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nixpkgs-suyu/pkgs/applications/science/biology
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Patrick Hilhorst 593e11fd94
treewide: fix redirected urls 
According to https://repology.org/repository/nix_unstable/problems, we have a
lot of packages that have http links that redirect to https as their homepage.
This commit updates all these packages to use the https links as their
homepage.

The following script was used to make these updates:

```

curl https://repology.org/api/v1/repository/nix_unstable/problems \
    | jq '.[] | .problem' -r \
    | rg 'Homepage link "(.+)" is a permanent redirect to "(.+)" and should be updated' --replace 's@$1@$2@' \
    | sort | uniq > script.sed

find -name '*.nix' | xargs -P4 -- sed -f script.sed -i
```
2020-01-22 11:26:22 +01:00
..
ants ants: use itk 4.x 2019-09-13 11:54:21 +02:00
aragorn aragorn: init at 1.2.38 (#58354) 2019-04-29 07:18:03 -04:00
bayescan bayescan: init at 2.1 (#68191) 2020-01-09 12:38:53 -05:00
bcftools bcftools: 1.9 -> 1.10.2 2019-12-22 20:00:29 -08:00
bedtools bedtools: 2.29.1 -> 2.29.2 2019-12-18 10:39:25 +11:00
bftools bftools: 5.9.2 -> 6.3.0 2019-12-06 02:11:00 -08:00
blast blast: init at 2.10.0 (#61430) 2020-01-07 20:14:18 +01:00
bowtie2 treewide: name -> pname (easy cases) (#66585) 2019-08-15 13:41:18 +01:00
bwa treewide: name -> pname (easy cases) (#66585) 2019-08-15 13:41:18 +01:00
cd-hit cd-hit: init at 4.8.1 2019-06-13 14:35:13 +02:00
clustal-omega treewide: name -> pname (easy cases) (#66585) 2019-08-15 13:41:18 +01:00
cmtk treewide: remove redundant rec 2019-08-28 11:07:32 +00:00
conglomerate
dcm2niix dcm2niix: 1.0.20190410 -> 1.0.20190902 2019-10-22 16:31:19 -07:00
deeptools deeptools: init at 3.3.1 2019-11-04 02:42:36 -08:00
delly delly: init at 0.8.1 (#70871) 2019-10-10 22:08:45 -04:00
diamond treewide: remove redundant rec 2019-08-28 11:07:32 +00:00
ecopcr
eggnog-mapper treewide: remove redundant quotes 2019-09-08 23:38:31 +00:00
emboss
est-sfs est-sfs: init at 2.03 2019-07-16 13:55:59 +02:00
exonerate exonerate: init at 2.4.0 2019-04-19 14:58:57 +02:00
EZminc EZminc: 2017-08-29 -> 2019-07-25; mark unbroken 2019-10-26 09:55:30 -07:00
freebayes freebayes: 2017-08-23 -> 1.3.1 (2019-06-03) 2019-11-20 09:10:31 -08:00
hisat2 treewide: name -> pname (easy cases) (#66585) 2019-08-15 13:41:18 +01:00
hmmer hmmer: 3.2.1 -> 3.3 2019-11-27 18:40:23 -08:00
igv maintainer: mimadrid: update github username and personal data 2019-09-14 12:15:46 +02:00
inormalize
itsx treewide: name -> pname (easy cases) (#66585) 2019-08-15 13:41:18 +01:00
iv iv: only use patchelf on linux 2019-06-05 23:42:58 -04:00
kallisto kallisto: 0.46.0 -> 0.46.1 (#74430) 2019-11-30 21:12:54 +01:00
kssd kssd: init at 1.0 2019-12-08 16:48:59 +01:00
last last: 1042 -> 1045 2020-01-06 11:46:28 -08:00
macse macse: init at 2.03 2019-09-24 08:24:07 +02:00
megahit megahit: 1.1.4 -> 1.2.9 2019-11-02 15:53:57 +01:00
messer-slim treewide: name -> pname (easy cases) (#66585) 2019-08-15 13:41:18 +01:00
migrate
minc-tools
minc-widgets
minia minia: init at 3.2.1 2019-12-20 11:27:04 +11:00
minimap2 treewide: name -> pname (easy cases) (#66585) 2019-08-15 13:41:18 +01:00
mni_autoreg
mosdepth treewide: name -> pname (easy cases) (#66585) 2019-08-15 13:41:18 +01:00
mrbayes
muscle
N3
ncbi-tools
neuron treewide: name -> pname (easy cases) (#66585) 2019-08-15 13:41:18 +01:00
niftyreg niftyreg: fix build with gcc9 2019-11-03 14:43:37 +01:00
niftyseg nifticlib and niftseg: change platform from linux to unix since these build on OSX 2019-11-14 21:25:10 -05:00
octopus treewide: name -> pname (easy cases) (#66585) 2019-08-15 13:41:18 +01:00
paml paml: 4.9i -> 4.9j 2019-12-01 18:43:58 +01:00
picard-tools picard-tools: 2.21.1 -> 2.21.3 (#74528) 2019-11-30 16:24:44 +01:00
platypus treewide: remove redundant rec 2019-08-28 11:07:32 +00:00
plink
plink-ng treewide: name -> pname (easy cases) (#66585) 2019-08-15 13:41:18 +01:00
poretools treewide: fix redirected urls 2020-01-22 11:26:22 +01:00
prodigal Prodigal: init at 2.6.3 2019-04-19 08:38:14 +02:00
raxml treewide: name -> pname (easy cases) (#66585) 2019-08-15 13:41:18 +01:00
samtools samtools: 1.9 -> 1.10 2020-01-19 13:13:01 -08:00
seaview treewide: name -> pname (easy cases) (#66585) 2019-08-15 13:41:18 +01:00
snpeff treewide: name -> pname (easy cases) (#66585) 2019-08-15 13:41:18 +01:00
somatic-sniper treewide: name -> pname (easy cases) (#66585) 2019-08-15 13:41:18 +01:00
sortmerna sortmerna: init at 3.0.3 2019-08-27 00:37:43 +02:00
spades SPAdes: init at 3.13.1 (#63082) 2019-10-03 09:18:48 +00:00
stacks stacks: 2.4 -> 2.41 2019-07-17 09:34:10 +02:00
star star: 2.7.2b -> 2.7.3a 2019-11-03 10:23:05 +01:00
strelka strelka: fix build w/ gcc9 2019-12-30 03:18:19 +01:00
sumatools treewide: replace make/build/configure/patchFlags with nix lists 2019-12-30 12:58:11 +01:00
svaba svaba: init at 1.1.0 2019-12-08 14:51:05 +01:00
tebreak tebreak: init at 1.0 2019-12-29 17:16:10 +11:00
trimal trimal: init at 1.4.1 2019-06-14 16:31:39 +02:00
truvari truvari: init at 1.3.2 (#70877) 2019-10-24 17:06:42 -04:00
varscan treewide: name -> pname (easy cases) (#66585) 2019-08-15 13:41:18 +01:00
vcftools treewide: name -> pname (easy cases) (#66585) 2019-08-15 13:41:18 +01:00
xenomapper python.pkgs wide: fix problematic urls 2020-01-10 21:02:12 -08:00