The ont_fast5_api is a simple interface to HDF5 files of the Oxford
Nanopore .fast5 file format. It provides:
o Implementation of the fast5 file schema using h5py library
o Methods to interact with and reflect the fast5 file schema
o Tools to convert between multi_read and single_read formats
o Tools to compress/decompress raw data in files
ErmineJ performs analyses of gene sets in high-throughput genomics data
such as gene expression profiling studies. A typical goal is to
determine whether particular biological pathways are "doing something
interesting" in an experiment that generates long lists of candidates.
The software is designed to be used by biologists with little or no
informatics background (but if you do, you might be interested in the
CLI or the R support).
When switching the build dependency from devel/gradle to devel/gradle6,
the build is accidentally broken. This attempts to revert part of the
change and fix build.
Fixes: 55044a2200
Approved by: lwhsu (mentor, implicit), portmgr (fix build)
When switching the build dependency from devel/gradle to devel/gradle6,
the build is accidentally broken. This attempts to revert part of the
change and fix build.
Fixes: 55044a2200
Approved by: lwhsu (mentor, implicit), portmgr (fix build)
devel/gradle needs to be updated to 7.x, while some ports build failed
under the newer version, including:
- biology/jalview
- biology/igv
Updated them to use this devel/gradle6 until they officially support 7.x.
No functional changes for these ports.
Approved by: lwhsu (mentor)
Unfortunately, this version of FAHClient is not able to daemonize
successfully anymore. Even though the --daemon flag is passed, FAHClient
does not detach from the controlling terminal. In addition to that it
does not go into background. The --log seems to be broken as well as
since all the logs are printed to the terminal instead of the log file.
In order to alleviate those problems, use daemon(8).
PR: 250463
Changes: https://foldingforum.org/viewtopic.php?t=36307
MMseqs2 (Many-against-Many sequence searching) is a software suite to search
and cluster huge protein and nucleotide sequence sets. MMseqs2 is open source
GPL-licensed software implemented in C++ for FreeBSD, Linux, MacOS, and (via
via cygwin) Windows. The software is designed to run on multiple cores and
servers and exhibits very good scalability. MMseqs2 can run 10000 times
faster than BLAST. At 100 times its speed it achieves almost the same
sensitivity. It can perform profile searches with the same sensitivity as
PSI-BLAST at over 400 times its speed.
Per discussion with bapt on helping pkg handle the changing of these
deps and avoiding impossible upgrade senarios.
PR: 246767
Reviewed by: manu, bapt
Approved by: x11
Differential Revision: https://reviews.freebsd.org/D30824
SRA tools is a toolkit for using data in the INSDC Sequence Read Archives.
SRAs operated by International Nucleotide Sequence Database Collaboration
houses sequence reads and alignments generated by "next-gen" sequencers.
This port is a bit convoluted due to the fact that the sra-tools build
requires access to the ncbi-vdb source tree. Hence, ncbi-vdb is treated
as a submodule here rather than a separate library port. We are working
with upstream with hope for long-term improvements.
Biostar-Tools is a metaport for installing all the tools necessary to work
through the Biostar Handbook, except for bedGrapToBigWig, which has license
restrictions. If you need bedGraphToBigWig, run
cd /usr/ports/biology/ucsc-userapps && make install clean
From [1]
* What is new in gsl-2.7:
* fixed doc bug for gsl_histogram_min_bin (lhcsky at 163.com)
* fixed bug #60335 (spmatrix test failure, J. Lamb)
* fixed bug #36577
* clarified documentation on interpolation accelerators (V. Krishnan)
* fixed bug #45521 (erroneous GSL_ERROR_NULL in ode-initval2, thanks to M. Sitte)
* fixed doc bug #59758
* fixed bug #58202 (rstat median for n=5)
* added support for native C complex number types in gsl_complex
when using a C11 compiler
* upgraded to autoconf 2.71, automake 1.16.3, libtool 2.4.6
* updated exponential fitting example for nonlinear least squares
* added banded LU decomposition and solver (gsl_linalg_LU_band)
* New functions added to the library:
- gsl_matrix_norm1
- gsl_spmatrix_norm1
- gsl_matrix_complex_conjtrans_memcpy
- gsl_linalg_QL: decomp, unpack
- gsl_linalg_complex_QR_* (thanks to Christian Krueger)
- gsl_vector_sum
- gsl_matrix_scale_rows
- gsl_matrix_scale_columns
- gsl_multilarge_linear_matrix_ptr
- gsl_multilarge_linear_rhs_ptr
- gsl_spmatrix_dense_add (renamed from gsl_spmatrix_add_to_dense)
- gsl_spmatrix_dense_sub
- gsl_linalg_cholesky_band: solvem, svxm, scale, scale_apply
- gsl_linalg_QR_UD: decomp, lssolve
- gsl_linalg_QR_UU: decomp, lssolve, QTvec
- gsl_linalg_QR_UZ: decomp
- gsl_multifit_linear_lcurvature
- gsl_spline2d_eval_extrap
* bug fix in checking vector lengths in gsl_vector_memcpy (dieggsy@pm.me)
* made gsl_sf_legendre_array_index() inline and documented
- gsl_sf_legendre_nlm()
[1] http://git.savannah.gnu.org/cgit/gsl.git/tree/NEWS
PR: 256423
Exp-run by: antoine
Classify ChIP/ATAC-Seq peaks based on features provided in a GFF
Peaks are provided in a BED file sorted by chromosome and position.
The GFF must be sorted by chromosome and position, with gene-level
features separated by ### tags and each gene organized into
subfeatures such as transcripts and exons. This is the default for
common data sources.
- Upgrade math/blas, math/cblas, math/lapack, math/lapacke and math/xlapack
to 3.9.1;
Latest release notes at <http://www.netlib.org/lapack/lapack-3.9.1.html>
- Chase this upgrade in biology/treekin;
- Add a test target;
- Remove a conflict with math/openblas (PR 244296);
- Fix the build with Gcc10 (PR 247485).
PR: 247542
Approved by: expr-run by antoine@
LLVM on powerpc doesn't have libomp.
Same issue happens on armv6 and armv7 but someone has to test whether doing the same for those architectures is enough.
Since the previous update changed USES=python from 3.6+ to 3.7+, all
dependent ports must have USES=python:3.7+ as well, otherwise it breaks
the @py36 flavor.
PR: 255347
Reported by: sunpoet
For ports that already use the licenses framwork, merge the content of
RESTRICTED/NO_CDROM/LEGAL* entries into LICENSEs.
Approved by: rene
Differential Revision: https://reviews.freebsd.org/D30010
These are the command-line bioinformatics utilities associated with the UCSC
genome browser. Care has been taken to install only the freely available
tools. However, the license information at https://genome.ucsc.edu/license/
is not entirely clear and we may add non-free utilities in the future.
Contact UCSC if you are using this port for commercial purposes.
Entrez Direct (EDirect) provides access to the NCBI's suite of interconnected
databases (publication, sequence, structure, gene, variation, expression, etc.)
from a UNIX terminal window.
* Add missing dependency devel/py-nose that is required to build. With
Python 3.6/3.7 there are no build issues because the sdist contains
Python Eggs of "nose" for these versions.
While I'm here:
* Set NO_ARCH because the port has no architecture specific files.
* Make it concurrent safe, package installs a script and bump
PORTREVISION due package change.
PR: 253815
Approved by: portmgr (build fix)
MFH: No (The port was added after the 2021Q1 branch)
* Apply the same fix as in 9cb5898561 by
stripping libraries by wildcard paths.
* Also use PYTHONPREFIX_SITELIBDIR instead PYTHON_SITELIBDIR to make
the port PREFIX safe while I'm here.
PR: 253815
Approved by: python (with hat)
Genetic variant annotation and functional effect prediction toolbox. It
annotates and predicts the effects of genetic variants on genes and proteins
(such as amino acid changes).
This package includes BBMap, a short read aligner, as well as various other
bioinformatic tools. It is written in pure Java, can run on any platform, and
has no dependencies other than Java being installed (compiled for Java 6 and
higher). All tools are efficient and multithreaded.
Sequence reading library developed by the Ribosomal Database Project. It can
handle genbank, embl, fasta, fastq, sff and sto files, can read from files or
streams, and can handle indexing files.
CrossMap is a program for genome coordinates conversion between different
assemblies (such as hg18 (NCBI36) <=> hg19 (GRCh37)). It supports commonly used
file formats including BAM, CRAM, SAM, Wiggle, BigWig, BED, GFF, GTF, MAF VCF,
and gVCF.
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.
2021-04-01 ftp/wzdftpd: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 astro/roadmap: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 games/cosmo: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 games/bomberinstinct: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 games/drm: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 games/bygfoot: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 games/cre: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 irc/hybserv: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 irc/xaric: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 mail/elmo: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 misc/cave: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 security/bugs: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 security/dmitry: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 security/doorman: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 shells/esh: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 sysutils/cpu: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 textproc/libcrm114: No known users, dead upstream
2021-04-01 x11/wmmatrix: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 x11/wmxss: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 x11/tycoon: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 x11/xgrab: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 x11/xbanner: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 x11/bricons: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 x11/xmon: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 games/cavezofphear: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 astro/saoimage: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 audio/ksmp3play: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 audio/jamin: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 audio/musicbox-tag-editor: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 audio/nspmod: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 audio/cdplay: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 audio/gimmix: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 audio/ghostess: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 audio/wmrecord: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 audio/toolame: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 audio/shout: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 biology/grappa: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 biology/phylip: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 biology/lagan: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 cad/varkon: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 cad/transcalc: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 comms/seyon: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 comms/efax: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 converters/vda2fbd: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 converters/shftool: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 devel/openzz: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 devel/sourcenav: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 devel/gb: Unmaintained and dead upstream
2021-04-01 dns/checkdns: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 dns/inadyn-mt: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 editors/gate: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 editors/thoteditor: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 emulators/cinc: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 emulators/e-uae: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 emulators/dtcyber: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 ftp/jftpgw: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 ftp/pureadmin: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-02 textproc/hs-pandoc-citeproc: Integrated into textproc/hs-pandoc
Use GCC for its SSE -> AltiVec translation:
In file included from src/ssw.cpp:38:
In file included from /usr/lib/clang/11.0.1/include/emmintrin.h:13:
In file included from /usr/lib/clang/11.0.1/include/xmmintrin.h:13:
/usr/lib/clang/11.0.1/include/mmintrin.h:33:5: error: use of undeclared identifier '__builtin_ia32_emms'; did you mean '__builtin_isless'?
__builtin_ia32_emms();
For ports optionally dependending on Python 2.7, just mark those options
as expired. Remove konquerer from the x11/kde-baseapps metaport and bump
its PORTREVISION.
Submitted by: rene
Reviewed by: portmgr, adridg, ehaupt, lme, madpilot, pizzamig, se, sunpoet, yuri
Approved by: portmgr
Differential Revision: https://reviews.freebsd.org/D28665
vcf2hap is a simple tool for generating a .hap file from a VCF. The .hap file
is required by haplohseq. vcf2hap is extremely fast and requires a trivial
amount of memory regardless of the size of the VCF file.
ad2vdf extracts allelic depth info from a SAM stream and adds it to a
corresponding single-sample VCF file. SAM input is read via stdin and the VCF
input file is taken as a command-line argument. This allows expensive BAM/CRAM
decoding to be performed in parallel by a separate samtools process.
Vcf-split splits a multi-sample VCF into single-sample VCFs, writing thousands
of output files simultaneously. Parsing the TOPMed human chromosome 1 BCF
with bcftools takes two days, so extracting the 137,977 samples one at a time
or using thousands of parallel readers of the same file is impractical.
Vcf-split solves this by generating thousands of single-sample outputs during
a single sweep through the multi-sample input.
Biolibc is a library of fast, memory-efficient, low-level functions for
processing biological data. Like libc, it consists of numerous disparate,
general-purpose functions which could be used by a wide variety of
applications. These include functions for streaming common file formats such
as SAM and VCF, string functions specific to bioinformatics, etc.
biology/samtools: Update to 1.12
biology/bcftools: Update to 1.12
Numerous enhancements, performance improvements, and bug fixes since 1.11
Build-tested all other htslib dependents, no revbumps should be needed
Reported by: portscout
Generate random genomic data in FASTA/FASTQ, SAM, or VCF format, suitable for
small academic examples or test inputs of arbitrary size. Output can be piped
directly to programs or redirected to a file and edited to taste.
GCC is also necessary on powerpc64:
In file included from skbio/alignment/_ssw_wrapper.c:626:
In file included from skbio/alignment/_lib/ssw.h:17:
In file included from /usr/lib/clang/11.0.1/include/emmintrin.h:13:
In file included from /usr/lib/clang/11.0.1/include/xmmintrin.h:13:
/usr/lib/clang/11.0.1/include/mmintrin.h:50:12: error: invalid conversion between vector type '__m64' (vector of 1 'long long' value) and integer type 'int' of different size
return (__m64)__builtin_ia32_vec_init_v2si(__i, 0);
Use GCC:
In file included from skbio/alignment/_ssw_wrapper.c:626:
In file included from skbio/alignment/_lib/ssw.h:17:
In file included from /usr/lib/clang/11.0.1/include/emmintrin.h:13:
In file included from /usr/lib/clang/11.0.1/include/xmmintrin.h:13:
/usr/lib/clang/11.0.1/include/mmintrin.h:50:12: error: invalid conversion between vector type '__m64' (vector of 1 'long long' value) and integer type 'int' of different size
return (__m64)__builtin_ia32_vec_init_v2si(__i, 0);
* PyQt5: update to 5.15.3
This is a minor feature and bug-fix release. There are corresponding releases of the other PyQt5-related packages.
- Added the missing QImage.setAlphaChannel().
- Support for the QtNetworkAuth library has been moved to a separate PyQtNetworkAuth package.
- Wheels no longer bundle the corresponding Qt libraries and instead automatically install them from an external wheel.
* QScintilla2: update to 2.12.0
This adds support for Qt6 and removes support for Qt4.
- Change the new distname (again)i due to a conflict
- Use the new sip-build system
* devel/py-qtbuilder: update to 1.9.0
* devel/py-sip: fix flavor for sip-distinfo
PR: 253865
Exp-run by: antoine
Numerous small bug fixes and enhancements, code refactoring
py-xopen: Update to 1.1.0
Required by cutadapt 3.3
Drop python 3.5 support
Add isal support (not yet utilized in FreeBSD port)
