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authorEfraim Flashner2023-09-19 19:24:04 +0300
committerEfraim Flashner2023-09-19 19:24:04 +0300
commitc2415bfa014892a56be9b621089a0a2ffab234f7 (patch)
tree5b4b601ebd94cd3d3d1cdac4764b9e5a46769169
parent90d0c931a585ec862151a11b6a88fce678670b9d (diff)
downloadguix-bioinformatics-c2415bfa014892a56be9b621089a0a2ffab234f7.tar.gz
Add fastix
-rw-r--r--gn/packages/bioinformatics.scm26
-rw-r--r--gn/packages/crates-io.scm25
2 files changed, 51 insertions, 0 deletions
diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm
index 2b1d514..4b37c8f 100644
--- a/gn/packages/bioinformatics.scm
+++ b/gn/packages/bioinformatics.scm
@@ -548,6 +548,32 @@ remove these, as they provide little information for many downstream
applications, such as haplotype panels or other imputation references.")
(license license:expat)))
+(define-public fastix
+ (package
+ (name "fastix")
+ (version "0.1.0")
+ (source (origin
+ (method url-fetch)
+ (uri (crate-uri "fastix" version))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32 "1mzk65mg8vx0hz39xis6zqdmq56abhmza656gn9pgmlsn151gpx2"))))
+ (build-system cargo-build-system)
+ (arguments
+ `(#:install-source? #f
+ #:cargo-inputs
+ (("rust-clap" ,rust-clap-2))
+ #:cargo-development-inputs
+ (("rust-assert-cmd" ,rust-assert-cmd-0.12)
+ ("rust-predicates" ,rust-predicates-1))))
+ (home-page "https://github.com/ekg/fastix")
+ (synopsis "Prefix-renaming FASTA records")
+ (description "A command line tool to add prefixes to FASTA headers. The
+idea is to support pangenomic applications, following the
+@url{https://github.com/pangenome/PanSN-spec, PanSN} hierarchical naming
+specification.")
+ (license license:expat)))
+
(define-public gafpack
(let ((commit "ad31875b6914d964c6fd72d1bf334f0843538fb6") ; November 10, 2022
(revision "1"))
diff --git a/gn/packages/crates-io.scm b/gn/packages/crates-io.scm
index 79832bc..557c980 100644
--- a/gn/packages/crates-io.scm
+++ b/gn/packages/crates-io.scm
@@ -10,6 +10,31 @@
#:use-module (gnu packages maths)
#:use-module (gnu packages python))
+(define-public rust-assert-cmd-0.12
+ (package
+ (name "rust-assert-cmd")
+ (version "0.12.2")
+ (source (origin
+ (method url-fetch)
+ (uri (crate-uri "assert-cmd" version))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "1xfn2spazxk3ljj9q3250a24gndja9vwa0h0rnbccdrbd4ncyvwk"))))
+ (build-system cargo-build-system)
+ (arguments
+ `(#:cargo-inputs
+ (("rust-doc-comment" ,rust-doc-comment-0.3)
+ ("rust-escargot" ,rust-escargot-0.5)
+ ("rust-predicates" ,rust-predicates-1)
+ ("rust-predicates-core" ,rust-predicates-core-1)
+ ("rust-predicates-tree" ,rust-predicates-tree-1)
+ ("rust-wait-timeout" ,rust-wait-timeout-0.2))))
+ (home-page "https://github.com/assert-rs/assert_cmd")
+ (synopsis "Test CLI Applications.")
+ (description "Test CLI Applications.")
+ (license (list license:expat license:asl2.0))))
+
(define-public rust-bgzip-0.2
(package
(name "rust-bgzip")