A standalone program for mapping and aligning cDNA sequences to a
genome. The program maps and aligns a single sequence with minimal
startup time and memory requirements, and provides fast batch
processing of large sequence sets. The program generates accurate
gene structures, even in the presence of substantial polymorphisms
and sequence errors, without using probabilistic splice site models.
Methodology underlying the program includes a minimal sampling
strategy for genomic mapping, oligomer chaining for approximate
alignment, sandwich DP for splice site detection, and microexon
identification with statistical significance testing.
===> The following configuration options are available for gmap-2025.07.31_1:
SIMD=off: Use CPU-specific optimizations
===> Use 'make config' to modify these settings
The default configuration for the gmap port disables all optimizations
to maintain compatibility with the widest range of systems.
To get a binary optimized for your system please deinstall gmap and
build from ports using "make config" to enable the SIMD option.
biology/gmap: enable on aarch64 and powerpc64
The aarch64 failure noted in the FIXME was the same broken __builtin_clz
probe that compiled x86 asm("bsr") on powerpc64le, so the configure
cache seeds from the previous commit fix it. powerpc64 builds as well;
the source has explicit big-endian support.
biology/gmap: fix build on powerpc64le
configure probes __builtin_clz and friends with AC_CHECK_DECL, which
always fails with clang, and its asm("bsr") probe is dead code at -O2,
so HAVE_ASM_BSR is defined on every architecture and x86 inline asm is
compiled on powerpc64le. Seed the declaration cache so the builtins are
detected and used.
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.
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: 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 )
Update CONFLICTS definitions in categories a* to c*
Update the CONFLICTS definitions of ports in the following categories:
- accessibility
- archivers
- audio
- benchmarks
- biology
- cad
- chinese
- comms
- converters
An attempt has been made to use generic conflicts patterns that do not
have to be updated whenever a new version of a conflicting port is
added to the ports system.
There is a misunderstanding that the port being built/installed has to
be omitted from the conflicts pattern. This is not true - the port
being built is implicitly non-conflicting due to logic in bsd.port.mk.
Approved by: portmgr (implicit)
Fix CONFLICTS entries of multiple ports
There have been lots of missing CONFLICTS_INSTALL entries, either
because conflicting ports were added without updating existing ports,
due to name changes of generated packages, due to mis-understanding
the format and semantics of the conflicts entries, or just due to
typoes in package names.
This patch is the result of a comparison of all files contained in
the official packages with each other. This comparison was based on
packages built with default options and may therefore have missed
further conflicts with optionally installed files.
Where possible, version numbers in conflicts entries have been
generalized, some times taking advantage of the fact that a port
(Only the first 15 lines of the commit message are shown above )
Style: improve ONLY_FOR_ARCHS_REASON (grammar, markup, etc.)
ONLY_FOR_ARCHS_REASON is used as part of the sentence and thus should
start with lower-case letter and not end with a period which is added
by the framework, similar to other knobs like BROKEN, IGNORE, et al.
While here, remove needless quoting, add missing Oxford comma, expand
contractions and jargonisms, use correct spelling for proper names.
biology/gmap: Upgrade to 2020.09.12
First upgrade in 5 years, so numerous improvements
Unsure if powerpc is still supported upstream
Code mentions power8, but does not build on my Mac G5
Enable workaround for building on powerpc64.
Autoconf reports that HAVE_ASM_BSR is true (1). However, it's a false
positive.
I do not have enough knowledge of autoconf to fix this problem correctly,
so fix src/config.h in post-configure. Patches welcome.
A proper fix will most likely also fix the build on other tier-2 archs,
but I have not taken the time to test that yet.
Approved by: portmgr (tier-2 blanket)
Multiple ports:
Change maintainer email bacon4000@gmail.com to jwb@FreeBSD.org
Remove Created by comments for same user
Approved by: jrm (mentor)
Differential Revision: https://reviews.freebsd.org/D14128
Try to bring some consistency to ports that have x86-specific pieces.
- in general, if we think that the code is not architecture-specific,
and instead just enables x86 assembler by default, those should
use BROKEN rather than IGNORE. This will allow them to be attempted
with TRYBROKEN.
- spell i386 as x86.
- spell asm as assembler.
- pet portlint.
These changes should have no effect on tier-1 builds.
Approved by: portmgr (tier-2 blanket)
For ports that are marked BROKEN on armv6, and also fail to build on
armv7, mark them so.
This is part two of a multipart commit to bring armv7 ports to parity
with armv6.
Approved by: portmgr (tier-2 blanket)
Obtained from: lonesome.com -exp run
Mark some ports failing on power64. In cases where the error message
was a stub, provide a real one.
While here, pet portlint.
Approved by: portmgr (tier-2 blanket)
- Update to 2015.09.21
- Add License
- Add SIMD option disabled by default to avoid creating official
packags with CPU specific optimizations
- Add pkg-message explaining how to get an optimized binary
- Assign maintainership to submitter
PR: 203334
Submitted by: jwbacon at tds.net
Approved by: Maintainer timeout
Support stage
Convert USE_GMAKE to USES=gmake
Add dependency on perl which the port need and was getting by chance
bump portrevision, dependencies has changed
Update CONFIGURE_ARGS for how we pass CONFIGURE_TARGET to configure script.
Specifically, newer autoconf (> 2.13) has different semantic of the
configure target. In short, one should use --build=CONFIGURE_TARGET
instead of CONFIGURE_TARGET directly. Otherwise, you will get a warning
and the old semantic may be removed in later autoconf releases.
To workaround this issue, many ports hack the CONFIGURE_TARGET variable
so that it contains the ``--build='' prefix.
To solve this issue, under the fact that some ports still have
configure script generated by the old autoconf, we use runtime detection
in the do-configure target so that the proper argument can be used.
Changes to Mk/*:
- Add runtime detection magic in bsd.port.mk
(Only the first 15 lines of the commit message are shown above )
Add gmap 2006.04.21, a Genomic Mapping and Alignment Program for mRNA
and EST Sequences.
PR: ports/103651
Submitted by: Bob Zimmermann <rpz at cse.wustl.edu>
