diff options
Diffstat (limited to 'gn/packages/bioinformatics.scm')
| -rw-r--r-- | gn/packages/bioinformatics.scm | 111 |
1 files changed, 111 insertions, 0 deletions
diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm index 2d1b55f..4e3c92b 100644 --- a/gn/packages/bioinformatics.scm +++ b/gn/packages/bioinformatics.scm @@ -54,6 +54,7 @@ #:use-module (gnu packages java) #:use-module (gnu packages jemalloc) #:use-module (gnu packages linux) + #:use-module (gnu packages llvm) #:use-module (gnu packages machine-learning) #:use-module (gnu packages maths) #:use-module (gnu packages mpi) @@ -510,6 +511,116 @@ reads.") collapses them into a non-redundant graph structure.") (license license:expat))) +(define-public pgr-tk + (package + (name "pgr-tk") + (version "0.3.6") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/Sema4-Research/pgr-tk") + (commit (string-append "v" version)) + (recursive? #t))) ; agc, WFA + (file-name (git-file-name name version)) + (sha256 + (base32 "160ngqbi8cbgaafq8crhfqv039mxr9jgl8hxxpwz0fh8mrh4003y")) + (snippet + #~(begin + (use-modules (guix build utils)) + (substitute* (find-files "." "Cargo.toml") + ;; Only use the major+minor version to decrease the number of + ;; special version crates. + (("(.*= \")([[:digit:]]+\\.[[:digit:]]+)\\.[[:digit:]]+(\".*)" + _ name version tail) + (string-append name version tail)) + ;; Then fix the version string for the actual package. + (("^version = \".*") + (string-append "version = \"" #$version "\"\n"))))))) + (build-system cargo-build-system) + (arguments + `(#:install-source? #f + #:cargo-test-flags + (list "--release" "--" + "--skip=get_aln_segements" + "--skip=get_shmmr_dots" + "--skip=AGCFile" + "--skip=SeqIndexDB") + #:cargo-inputs + (("rust-bindgen" ,rust-bindgen-0.58) + ("rust-bgzip" ,rust-bgzip-0.2) + ("rust-byteorder" ,rust-byteorder-1) + ("rust-clap" ,rust-clap-3.1) + ("rust-cuckoofilter" ,rust-cuckoofilter-0.5) + ("rust-flate2" ,rust-flate2-1) + ("rust-libc" ,rust-libc-0.2) + ("rust-log" ,rust-log-0.4) + ("rust-petgraph" ,rust-petgraph-0.6) + ("rust-pyo3" ,rust-pyo3-0.14) + ("rust-rayon" ,rust-rayon-1) + ("rust-regex" ,rust-regex-1) + ("rust-rustc-hash" ,rust-rustc-hash-1) + ("rust-serde" ,rust-serde-1) + ("rust-serde-json" ,rust-serde-json-1) + ("rust-simple-logger" ,rust-simple-logger-1)) + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'insert-wfa-source + (lambda* (#:key inputs #:allow-other-keys) + (copy-recursively (assoc-ref inputs "wfa-src") + "rs-wfa/WFA"))) + (add-after 'unpack 'adjust-source + (lambda _ + (substitute* '("pgr-bin/build.rs" + "pgr-db/build.rs" + "pgr-tk/build.rs") + (("git") "ls") + (("bioconda") "Guix")) + ;; Build with zlib, not zlib-ng + (substitute* '("pgr-bin/Cargo.toml" + "pgr-db/Cargo.toml") + (("zlib-ng-compat") "zlib")))) + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let ((out (assoc-ref outputs "out"))) + (with-directory-excursion "target/release" + (install-file "libpgrtk.so" (string-append out "/lib")) + (for-each + (lambda (file) + (install-file file (string-append out "/bin"))) + (list "pgr-filter" + "pgr-mdb" + "pgr-multifilter" + "pgr-probe-match" + "pgr-shmmr-pair-count"))))))))) + (inputs (list clang python zlib)) + (native-inputs + `(("pkg-config" ,pkg-config) + ("wfa-src" + ,(origin + (method git-fetch) + (uri (git-reference + ;; forPYO3 branch, 14-03-2021 + (url "https://github.com/cschin/WFA") + (commit "1f8c8d2905ed482cd2d306a1676d60c2a45cb098"))) + (file-name "wfa-for-pgr-tk") + (sha256 + (base32 "19h1cjp2bdlcfq5c6rsbk8bc0f8zn64b471dhj4xlfxd1prv2dpk")))))) + (home-page "https://github.com/Sema4-Research/pgr-tk") + (synopsis "Pangenome Research Tool Kit") + (description + "PGR-TK provides pangenome assembly management, query and +@acronym{Minimizer Anchored Pangenome, MAP} Graph Generation. It is a project +to provide Python and Rust libraries to facilitate pangenomics analysis. +Several algorithms and data structures used for the Peregrine Genome Assembler +are useful for Pangenomics analysis as well. This repo takes those algorithms +and data structure, combining other handy 3rd party tools to expose them as a +library in Python (with Rust code for those computing parts that need +performance.)") + (license (license:non-copyleft + "file:///LICENSE" + "CC-BY-NC-SA 4.0")))) + (define-public pangenie (let ((commit "e779076827022d1416ab9fabf99a03d8f4725956") ; September 2, 2021 from phasing-tests branch (revision "2")) |