Merge pull request #4 from jonalm/dev/use_ncbi_artifacts_instead_of_b…

…ioconda

use artifacts from NCBI directly

.github/workflows/CI.yml

@@ -27,6 +27,8 @@ jobs:
           - 'nightly'
         os:
           - ubuntu-latest
+          - windows-latest
+          - macOS-latest
         arch:
           - x64
     steps:

.gitignore

@@ -6,3 +6,5 @@
 /docs/build/
 .CondaPkg
 test/example_files/dna2.fasta.*
+.DS_Store
+Manifest*

Artifacts.toml

@@ -0,0 +1,42 @@
+[[ncbi-blast]]
+arch = "aarch64"
+git-tree-sha1 = "0406b91031ce302fa9117606d007d04635279fef"
+os = "macos"
+
+    [[ncbi-blast.download]]
+    sha256 = "e8da4f34b0421da051b1c2d9e5f8e1e43bf76e38cf9361a1dbe2fbc44b6224db"
+    url = "https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.16.0/ncbi-blast-2.16.0+-aarch64-macosx.tar.gz"
+[[ncbi-blast]]
+arch = "x86_64"
+git-tree-sha1 = "690abc170201bc029d0e7386da0791d7a76d98ff"
+os = "macos"
+
+    [[ncbi-blast.download]]
+    sha256 = "7eee1e7720f5daaf06e39d9c92b125d9072de7eb81f499c005dedb08b932324c"
+    url = "https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.16.0/ncbi-blast-2.16.0+-x64-macosx.tar.gz"
+[[ncbi-blast]]
+arch = "aarch64"
+git-tree-sha1 = "39394a0d1959ae677fde91f3148e1a6bc94f11eb"
+libc = "glibc"
+os = "linux"
+
+    [[ncbi-blast.download]]
+    sha256 = "d447a232ed3c47d1a5abca91932e0e4d3e6540f2c970cee26aa52b994392e0c2"
+    url = "https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.16.0/ncbi-blast-2.16.0+-aarch64-linux.tar.gz"
+[[ncbi-blast]]
+arch = "x86_64"
+git-tree-sha1 = "401cfe44557a4063e16671896f0834e2648b67af"
+libc = "glibc"
+os = "linux"
+
+    [[ncbi-blast.download]]
+    sha256 = "b0b13098c901d23b324ad1700e7471bb7408a7f7f517d74d5faad711be76e8f4"
+    url = "https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.16.0/ncbi-blast-2.16.0+-x64-linux.tar.gz"
+[[ncbi-blast]]
+arch = "x86_64"
+git-tree-sha1 = "f8f04f978f874b0a2a50ba3ebcfe97f29eaa740d"
+os = "windows"
+
+    [[ncbi-blast.download]]
+    sha256 = "3b6f27a72e9a875f1c02119704775a8e04ae97b5e4a148b560f9be9acd39e943"
+    url = "https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.16.0/ncbi-blast-2.16.0+-x64-win64.tar.gz"

Project.toml

@@ -1,11 +1,11 @@
 name = "NCBIBlast"
 uuid = "dcaf3faf-48b5-45a7-abb1-fcfd75344536"
 authors = ["Kevin Bonham <[email protected]> and contributors"]
-version = "0.1.0"
+version = "0.2.0"
 
 [deps]
-CondaPkg = "992eb4ea-22a4-4c89-a5bb-47a3300528ab"
+Pkg = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f"
 
 [compat]
-CondaPkg = "0.2.23"
+Pkg = "1.10.0"
 julia = "1.10"

dev/generate_artifact_toml.jl

@@ -0,0 +1,18 @@
+using Pkg: BinaryPlatforms
+using ArtifactUtils: add_artifact!
+
+blast_version = "2.16.0"
+url_common = "https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/$(blast_version)/ncbi-blast-$(blast_version)+-"
+platform_url_pairs = [
+    BinaryPlatforms.MacOS(:aarch64)  => "$(url_common)aarch64-macosx.tar.gz",
+    BinaryPlatforms.MacOS(:x86_64)   => "$(url_common)x64-macosx.tar.gz",
+    BinaryPlatforms.Linux(:aarch64)  => "$(url_common)aarch64-linux.tar.gz",
+    BinaryPlatforms.Linux(:x86_64)   => "$(url_common)x64-linux.tar.gz",
+    BinaryPlatforms.Windows(:x86_64) => "$(url_common)x64-win64.tar.gz"
+]
+
+foreach(platform_url_pairs) do (platform, url)
+    add_artifact!("Artifacts.toml", "ncbi-blast", url; platform, force=true)
+end
+
+##

src/NCBIBlast.jl

@@ -7,7 +7,17 @@ export blastn,
        tblastx,
        makeblastdb
 
-using CondaPkg
+using Pkg.Artifacts: @artifact_str
+
+const BLAST_VERSION = "2.16.0"
+const BIN_PATH = joinpath(artifact"ncbi-blast", "ncbi-blast-$(BLAST_VERSION)+", "bin")
+
+_blastn_exe() = joinpath(BIN_PATH, "blastn")
+_blastx_exe() = joinpath(BIN_PATH, "blastx")
+_blastp_exe() = joinpath(BIN_PATH, "blastp")
+_tblastn_exe() = joinpath(BIN_PATH, "tblastn")
+_tblastx_exe() = joinpath(BIN_PATH, "tblastx")
+_makeblastdb_exe() = joinpath(BIN_PATH, "makeblastdb")
 
 function add_cli_kwargs!(cmd::Vector{String}, kwargs)
     for (key,val) in pairs(kwargs)
@@ -85,11 +95,9 @@ Use '-help' to print detailed descriptions of command line arguments
 ```
 """
 function blastn(stdin = nothing; stdout=stdout, kwargs...)
-    cmd = ["blastn"]
+    cmd = [_blastn_exe()]
     add_cli_kwargs!(cmd, kwargs)
-    CondaPkg.withenv() do
-        run(pipeline(Cmd(cmd); stdout, stdin))
-    end
+    run(pipeline(Cmd(cmd); stdout, stdin))
 end
 
 
@@ -141,11 +149,9 @@ DESCRIPTION
 ```
 """
 function blastp(stdin = nothing; stdout=stdout, kwargs...)
-    cmd = ["blastp"]
+    cmd = [_blastp_exe()]
     add_cli_kwargs!(cmd, kwargs)
-    CondaPkg.withenv() do
-        run(pipeline(Cmd(cmd); stdout, stdin))
-    end
+    run(pipeline(Cmd(cmd); stdout, stdin))
 end
 
 """
@@ -199,11 +205,9 @@ Use '-help' to print detailed descriptions of command line arguments
 ```
 """
 function blastx(stdin = nothing; stdout=stdout, kwargs...)
-    cmd = ["blastx"]
+    cmd = [_blastx_exe()]
     add_cli_kwargs!(cmd, kwargs)
-    CondaPkg.withenv() do
-        run(pipeline(Cmd(cmd); stdin, stdout))
-    end
+    run(pipeline(Cmd(cmd); stdin, stdout))
 end
 
 
@@ -258,11 +262,9 @@ Use '-help' to print detailed descriptions of command line arguments
 ```
 """
 function tblastn(stdin = nothing; stdout=stdout, kwargs...)
-    cmd = ["tblastn"]
+    cmd = [_tblastn_exe()]
     add_cli_kwargs!(cmd, kwargs)
-    CondaPkg.withenv() do
-        run(pipeline(Cmd(cmd); stdout, stdin))
-    end
+    run(pipeline(Cmd(cmd); stdout, stdin))
 end
 
 """
@@ -311,11 +313,9 @@ Use '-help' to print detailed descriptions of command line arguments
 ```
 """
 function tblastx(stdin = nothing; stdout=stdout, kwargs...)
-    cmd = ["tblastx"]
+    cmd = [_tblastx_exe()]
     add_cli_kwargs!(cmd, kwargs)
-    CondaPkg.withenv() do
-        run(pipeline(Cmd(cmd); stdout, stdin))
-    end
+    run(pipeline(Cmd(cmd); stdout, stdin))
 end
 
 
@@ -345,11 +345,9 @@ Use '-help' to print detailed descriptions of command line arguments
 ```
 """
 function makeblastdb(; kwargs...)
-    cmd = ["makeblastdb"]
+    cmd = [_makeblastdb_exe()]
     add_cli_kwargs!(cmd, kwargs)
-    CondaPkg.withenv() do
-        run(Cmd(cmd))
-    end
+    run(Cmd(cmd))
 end
 
 end