigToBedGraph [args] |
414
15 May 2021 15:23:08
|
Jason W. Bacon (jwb) |
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. |
413
06 May 2021 11:47:41
|
Mathieu Arnold (mat) |
Deorbit RESTRICTED && NO_CDROM, part one.
For ports that already use the licenses framwork, merge the content of
RESTRICTED/NO_CDROM/LEGAL* entries into LICENSEs.
Approved by: rene
Differential Revision: https://reviews.freebsd.org/D30010 |
413
25 Apr 2021 17:18:38
|
Jason W. Bacon (jwb) |
biology/ucsc-userapps: Command line tools from the UCSC Genome Browser project
These are the command-line bioinformatics utilities associated with the UCSC
genome browser. Care has been taken to install only the freely available
tools. However, the license information at https://genome.ucsc.edu/license/
is not entirely clear and we may add non-free utilities in the future.
Contact UCSC if you are using this port for commercial purposes. |
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