| Port details |
- snpeff Genetic variant annotation and effect prediction toolbox
- 5.1 biology
 =0      5.1Version of this port present on the latest quarterly branch. - Maintainer: jwb@FreeBSD.org
- Port Added: 2021-04-18 18:48:08
- Last Update: 2023-11-06 10:03:47
- Commit Hash: 06df180
- Also Listed In: java python
- License: MIT
- WWW:
- https://snpeff.sourceforge.net/
- Description:
- Genetic variant annotation and functional effect prediction toolbox. It
annotates and predicts the effects of genetic variants on genes and proteins
(such as amino acid changes).
Features:
Supports over 38,000 genomes
Standard ANN annotation format
Cancer variants analysis
GATK compatible (-o gatk)
HGVS notation
Sequence Ontology standardized terms
  ¦  ¦  ¦  ¦ 
- Manual pages:
- FreshPorts has no man page information for this port.
- pkg-plist: as obtained via:
make generate-plist - Dependency lines:
-
- To install the port:
- cd /usr/ports/biology/snpeff/ && make install clean
- To add the package, run one of these commands:
- pkg install biology/snpeff
- pkg install snpeff
NOTE: If this package has multiple flavors (see below), then use one of them instead of the name specified above.- PKGNAME: snpeff
- Flavors: there is no flavor information for this port.
- distinfo:
- TIMESTAMP = 1671473460
SHA256 (snpeff-5.1/snpEff_latest_core.zip) = 919e0595c08e86d1dd82279723c83cb872070244ee4ce0cb3167bde2b272893b
SIZE (snpeff-5.1/snpEff_latest_core.zip) = 67191760
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:
-
- python3.9 : lang/python39
- Test dependencies:
-
- python3.9 : lang/python39
- Runtime dependencies:
-
- bash : shells/bash
- java : java/openjdk17
- python3.9 : lang/python39
- This port is required by:
- for Run
-
- biology/biostar-tools
Configuration Options:- No options to configure
- Options name:
- biology_snpeff
- USES:
- python shebangfix zip
- FreshPorts was unable to extract/find any pkg message
- Master Sites:
|
Number of commits found: 8
| Commit History - (may be incomplete: for full details, see links to repositories near top of page) |
| Commit | Credits | Log message |
|---|
5.1
06 Nov 2023 10:03:47
 |
Rodrigo Osorio (rodrigo) |
*/*: Update WWW to use HTTPS for sourceforge.net projects
Homepage link is permanent redirected to its HTTPS counterpart
Issue reported by repology : https://repology.org/repository/freebsd/problems
Approved by: portmgr (blanket)
PR: 274888 |
5.1
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> |
5.1
19 Dec 2022 18:50:00
|
Jason W. Bacon (jwb) |
biology/snpeff: Update to 5.1
Unbreak fetch, which depends on an unversioned distfile
Requested version tags upstream and looking at other build options |
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) |
5.0
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  ) |
5.0
24 May 2022 20:09:35
|
Rene Ladan (rene) |
cleanup: remove expired versions of OpenJDK (12 through 16)
Adjust ports depending on expired versions of OpenJDK:
- biology/snpeff: 12+ -> 17+
- devel/RStudio: 12 -> 11
- www/closure-compiler: 13 -> 11+
Allow java/openjdk17 to use java/openjdk17-bootstrap on i386
too, this builds just fine on 13.1-i386
Remove jdk12-doc as it is no longer relevant.
Clean up Java version calculations in bsd.java.mk
Reviewed by: jwb, java (glewis)
Differential Revision: https://reviews.freebsd.org/D35280 |
5.0
19 Apr 2021 16:41:58
|
Jason W. Bacon (jwb) |
biology/snpeff: Improvements to Makefile and patches
Reported by: Omp |
5.0
18 Apr 2021 18:46:29
|
Jason W. Bacon (jwb) |
biology/snpeff: Genetic variant annotation and effect prediction toolbox
Genetic variant annotation and functional effect prediction toolbox. It
annotates and predicts the effects of genetic variants on genes and proteins
(such as amino acid changes). |
Number of commits found: 8
|
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