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* biology/py-bx-python: update to 0.10.0Ruslan Makhmatkhanov2024-01-282-5/+4
| | | | | | | | | | Update to 0.10.0. This release adds support for python 3.11 Changes: https://github.com/bxlab/bx-python/releases/tag/v0.10.0 PR: 276683 PR: 275494 Approved by: yuri (maintainer)
* */*: bump PORTREVISION after the upgrade to SuiteSparseThierry Thomas2024-01-282-2/+2
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* biology/htslib: Moved man to share/manMuhammad Moinur Rahman2024-01-272-7/+9
| | | | Approved by: portmgr (blanket)
* biology/biolibc: Impelled to share/manMuhammad Moinur Rahman2024-01-232-472/+475
| | | | Approved by: portmgr (blanket)
* biology/vsearch: Update to 2.27.0Jason W. Bacon2024-01-232-4/+4
| | | | | | | Add FASTQ support to usearch_global and search_exact Code cleanup and manual clarifications Reported by: portscout
* biology/py-pyrodigal: update 3.2.1 → 3.2.2Yuri Victorovich2024-01-212-4/+4
| | | | Reported by: portscout
* biology/py-htseq: Fix build with python-3.11Wen Heping2024-01-211-2/+2
| | | | | PR: 275494 Approved by: portmgr@(blanket, fix build)
* biology/ncbi-cxx-toolkit: Broken on armv7Yuri Victorovich2024-01-211-0/+1
| | | | Reported by: fallout
* biology/py-mrcfile: update 1.4.3 → 1.5.0Yuri Victorovich2024-01-202-5/+4
| | | | Reported by: portscout
* biology/bowtie2: Update to 2.5.3Jason W. Bacon2024-01-182-4/+4
| | | | | | | A few bug fixes Add option for faster indexing of small indexes Reported by: portscout
* biology/recombine: Remove expired portRene Ladan2024-01-186-268/+0
| | | | 2024-01-17 biology/recombine: Upstream advises to use biology/lamarc
* biology/seqio: Remove expired portMuhammad Moinur Rahman2024-01-188-354/+0
| | | | 2024-01-17 biology/seqio: Upstream last release was in 2000
* biology/sim4: Remove expired portMuhammad Moinur Rahman2024-01-184-40/+0
| | | | 2024-01-17 biology/sim4: Upstream last update was in 2005
* biology/metaeuk: fix build on powerpc64le by disabling openmp until libomp ↵Piotr Kubaj2024-01-161-2/+3
| | | | is fixed
* */*: bump PORTREVISION after the upgrade of SuiteSparse to v7.5.0Thierry Thomas2024-01-132-2/+2
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* biology/mashmap: Broken on armv7Yuri Victorovich2024-01-131-0/+1
| | | | Reported by: https://portsfallout.com/
* MANPREFIX: eliminate its usageBaptiste Daroussin2024-01-125-50/+51
| | | | While here move manpages to share/man
* biology/metaeuk: Add to NOT_FOR_ARCHS, and correct BROKENxx linesYuri Victorovich2024-01-121-1/+2
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* biology/metaeuk: Correct the reason in the BROKEN_xx lineYuri Victorovich2024-01-121-1/+1
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* biology/metaeuk: Not for 32-bit architecturesYuri Victorovich2024-01-121-2/+1
| | | | metaeuk produces wrong results there.
* biology/metaeuk: Broken on i386, armv7, powerpc64Yuri Victorovich2024-01-121-0/+4
| | | | Reported by: https://portsfallout.com/
* biology/btllib: Temporarily not for non-64-bit architecturesYuri Victorovich2024-01-121-0/+2
| | | | | | Until the breakage is fixed by the upstream. Reported by: https://portsfallout.com/
* biology/atac-seq: Update to 0.2.0Jason W. Bacon2024-01-102-2/+8
| | | | Add biology/py-macs3 dep to metaport
* biology/py-macs3: Peak caller for TF binding sitesJason W. Bacon2024-01-108-0/+104
| | | | | | | | | MACS (Model-based Analysis of ChIP-Seq) is a tool for identifying transcription factor (TF) binding sites. Such sites are generated by CHiP-Seq (CHromatin immuno-Precipitation sequencing) and ATAC-Seq (Assay for Transposase Accessible Chromatin Sequencing). MACS identifies "peaks" in the genome sequence, which are areas enriched in bound TFs or accessible chromatin.
* MAN?PREFIX: eleminate its usage and move man to share/manBaptiste Daroussin2024-01-105-33/+32
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* MAN[1-5]PREFIX: eleminate its usage and move man to share/manBaptiste Daroussin2024-01-094-22/+24
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* biology/mashmap: update 3.1.2 → 3.1.3Yuri Victorovich2024-01-052-5/+8
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* biology/ncbi-cxx-toolkit: update 27.0.0 → 28.0.0Yuri Victorovich2024-01-053-17/+6
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* */*: chase the upgrade of BLAS / LAPACK to 3.12.0Thierry Thomas2024-01-012-1/+2
| | | | PR: 275860
* lang/zig: update to 0.11.0Nathan Fisher2024-01-011-1/+1
| | | | | | Changes: https://ziglang.org/download/0.11.0/release-notes.html PR: 273124 Approved by: dch (maintainer)
* */*: chase the upgrade of SuiteSparseThierry Thomas2023-12-312-2/+2
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* */*: Sunset 12.4-RELEASE/12-STABLE from ports treeMuhammad Moinur Rahman2023-12-314-12/+1
| | | | | | | | | | | | | | | | | | | | | - Remove all references to defunct ARCH arm - Remove all references to defunct ARCH sparc64 - Remove x11-drivers/xf86-video-sunffb which requires defunct sparc64 ARCH - Remove sysutils/afbinit requires defunct sparc64 ARCH - Remove all references to bktr driver - Remove all references to defunct FreeBSD_12 - Remove all references to OSVERSION/OSREL corresponding to 12 - Remove conditionals in Mk/Uses/cabal.mk - Remove sparc reference from Mk/Uses/qt-dist.mk - Remove BROKEN_sparc64/NOT_FOR_ARCH=sparc64 - Remove BROKEN_FreeBSD_12* from: - Remove OpenSSL patches from: - Remove conditional flags for OSVERSION >= 1300000 to fixed flags. Also move conditional flags for non sparc64/arm ARCH to fixed flags. Reviewed by: brooks, jbeich, rene, salvadore Differential Revision: https://reviews.freebsd.org/D42068
* biology/ucsc-userapps: Replace dependenciesMuhammad Moinur Rahman2023-12-301-2/+1
| | | | | | | | | | Currently their is a hardcoded dependency on mysql57-client which is about to be removed. Ports depending on mysql should always use USES=mysql rather than hardcoded *_DEPENDS. As I do not have a licensed version of this application for now switch to USES=mysql. This should not affect the cluster build at all as this is a RESTRICTED ports. Approved by: portmgr (blanket)
* biology/diamond: Fix build on main after import of clang 17Dimitry Andric2023-12-292-0/+15
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* */*: Refactor with IGNORE_WITH_MYSQLMuhammad Moinur Rahman2023-12-291-1/+1
| | | | | | | | | | | | | | | | | | | | | | | | | - There are multiple ports which has MYSQL options and are non-DEFAULT. Most of the time committers actually forget to check with the OPTION enabled and in some cases they are BROKEN with newr versions of mysql. So test with different versions of mysql and mark IGNOPRE_WITH_MYSQL appropriately. Due to the EOL of 5.7 this has not been checked. - Unbreak sysutils/cfengine* with MySQL 8.0 and later - The primary purpose of running this check is having statistics of the MySQL usability over MariaDB to explore the future possibility of shifting to MariaDB as the default as major ports upstream have moved their codebase to support MariaDB over MySQL. - The following actions will also be taken after the sunset of MySQL 5.7 If a port is broken on all instances of MySQL/MariaDB: - If a port has the option of multiple DB backends and MySQL is the default then the DEFAULT will be changed to PGSQL/SQLITE before 2024Q1. And the OPTION will be removed before 2024Q2. If a MAINTAINER is aware about such cases and want to prefer PGSQL over SQLITE or vice versa please do so at your own accord. Otherwise PGSQL will be preferred over SQLITE. - If a port has the option of multiple DB backends and MySQL is not the default then the the OPTION will be removed before 2024Q1. Approved by: portmgr (blanket)
* biology/libbigwig: Fix name-clashing in roundupJason E. Hale2023-12-281-0/+29
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Rename the roundup method defined in bwValues.c as it clashes with the roundup macro defined in sys/param.h /wrkdirs/usr/ports/biology/libbigwig/work/libBigWig-0.4.7/bwValues.c:9:35: error: too few arguments provided to function-like macro invocation static uint32_t roundup(uint32_t v) { ^ /usr/include/sys/param.h:300:9: note: macro 'roundup' defined here ^ /wrkdirs/usr/ports/biology/libbigwig/work/libBigWig-0.4.7/bwValues.c:9:24: error: expected ';' after top level declarator static uint32_t roundup(uint32_t v) { ^ ; /wrkdirs/usr/ports/biology/libbigwig/work/libBigWig-0.4.7/bwValues.c:350:30: error: too few arguments provided to function-like macro invocation o->m = roundup(o->l+1); ^ /usr/include/sys/param.h:300:9: note: macro 'roundup' defined here ^ /wrkdirs/usr/ports/biology/libbigwig/work/libBigWig-0.4.7/bwValues.c:370:30: error: too few arguments provided to function-like macro invocation o->m = roundup(o->l+1); ^ /usr/include/sys/param.h:300:9: note: macro 'roundup' defined here ^ 4 errors generated. Approved by: portmgr (blanket)
* biology/p5-Bio-DB-NCBIHelper: Update to 1.7.8Po-Chuan Hsieh2023-12-252-5/+5
| | | | | | - Update LICENSE_FILE Changes: https://metacpan.org/dist/Bio-DB-NCBIHelper/changes
* biology/hyphy: Update to 2.5.58Joseph Mingrone2023-12-233-4/+6
| | | | | Changes: https://github.com/veg/hyphy/releases/tag/2.5.58 Sponsored by: The FreeBSD Foundation
* biology/taxonkit: update 0.15.0 → 0.15.1Yuri Victorovich2023-12-202-7/+6
| | | | Reported by: portscout
* biology/py-pyrodigal: update 3.1.1 → 3.2.1Yuri Victorovich2023-12-202-4/+4
| | | | Reported by: portscout
* biology/gatk: update 4.4.0.0 → 4.5.0.0Yuri Victorovich2023-12-182-8/+8
| | | | ChangeLog: https://github.com/broadinstitute/gatk/releases/tag/4.5.0.0
* biology/sim4: fix EXPIRATION_DATERene Ladan2023-12-181-1/+1
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* biology/recombine: Mark DEPRECATEDMuhammad Moinur Rahman2023-12-171-4/+8
| | | | | | | - Upstream last release was in 2002 - Upstream advises to use bioloby/lamarc - Set EXPIRATION_DATE 2024-01-17 - Pet portclippy
* biology/seqio: Mark DEPRECATEDMuhammad Moinur Rahman2023-12-171-7/+11
| | | | | | - Upstream last release was in 2000 - Set EXPIRATION_DATE 2024-01-17 - Pet portclippy
* biology/sim4: Mark DEPRECATEDMuhammad Moinur Rahman2023-12-171-0/+3
| | | | | - Upstream last update was in 2005 - Set EXPIRATION_DATE 2024-01-17
* biology/py-pybigwig: Update to 0.3.22Jason W. Bacon2023-12-163-4/+33
| | | | | | | No real changes from 0.3.21 Add patch to resolve conflict with roundup() macro in sys/param.h Reported by: pkg-fallout
* biology/R-cran-Biobase: New portMuhammad Moinur Rahman2023-12-154-0/+24
| | | | | | | Functions that are needed by many other packages or which replace R functions. WWW: https://bioconductor.org/packages/Biobase
* biology/R-cran-BiocGenerics: New portMuhammad Moinur Rahman2023-12-154-0/+21
| | | | | | The package defines many S4 generic functions used in Bioconductor. WWW: https://bioconductor.org/packages/release/bioc/html/BiocGenerics.html
* biology/R-cran-BiocManager: New portMuhammad Moinur Rahman2023-12-154-0/+22
| | | | | | | | | The BiocManager package, as the modern successor package to BiocInstaller, allows users to install and manage packages from the Bioconductor project. Bioconductor focuses on the statistical analysis and comprehension of high-throughput genomic data. WWW: https://bioconductor.github.io/BiocManager/
* devel/grpc: Update to 1.60.0Po-Chuan Hsieh2023-12-141-0/+1
| | | | | | - Bump PORTREVISION of dependent ports for shlib change Changes: https://github.com/grpc/grpc/releases
generated by cgit v1.2.3 (git 2.25.1) at 2024-06-22 14:39:43 +0000