MoChA is a bcftools plugin released under the MIT license for mosaic
chromosomal alteration detection and analysis from DNA microarray or
whole genome sequence data. It can be used both with Illumina and
Affymetrix data. It can also be used for detection of germline copy
number variants. Data can be prepared in usable file formats using the
gtc2vcf plugin.
Only sra-tools is still non-portable, but it will take some time to
add support for other architectures. In the meantime, allow aarch64
and powerpc64 users to have a biostar-tools package.
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)
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").
Approved by: portmgr (blanket)
pkg-static: Unable to access file /wrkdirs/usr/ports/biology/hhsuite/work/stage/usr/local/bin/hhalign_omp:No such file or directory
pkg-static: Unable to access file /wrkdirs/usr/ports/biology/hhsuite/work/stage/usr/local/bin/hhblits_ca3m:No such file or directory
pkg-static: Unable to access file /wrkdirs/usr/ports/biology/hhsuite/work/stage/usr/local/bin/hhblits_omp:No such file or directory
pkg-static: Unable to access file /wrkdirs/usr/ports/biology/hhsuite/work/stage/usr/local/bin/hhsearch_omp:No such file or directory
powerpc doesn't have LLVM with libomp.
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.
