millironx/docker-BioJulia
1
0
Fork 0
mirror of https://github.com/MillironX/docker-BioJulia.git synced 2024-12-22 01:18:17 +00:00
Code Issues Releases Packages Activity

Update to BioAlignments v3

Browse source
This commit is contained in:
Thomas A. Christensen II 2022-11-19 15:32:40 -06:00
parent 4ab07c6857
commit a3cbfcaaee
Signed by: millironx
GPG key ID: 139C07724802BC5D
3 changed files with 328 additions and 368 deletions
Show stats Download patch file Download diff file Expand all files Collapse all files

684
Manifest.toml
View file

File diff suppressed because it is too large Load diff

4
Project.toml
View file

@ -9,7 +9,6 @@ BioAlignments = "00701ae9-d1dc-5365-b64a-a3a3ebf5695e"
BioGenerics = "47718e42-2ac5-11e9-14af-e5595289c2ea"
BioSequences = "7e6ae17a-c86d-528c-b3b9-7f778a29fe59"
BioServices = "a0d4ced5-b29c-5395-b614-ca030a679c4b"
BioStructures = "de9282ab-8554-53be-b2d6-f6c222edabfc"
BioSymbols = "3c28c6f8-a34d-59c4-9654-267d177fcfa9"
BusinessDays = "4f18b42c-503e-5345-9536-bb0f25fc7038"
CSV = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b"
@ -33,7 +32,6 @@ FASTX = "c2308a5c-f048-11e8-3e8a-31650f418d12"
Formatting = "59287772-0a20-5a39-b81b-1366585eb4c0"
GFF3 = "af1dc308-cb6b-11e8-32f0-31192efa90f6"
GLM = "38e38edf-8417-5370-95a0-9cbb8c7f171a"
GenomeGraphs = "3aa97884-90e5-11e8-2134-af657ec4f203"
GenomicAnnotations = "4f8a0a0a-376d-5ac0-ab14-e88793df67f0"
GenomicFeatures = "899a7d2d-5c61-547b-bef9-6698a8d05446"
HTTP = "cd3eb016-35fb-5094-929b-558a96fad6f3"
@ -50,7 +48,6 @@ JSON3 = "0f8b85d8-7281-11e9-16c2-39a750bddbf1"
JuliaWebAPI = "480116ec-64ea-5dec-baca-db6b11e96e37"
Kelpie = "1b112299-d6bc-44e2-912a-478f25731460"
KernelDensity = "5ab0869b-81aa-558d-bb23-cbf5423bbe9b"
KmerAnalysis = "a20136b7-8e32-4c10-91d3-7060c0bd8ec7"
LaTeXStrings = "b964fa9f-0449-5b57-a5c2-d3ea65f4040f"
Libz = "2ec943e9-cfe8-584d-b93d-64dcb6d567b7"
LightGraphs = "093fc24a-ae57-5d10-9952-331d41423f4d"
@ -72,7 +69,6 @@ PopGen = "af524d12-c74b-11e9-22a8-3b091653023f"
PopGenCore = "45b36091-5ef7-4b08-b448-aaf24c763a14"
ProtoBuf = "3349acd9-ac6a-5e09-bcdb-63829b23a429"
QuantEcon = "fcd29c91-0bd7-5a09-975d-7ac3f643a60c"
ReadDatastores = "70a005b8-9d8a-11e9-0d98-c909fa2e52d2"
Roots = "f2b01f46-fcfa-551c-844a-d8ac1e96c665"
SequenceVariation = "eef6e190-9969-4f06-a38f-35a110a8fdc8"
StaticArrays = "90137ffa-7385-5640-81b9-e52037218182"

8
README.md
View file

@ -53,9 +53,9 @@ plus
- [x] [BioAlignments](https://github.com/MillironX/BioAlignments.jl)
- [x] [BioSequences](https://github.com/BioJulia/BioSequences.jl)
- [x] [BioStructures](https://github.com/BioJulia/BioStructures.jl)
- ~~[ ] [BioStructures](https://github.com/BioJulia/BioStructures.jl)~~ (Dependency mismatch with BioAlignments)
- [x] [BioSymbols](https://github.com/BioJulia/BioSymbols.jl)
- [x] [GenomeGraphs](https://github.com/BioJulia/GenomeGraphs.jl)
- ~~[ ] [GenomeGraphs](https://github.com/BioJulia/GenomeGraphs.jl)~~ (Dependency mismatch with BioAlignments)
- [x] [IntervalTrees](https://github.com/BioJulia/IntervalTrees.jl)
- [x] [SubstitutionModels](https://github.com/BioJulia/SubstitutionModels.jl)
@ -76,7 +76,7 @@ plus
### Analyses
- [x] [KmerAnalysis](https://github.com/BioJulia/KmerAnalysis.jl)
- ~~[ ] [KmerAnalysis](https://github.com/BioJulia/KmerAnalysis.jl)~~ (Dependency mismatch with BioAlignments)
- [x] [PopGen](https://github.com/BioJulia/PopGen.jl.git)
- [x] [SequenceVariation](https://BioJulia/SequenceVariation.jl)
@ -95,7 +95,7 @@ plus
### Data Storage and Retrieval
- [x] [BioServices](https://github.com/BioJulia/BioServices.jl)
- [x] [ReadDatastores](https://github.com/BioJulia/ReadDatastores.jl)
- ~~[ ] [ReadDatastores](https://github.com/BioJulia/ReadDatastores.jl)~~ (Dependency mismatch with BioAlignments)
[`JULIA_DEPOT_PATH`]: https://docs.julialang.org/en/v1/manual/environment-variables/#JULIA_DEPOT_PATH
[biojulia]: https://biojulia.net