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.
Entrez Direct (EDirect) provides access to the NCBI's suite of interconnected
databases (publication, sequence, structure, gene, variation, expression, etc.)
from a UNIX terminal window.
* Add missing dependency devel/py-nose that is required to build. With
Python 3.6/3.7 there are no build issues because the sdist contains
Python Eggs of "nose" for these versions.
While I'm here:
* Set NO_ARCH because the port has no architecture specific files.
* Make it concurrent safe, package installs a script and bump
PORTREVISION due package change.
PR: 253815
Approved by: portmgr (build fix)
MFH: No (The port was added after the 2021Q1 branch)
* Apply the same fix as in 9cb5898561 by
stripping libraries by wildcard paths.
* Also use PYTHONPREFIX_SITELIBDIR instead PYTHON_SITELIBDIR to make
the port PREFIX safe while I'm here.
PR: 253815
Approved by: python (with hat)
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).
This package includes BBMap, a short read aligner, as well as various other
bioinformatic tools. It is written in pure Java, can run on any platform, and
has no dependencies other than Java being installed (compiled for Java 6 and
higher). All tools are efficient and multithreaded.
Sequence reading library developed by the Ribosomal Database Project. It can
handle genbank, embl, fasta, fastq, sff and sto files, can read from files or
streams, and can handle indexing files.
CrossMap is a program for genome coordinates conversion between different
assemblies (such as hg18 (NCBI36) <=> hg19 (GRCh37)). It supports commonly used
file formats including BAM, CRAM, SAM, Wiggle, BigWig, BED, GFF, GTF, MAF VCF,
and gVCF.
A python extension, written in C, for quick access to bigBed files and access
to and creation of bigWig files. This extension uses libBigWig for local and
remote file access.
2021-04-01 ftp/wzdftpd: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 astro/roadmap: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 games/cosmo: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 games/bomberinstinct: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 games/drm: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 games/bygfoot: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 games/cre: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 irc/hybserv: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 irc/xaric: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 mail/elmo: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 misc/cave: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 security/bugs: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 security/dmitry: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 security/doorman: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 shells/esh: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 sysutils/cpu: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 textproc/libcrm114: No known users, dead upstream
2021-04-01 x11/wmmatrix: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 x11/wmxss: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 x11/tycoon: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 x11/xgrab: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 x11/xbanner: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 x11/bricons: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 x11/xmon: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 games/cavezofphear: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 astro/saoimage: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 audio/ksmp3play: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 audio/jamin: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 audio/musicbox-tag-editor: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 audio/nspmod: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 audio/cdplay: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 audio/gimmix: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 audio/ghostess: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 audio/wmrecord: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 audio/toolame: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 audio/shout: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 biology/grappa: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 biology/phylip: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 biology/lagan: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 cad/varkon: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 cad/transcalc: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 comms/seyon: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 comms/efax: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 converters/vda2fbd: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 converters/shftool: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 devel/openzz: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 devel/sourcenav: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 devel/gb: Unmaintained and dead upstream
2021-04-01 dns/checkdns: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 dns/inadyn-mt: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 editors/gate: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 editors/thoteditor: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 emulators/cinc: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 emulators/e-uae: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 emulators/dtcyber: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 ftp/jftpgw: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 ftp/pureadmin: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-02 textproc/hs-pandoc-citeproc: Integrated into textproc/hs-pandoc
Use GCC for its SSE -> AltiVec translation:
In file included from src/ssw.cpp:38:
In file included from /usr/lib/clang/11.0.1/include/emmintrin.h:13:
In file included from /usr/lib/clang/11.0.1/include/xmmintrin.h:13:
/usr/lib/clang/11.0.1/include/mmintrin.h:33:5: error: use of undeclared identifier '__builtin_ia32_emms'; did you mean '__builtin_isless'?
__builtin_ia32_emms();
For ports optionally dependending on Python 2.7, just mark those options
as expired. Remove konquerer from the x11/kde-baseapps metaport and bump
its PORTREVISION.
Submitted by: rene
Reviewed by: portmgr, adridg, ehaupt, lme, madpilot, pizzamig, se, sunpoet, yuri
Approved by: portmgr
Differential Revision: https://reviews.freebsd.org/D28665
