bacon b3c5608461 biology/bowtie2: Update to 2.5.4 ... A few bug fixes and minor enhancements Changes: https://github.com/BenLangmead/bowtie2/releases		2024-05-24 11:32:57 +00:00
..
R-popbio	…
ad2vcf	biology/ad2vcf: Update to 0.1.6.19	2024-05-19 12:56:54 +00:00
arka	…
atac-seq	biology/atac-seq: Update to 1.5.0	2024-04-11 14:49:41 +00:00
azara	Bump all dependent packages of wayland (belatedly)	2022-08-11 05:08:00 +00:00
balance-tui	biology/balance-tui: update to 0.1.2	2023-06-06 19:25:14 +00:00
bcftools	*: recursive bump for Python 3.11 as new default	2023-08-14 05:23:45 +00:00
beagle	…
bedtools	biology/bedtools: Update to 2.31.1	2023-11-08 16:46:44 +00:00
biolibc	biology/biolibc: Update to 0.2.6.4	2024-05-19 12:54:59 +00:00
biolibc-tools	biolibc-tools: fix installation of manpages for users of a custom PKGMANDIR	2023-12-21 08:50:24 +00:00
bioperl	*: recursive bump for perl 5.38	2023-07-06 09:38:07 +00:00
bodr	*: recursive bump for icu 74.1	2023-11-08 13:18:02 +00:00
bowtie2	biology/bowtie2: Update to 2.5.4	2024-05-24 11:32:57 +00:00
bwa	biology/bwa: Add support for aarch64 via devel/simde	2023-05-18 14:05:15 +00:00
canu	biology/canu: Update to 2.2nb3	2024-02-23 14:30:58 +00:00
cdhit	*: recursive bump for perl 5.36	2022-06-28 11:30:51 +00:00
chemtool	*: bump for cairo buildlink3.mk change	2024-04-07 07:33:26 +00:00
chip-seq	biology/chip-seq: Update to 1.2	2023-12-23 16:35:38 +00:00
clustalw	…
coalesce	…
coordgenlibs	revbump for boost-libs	2023-12-29 18:24:34 +00:00
fasda	biology/fasda: Update to 0.1.5	2023-10-28 20:33:41 +00:00
fastDNAml	…
fastp	biology/fastp: Update to 0.22.0	2023-06-01 13:03:53 +00:00
fastq-trim	fastq-trim: fix installation when using custom PKGMANDIR	2023-12-24 10:18:27 +00:00
fastqc	*: recursive bump for perl 5.36	2022-06-28 11:30:51 +00:00
fastx-toolkit	biology/fastx-toolkit: Unbreak build on Darwin	2023-09-25 18:01:35 +00:00
filter-fastq	*: recursive bump for Python 3.11 as new default	2023-08-14 05:23:45 +00:00
fluctuate	…
gabedit	*: bump for cairo buildlink3.mk change	2024-04-07 07:33:26 +00:00
generand	Change MAINTAINER= to OWNER= on mission-critical packages	2022-12-28 15:27:15 +00:00
genesplicer	…
gffread	biology/gffread: GFF/GTF format conversions, filtering, etc	2022-11-06 23:01:17 +00:00
glimmer	…
gp	…
gromacs	*: recursive bump for icu 74.1	2023-11-08 13:18:02 +00:00
hisat2	*: recursive bump for Python 3.11 as new default	2023-08-14 05:23:45 +00:00
hmmer	biology/hmmer: fix build on NetBSD/powerpc.	2024-04-22 13:44:10 +00:00
htslib	*: recursive bump for gnutls p11-kit option	2024-05-16 06:14:30 +00:00
igv	Switch USE_JAVA2 from 9 to 11, as actually requires 11	2023-11-18 15:02:53 +00:00
kallisto	biology/kallisto: Update to 0.50.1	2023-11-04 14:35:07 +00:00
libpll	biology/libpll: only works on Linux	2024-01-24 17:35:53 +00:00
lucy	…
maeparser	revbump for boost-libs	2023-12-29 18:24:34 +00:00
microsynteny-tools	microsynteny-tools: propagate python limitations	2023-11-06 20:21:32 +00:00
miniasm	miniasm: Honour LDFLAGS. Hopefully fixes build on platforms where zlib	2023-07-09 08:31:06 +00:00
minimap2	minimap2: Honour LDFLAGS when linking	2024-05-18 00:27:16 +00:00
molsketch	*: bump for cairo buildlink3.mk change	2024-04-07 07:33:26 +00:00
mopac	mopac: pkgsrc-users can't be OWNER, make it MAINTAINER	2023-12-15 13:50:36 +00:00
mpqc	*: recursive bump for perl 5.36	2022-06-28 11:30:51 +00:00
mummer	*: recursive bump for perl 5.36	2022-06-28 11:30:51 +00:00
ncbi-blast+	*: recursive bump for gnutls p11-kit option	2024-05-16 06:14:30 +00:00
nutsqlite	nutsqlite: make PKGNAME match directory name	2024-04-11 18:21:04 +00:00
openbabel	*: bump for cairo buildlink3.mk change	2024-04-07 07:33:26 +00:00
p5-Bio-ASN1-EntrezGene	*: recursive bump for perl 5.38	2023-07-06 09:38:07 +00:00
pdbalign	…
peak-classifier	biology/peak-classifier: Update to 0.1.4.13	2023-10-28 20:37:17 +00:00
phylip	…
plink	biology/plink: Unbreak build on Darwin	2023-12-24 16:26:42 +00:00
plinkseq	*: recursive bump for protobuf 26.1	2024-04-05 14:00:56 +00:00
primer3	*: Mark packages that were originally identified as requiring	2023-08-02 19:20:16 +00:00
profit	fetch from backup	2023-12-23 02:13:49 +00:00
puzzle	…
py-bcbio-gff	biology/py-bcbio-gff: Read and write GFF files	2023-11-05 17:51:31 +00:00
py-biopython	py-biopython: add missing setuptools tool	2023-11-15 08:58:06 +00:00
py-cutadapt	biology/py-cutadapt: Release to pkgsrc-users@	2024-04-10 23:47:55 +00:00
py-dna-features-viewer	py-dna-features-viewer: Fix PYTHON_VERSIONS_INCOMPATIBLE.	2023-11-06 20:05:34 +00:00
py-dnaio	biology/py-dnaio: Release to pkgsrc-users@	2024-04-10 23:48:52 +00:00
py-macs2	py-macs2: add missing tool dependencies	2023-12-25 10:21:17 +00:00
py-macs3	biology/py-macs3: Update to 3.0.1	2024-02-28 13:38:48 +00:00
py-multiqc	biology/py-multiqc: PYTHON_VERSIONS_INCOMPATIBLE+=38	2023-07-23 00:26:31 +00:00
py-pydicom	py-pydicom: updated to 2.4.4	2024-01-14 18:29:06 +00:00
racon	*: remove pkg-config from tools where no buildlink3.mk file is included	2022-07-25 11:12:18 +00:00
rasmol	*: Remove many GCC_REQD for particularly old GCCs	2023-07-17 22:00:22 +00:00
rna-seq	biology/rna-seq: Update to 1.3.0	2024-04-11 14:46:53 +00:00
rna-star	biology/rna-star: Fix build on Darwin 21.6.0 x86	2023-08-29 21:49:56 +00:00
samtools	*: recursive bump for Python 3.11 as new default	2023-08-14 05:23:45 +00:00
seqtk	seqtk: Add missing zlib dependency	2023-07-09 08:41:40 +00:00
sewer	…
sra-tools	sra-tools: add missing Python dependency	2023-11-24 16:37:29 +00:00
stacks	*: recursive bump for Python 3.11 as new default	2023-08-14 05:23:45 +00:00
stride	…
stringtie	biology/stringtie: RNA-Seq assembly and quantification	2023-08-12 14:58:35 +00:00
trimmomatic	…
vcf-split	biology/vcf-split: Update to 0.1.5.10	2023-10-28 20:39:31 +00:00
vcf2hap	biology/vcf2hap: Update to 0.1.6.7	2023-10-28 20:41:05 +00:00
vsearch	biology/vsearch: Update to 2.27.1	2024-04-08 21:53:32 +00:00
xmakemol	biology/xmakemol: import package from wip.	2022-12-30 18:17:48 +00:00
xylem	…
Makefile	biology/Makefile: update for nut -> nutsqlite	2024-04-11 18:47:42 +00:00