HISAT2 is a fast and sensitive alignment program for mapping next-generation
sequencing reads (both DNA and RNA) to a population of human genomes (as well
as to a single reference genome).
Release numerous ports to ports@
I've been retired for a few years, and it is unlikely I will be doing
any more scientific computing support in the future. I have continued
to maintain ~160 ports to the best of my ability, mainly as a favor to
the community, but I can no longer justify the time and effort
required. I am therefore releasing most of my scientific ports, along
with a few others, to ports@. I will continue to maintain ports I am
actively using and those for which I am upstream.
biology/hisat2: Update to 2.2.3
No functional changes. Upstream added explicit support for ARM,
which is not relevant since the FreeBSD port has been using SIMDE
patches for some time. Still waiting on upstream to act:
https://github.com/DaehwanKimLab/hisat2/pull/251
Upgrading the port just to silence portscout.
Reported by: portscout
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)
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 )
biology/hisat2: Add support for powerpc64* and aarch64
Minor patches to utilize simde to emulate SSE (from Debian package)
Add -fsigned-char since clang defaults to unsigned on aarch64
Remove -DPOPCNT_CAPABILITY (not truly safe even on amd64)
