| Port details |
- biolibc-tools High-performance bioinformatics tools based on biolibc
- 0.1.5 biology
 =2      0.1.4.13_1Version of this port present on the latest quarterly branch. - Maintainer: jwb@FreeBSD.org
- Port Added: 2021-08-30 13:12:06
- Last Update: 2025-04-26 20:40:24
- Commit Hash: 0bef7dd
- People watching this port, also watch:: jdictionary, py311-Automat, py311-python-gdsii, py311-PyOpenGL, p5-Sane
- License: BSD2CLAUSE
- WWW:
- https://github.com/auerlab/biolibc-tools
- Description:
- Biolibc-tools is a collection of simple fast, memory-efficient,
programs for processing biological data. These are simple programs
built on biolibc that are not complex enough to warrant a separate
project.
  ¦  ¦  ¦  ¦ 
- Manual pages:
- FreshPorts has no man page information for this port.
- pkg-plist: as obtained via:
make generate-plist - Dependency lines:
-
- biolibc-tools>0:biology/biolibc-tools
- To install the port:
- cd /usr/ports/biology/biolibc-tools/ && make install clean
- To add the package, run one of these commands:
- pkg install biology/biolibc-tools
- pkg install biolibc-tools
NOTE: If this package has multiple flavors (see below), then use one of them instead of the name specified above.- PKGNAME: biolibc-tools
- Flavors: there is no flavor information for this port.
- distinfo:
- TIMESTAMP = 1745688119
SHA256 (auerlab-biolibc-tools-0.1.5_GH0.tar.gz) = c9456237ef16907488488e596efb08056e8a2ca0a8752642ae4dc47163bd6214
SIZE (auerlab-biolibc-tools-0.1.5_GH0.tar.gz) = 28822
Packages (timestamps in pop-ups are UTC):
- Dependencies
- NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
- Build dependencies:
-
- uthash>0 : devel/uthash
- Library dependencies:
-
- libbiolibc.so : biology/biolibc
- libxtend.so : devel/libxtend
- libxxhash.so : devel/xxhash
- This port is required by:
- for Run
-
- biology/atac-seq
- biology/chip-seq
- biology/rna-seq
Configuration Options:- No options to configure
- Options name:
- biology_biolibc-tools
- FreshPorts was unable to extract/find any pkg message
- Master Sites:
|
| Commit History - (may be incomplete: for full details, see links to repositories near top of page) |
| Commit | Credits | Log message |
|---|
0.1.5
26 Apr 2025 20:40:24
 |
Jason W. Bacon (jwb) |
biology/biolibc-tools: Update to 0.1.5
A few enhancements and updates for libxtend and biolibc APIs
Changes: https://github.com/auerlab/biolibc-tools/releases |
0.1.4.13_1
02 Mar 2024 18:44:44
|
Nuno Teixeira (eduardo) |
biology/biolibc-tools: Move man pages to share/man
Approved by: portmgr (blanket) |
0.1.4.13
29 Oct 2023 22:41:02
|
Jason W. Bacon (jwb) |
biology/biolibc-tools: Update to 0.1.4.13
Updates for new libxtend API |
0.1.4.9
11 Aug 2023 20:40:49
|
Jason W. Bacon (jwb) |
biology/biolibc-tools: Update to 0.1.4.9
Update for biolibc GFF3 API changes |
0.1.4.6
10 Jun 2023 11:57:56
|
Jason W. Bacon (jwb) |
biology/biolibc-tools: Update to 0.1.4.6
Improvements to deromanize
Updates for libxtend API changes |
0.1.4.1
14 Dec 2022 00:11:56
|
Jason W. Bacon (jwb) |
biology/biolibc-tools: Update to 0.1.4.1
deromanize:
Check for NULL field to prevent crash in some situations
Take optional input file as second argument |
0.1.4
13 Dec 2022 00:47:59
|
Jason W. Bacon (jwb) |
biology/biolibc-tools: Update to 0.1.4
Add deromanize subcommand to convert Roman numeral chromosome IDs
fastx-stats: Report standard deviation for read length
Changes: https://github.com/auerlab/biolibc-tools/releases |
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) |
0.1.3_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  ) |
0.1.3_1
13 Aug 2022 18:51:14
|
Matthias Andree (mandree) |
*: bump PORTREVISION of all devel/xxhash users...
...except archivers/py-borgbackup, which requires a more complete fix. |
0.1.3
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 ) |
0.1.3
11 Jun 2022 14:26:56
|
Jason W. Bacon (jwb) |
biology/biolibc-tools: Update to 0.1.3
Add vcf-downsample subcommand
Improvements to build system
extract-seq: Recurse to output subfeatures
Numerous other minor enhancements and fixes
Changes: https://github.com/auerlab/biolibc-tools/tags |
0.1.2
15 Mar 2022 21:36:49
|
Jason W. Bacon (jwb) |
biology/biolibc-tools: Update to 0.1.2
New fastx-stats and ensembl2gene subcommands
Minor updates for biolibc 0.2.2 API changes
Minor bug fixes and ennancements |
0.1.1
14 Dec 2021 19:45:32
|
Jason W. Bacon (jwb) |
biology/biolibc-tools: Update to 0.1.1
Make all programs subcommands of "blt"
Several new commands
Updates for evolving libxtend and biolibc APIs
Add --version flag
Numerous minor fixes and enhancements
Changes: https://github.com/auerlab/biolibc-tools/releases/tag/0.1.1 |
0.1.0.34
30 Aug 2021 13:09:23
|
Jason W. Bacon (jwb) |
biology/biolibc-tools: High-performance tools based on biolibc
Biolibc-tools is a collection of simple fast, memory-efficient,
programs for processing biological data. These are simple programs
built on biolibc that are not complex enough to warrant a separate
project. |
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