genome (e.g. human genome). It has two major components, one for read shorter
than 150bp and the other for longer reads.
WWW: http://sourceforge.net/projects/bio-bwa/
PR: 203158
Submitted by: Jason Bacon <jwbacon@tds.net>
alignments of nucleotide or protein sequences. FastTree can handle alignments
with up to a million of sequences in a reasonable amount of time and memory.
WWW: http://www.microbesonline.org/fasttree/
PR: 203295
Submitted by: Jason Bacon <jwbacon@tds.net>
Some ports were already installing in the System domain, for these just remove the Makefile lines explicitly specifying the install domain.
The rest are installed in the Local domain, remove any overrides, update their pkg-plists and any explicit paths in the Makefiles and then bump port revision.
Approved by: bapt (mentor)
Differential Revision: https://reviews.freebsd.org/D2977
All applications in the ports tree works correctly with unicode version of wxGTK
Newer version of wxGTK are unicode only (3.0+)
Note that now WX_UNICODE macro is noop
- Move Perl's man1 files along with its man3 files.
- Move where Perl installs its modules man1 pages.
- Convert the ports installing man1 pages.
- Make different Perl versions installable at the same time.
Though you should note that only the default version can be used to
install Perl modules, and the non default Perl versions cannot use the
modules installed via ports if they contain .so as they are installed
in a version specific directory.
Reviewed by: bapt (the Mk bits)
Exp-run by: antoine
Sponsored by: Absolight
Differential Revision: https://reviews.freebsd.org/D3542
__sync_* functions family
- Remove BROKEN_ia64: it never had been first-class architecture, killed
officially in -CURRENT for a while now
- Sanitize installation commands and sort the knobs while I am here
configure script was passing `-faltivec' to the compiler, while this flag is
non-standard and only supported on Mac OS X/Darwin systems.
Also replace Apple-specific Altivec detection with querying the "hw.altivec"
sysctl instead.
UNIQUENAME was never unique, it was only used by USE_LDCONFIG and now,
we won't have conflicts there.
Use PKGBASE instead of LATEST_LINK in PKGLATESTFILE, the *only* consumer
is pkg-devel, and it works just fine without LATEST_LINK as pkg-devel
has the correct PKGNAME anyway.
Now that UNIQUENAME is gone, OPTIONSFILE is too. (it's been called
OPTIONS_FILE now.)
Reviewed by: antoine, bapt
Exp-run by: antoine
Sponsored by: Absolight
Differential Revision: https://reviews.freebsd.org/D3336
- While here: move knobs to their expected location, remove useless check
for ${PORT_OPTIONS:MDOCS} when installing documentation, standardize
Makefile headers
- Blixem bug fix in sorting features, RT 473624
- Compilation of the seqtools in parallel, RT 467905
- Fix bug with sorting by similarity/identity to first sequence (RT:473624)
- Fix an error compiling with multiple threads (RT:467905)
downside to having this set is that portscout cannot find new releases
when the username changes (which happens often in large projects with
multiple maintainers).
BCFtools is a set of utilities that manipulate variant calls in the
Variant Call Format (VCF) and its binary counterpart BCF. All
commands work transparently with both VCFs and BCFs, both
uncompressed and BGZF-compressed.
WWW: http://www.htslib.org/
PR: 199747
Submitted by: cartwright@asu.edu
