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pkgsrc/biology
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mrg 0a843265c7 various fixes for arm64 big endian support. 
most of these simply extend matching from "aarch64" to "aarch64eb"
in various forms of code.  most remaining uses in pkgsrc of
"MACHINE_ARCH == aarch64" are because of missing aarch64eb support,
such as most of the binary-bootstrap requiring languages like rust,
go, and java.

no pkg-bump because this shouldn't change packages on systems that
could already build all of these.
2021-04-25 07:51:24 +00:00
..
ad2vcf biology/ad2vcf: import ad2vcf-0.1.2 2021-03-24 18:19:21 +00:00
arka biology/arka: document 2 instances of char as array index 2020-05-03 14:58:18 +00:00
azara *: recursive bump for libffi 2020-03-08 16:47:24 +00:00
bcftools biology/htslib: Update to 1.12 2021-03-20 18:17:07 +00:00
bedtools biology/bedtools: Update to 2.30.0 2021-02-08 01:49:25 +00:00
biolibc biology/biolibc: import biolibc-0.1.1 2021-03-24 15:20:08 +00:00
bioperl bioperl: update to 1.7.7. 2020-09-06 20:07:47 +00:00
bodr revbump for textproc/icu 2021-04-21 11:40:12 +00:00
bowtie2 biology/bowtie2: import bowtie2-2.4.2 2021-01-21 17:30:12 +00:00
bwa *: bump PKGREVISION for perl-5.32. 2020-08-31 18:06:29 +00:00
canu revbump for boost-libs 2021-04-21 13:24:06 +00:00
cdhit *: bump PKGREVISION for perl-5.32. 2020-08-31 18:06:29 +00:00
chemical-mime-data chemical-mime-data: comment out dead sites 2017-12-24 09:42:12 +00:00
chemtool *: revbump after fontconfig bl3 changes (libuuid removal) 2020-08-17 20:17:15 +00:00
clustalw
coalesce *: remove dead download locations 2021-04-21 09:12:23 +00:00
coordgenlibs revbump for boost-libs 2021-04-21 13:24:06 +00:00
fastDNAml *: remove dead download location 2021-04-21 09:11:13 +00:00
fastp biology/fastp: document possible array[char] bug 2020-05-25 05:18:35 +00:00
fastqc biology/fastqc: import fastqc-0.11.9 2021-01-20 15:57:17 +00:00
fluctuate
gabedit *: revbump after fontconfig bl3 changes (libuuid removal) 2020-08-17 20:17:15 +00:00
generand biology/generand: import generand-0.1.2 2021-03-21 14:23:46 +00:00
genesplicer
glimmer Sort PLIST files. 2018-01-01 22:29:15 +00:00
gnome-chemistry-utils revbump for textproc/icu 2021-04-21 11:40:12 +00:00
gp all: migrate homepages from http to https 2020-01-26 17:30:40 +00:00
gromacs revbump for textproc/icu 2021-04-21 11:40:12 +00:00
hisat2 Revbump packages with a runtime Python dep but no version prefix. 2020-12-04 20:44:57 +00:00
hmmer
htslib revbump for boost-libs 2021-04-21 13:24:06 +00:00
igv biology/igv: import igv-2.9.2 2021-02-24 13:54:25 +00:00
kallisto kallisto: remove patches that were removed from distinfo during update 2020-07-30 07:59:19 +00:00
lucy mark packages that fail with -Werror=char-subscripts 2020-05-20 06:09:03 +00:00
maeparser revbump for boost-libs 2021-04-21 13:24:06 +00:00
molsketch revbump for textproc/icu 2021-04-21 11:40:12 +00:00
mopac
mpqc math/blas, math/lapack: Install interchangeable BLAS system 2020-10-12 21:51:57 +00:00
mummer *: bump PKGREVISION for perl-5.32. 2020-08-31 18:06:29 +00:00
ncbi-blast+ revbump for boost-libs 2021-04-21 13:24:06 +00:00
nut all: migrate some SourceForge homepage URLs back from https to http 2020-01-26 05:26:08 +00:00
openbabel revbump for boost-libs 2021-04-21 13:24:06 +00:00
p5-Bio-ASN1-EntrezGene p5-Bio-ASN1-EntrezGene: update to 1.73. 2020-09-06 19:43:03 +00:00
pdbalign
phylip *: remove dead download locations 2021-04-21 09:12:23 +00:00
plink math/blas, math/lapack: Install interchangeable BLAS system 2020-10-12 21:51:57 +00:00
plinkseq Multiple packages: Replace obsolete maintainer email 2019-01-13 22:06:42 +00:00
primer3 *: Convert broken sourceforge HOMEPAGEs back to http 2020-03-20 11:57:22 +00:00
profit
puzzle biology: align variable assignments 2019-11-02 22:09:00 +00:00
py-biopython math/blas, math/lapack: Install interchangeable BLAS system 2020-10-12 21:51:57 +00:00
py-cutadapt py-cutadpt: add missing build dependency 2021-04-22 08:36:59 +00:00
py-dnaio py-dnaio: mark incompatible with python 2 2021-04-22 08:38:59 +00:00
py-mol math/blas, math/lapack: Install interchangeable BLAS system 2020-10-12 21:51:57 +00:00
py-pydicom py-pydicom: Update to 1.3.0 2019-10-01 14:45:29 +00:00
R-popbio biology/R-popbio: import R-popbio-2.7 2020-08-10 18:18:46 +00:00
rasmol
samtools biology/htslib: Update to 1.12 2021-03-20 18:17:07 +00:00
sewer *: remove dead download location 2021-04-21 09:11:13 +00:00
stacks Revbump packages with a runtime Python dep but no version prefix. 2020-12-04 20:44:57 +00:00
stride Comment out dead sites. 2017-09-04 18:00:49 +00:00
trimmomatic biology/trimmomatic: import Trimmomatic-0.38 2018-07-25 15:14:32 +00:00
vcf-split biology/vcf-split: import vcf-split-0.1.1 2021-03-24 15:22:29 +00:00
vcf2hap biology/vcf2hap: import vcf2hap-0.1.2 2021-03-24 18:22:53 +00:00
vsearch various fixes for arm64 big endian support. 2021-04-25 07:51:24 +00:00
xylem all: migrate homepages from http to https 2020-01-26 17:30:40 +00:00
Makefile biology/Makefile: Add vcf2hap 2021-03-24 18:23:33 +00:00