Switch to github submodules for most deps rather than patch build system
Fixes build on powerpc64 and aarch64, possibly others
Changes: https://github.com/vcflib/vcflib/tags
PR: 259622
Reported by: pkubaj
- Cap supported python verions with 3.9. Fails with 3.10:
Traceback (most recent call last):
File "/wrkdirs/usr/ports/biology/py-python-libsbml/work-py310/python-libsbml-5.19.0/libsbml_source/src/bindings/python/doc-converter/rewrite_pydoc.py", line 121, in <module>
from formatter import NullWriter, AbstractFormatter
ModuleNotFoundError: No module named 'formatter'
- Fix library stripping to unbreak port with python != 3.8
Approved by: portmgr blanket
File "/wrkdirs/usr/ports/biology/libsbml/work/libsbml-5.19.0/src/bindings/python/doc-converter/rewrite_pydoc.py", line 121, in <module>
from formatter import NullWriter, AbstractFormatter
ModuleNotFoundError: No module named 'formatter'
Approved by: portmgr blanket
The conflict checks compare the patterns first against the package
names without version (as reported by "pkg query "%n"), then - if
there was no match - agsinst the full package names including the
version (as reported by "pkg query "%n-%v").
Many CONFLICTS definitions used patterns like "bash-[0-9]*" to filter
for the bash package in any version. But that pattern is functionally
identical with just "bash".
Approved by: portmgr (blanket)
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.
deepTools contains useful modules to process the mapped reads data for
multiple quality checks, creating normalized coverage files in standard
bedGraph and bigWig file formats, that allow comparison between
different files (for example, treatment and control). Finally, using
such normalized and standardized files, deepTools can create many
publication-ready visualizations to identify enrichments and for
functional annotations of the genome.
py-bigwig is 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.
py2bit is a python extension, written in C, for quick access to 2bit
files for randomly accessible, packed nucleotide sequences. The
extension uses lib2bit for file access.
Utilities for working on SAM/BAM files from The Center for Statistical
Genetics at the University of Michigan School of Public Health. It
includes numerous functions such as splitting, merging, trimming reads,
filtering, validation, diff, etc.
In file included from bit-common.c:63:
In file included from ./bit-choice.h:23:
In file included from ./triangle.h:44:
./openmp.h:19:10: fatal error: 'omp.h' file not found
The option implied a dependency on gcc but clang got openmp support long ago.
Remove compiler:openmp from Mk/Uses/compiler.mk
For ports using USE=compiler:openmp, just remove it and make them build with
clang.
Fix conditionals when necessary
Bump PORTREVISION where appropriate
If problem arises, they can be addressed by using USE_GCC=yes
An update to the Porter's Handbook will follow.
Approved by: portmgr (bapt)
Differential Revision: https://reviews.freebsd.org/D31971
Standard kent userapps commands are installed under ${PREFIX}/userapps
because of multiple conflicts. The kent command turns the standard
commands into subcommands, so no special PATH is needed.
/usr/local/ucsc-userapps/bin/bigWigToBedGraph [args]
can be run as
kent bigWigToBedGraph [args]
Standard emboss commands are installed under a special prefix because
of multiple conflicts. The emboss command turns the standard commands
into subcommands, so no special PATH is needed.
/usr/local/emboss/bin/needle [args]
can be run as
emboss needle [args]
PREFIX is overridden by default in the port Makefile, so PREFIX/bin
is not normally in PATH. The purpose of emboss-shell is to prepend
PREFIX/bin to PATH to give access to emboss tools.
Also fix tcsh detection.
PR: 258316
pywgsim is a modified version of the wgsim short read simulator. The
code for wgsim has been modified to allow visualizing the simulated
mutations as a GFF file.
Biolibc-tools is a collection of simple fast, memory-efficient,
programs for processing biological data. These are simple programs
built on biolibc that are not complex enough to warrant a separate
project.
Major API overhaul
New classes for FASTA and FASTQ
Generate accessor and mutator functions for all classes
Generate man pages for all functions and macros
Export delimiter-separated-value class to libxtend
BFC is a standalone high-performance tool for correcting sequencing
errors from Illumina sequencing data. It is specifically designed for
high-coverage whole-genome human data, though also performs well for
small genomes.
FLASH (Fast Length Adjustment of SHort reads) is a very fast and
accurate software tool to merge paired-end reads from next-generation
sequencing experiments. FLASH is designed to merge pairs of reads when
the original DNA fragments are shorter than twice the length of reads.
The resulting longer reads can significantly improve genome assemblies.
They can also improve transcriptome assembly when FLASH is used to
merge RNA-seq data.
