diff options
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 66 |
1 files changed, 66 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 55b7cb1c86..82506c1c3a 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -48,6 +48,7 @@ #:use-module (gnu packages maths) #:use-module (gnu packages mpi) #:use-module (gnu packages ncurses) + #:use-module (gnu packages pcre) #:use-module (gnu packages perl) #:use-module (gnu packages pkg-config) #:use-module (gnu packages popt) @@ -1425,6 +1426,71 @@ genes in incomplete assemblies or complete genomes.") ;; GPL3+ according to private correspondense with the authors. (license license:gpl3+))) +(define-public fxtract + (let ((util-commit "776ca85a18a47492af3794745efcb4a905113115")) + (package + (name "fxtract") + (version "2.3") + (source + (origin + (method url-fetch) + (uri (string-append + "https://github.com/ctSkennerton/fxtract/archive/" + version ".tar.gz")) + (file-name (string-append "ctstennerton-util-" + (string-take util-commit 7) + "-checkout")) + (sha256 + (base32 + "0275cfdhis8517hm01is62062swmi06fxzifq7mr3knbbxjlaiwj")))) + (build-system gnu-build-system) + (arguments + `(#:make-flags (list + (string-append "PREFIX=" (assoc-ref %outputs "out")) + "CC=gcc") + #:test-target "fxtract_test" + #:phases + (modify-phases %standard-phases + (delete 'configure) + (add-before 'build 'copy-util + (lambda* (#:key inputs #:allow-other-keys) + (rmdir "util") + (copy-recursively (assoc-ref inputs "ctskennerton-util") "util") + #t)) + ;; Do not use make install as this requires additional dependencies. + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out")) + (bin (string-append out"/bin"))) + (install-file "fxtract" bin) + #t)))))) + (inputs + `(("pcre" ,pcre) + ("zlib" ,zlib))) + (native-inputs + ;; ctskennerton-util is licensed under GPL2. + `(("ctskennerton-util" + ,(origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/ctSkennerton/util.git") + (commit util-commit))) + (file-name (string-append + "ctstennerton-util-" util-commit "-checkout")) + (sha256 + (base32 + "0cls1hd4vgj3f36fpzzg4xc77d6f3hpc60cbpfmn2gdr7ykzzad7")))))) + (home-page "https://github.com/ctSkennerton/fxtract") + (synopsis "Extract sequences from FASTA and FASTQ files") + (description + "Fxtract extracts sequences from a protein or nucleotide fastx (FASTA +or FASTQ) file given a subsequence. It uses a simple substring search for +basic tasks but can change to using POSIX regular expressions, PCRE, hash +lookups or multi-pattern searching as required. By default fxtract looks in +the sequence of each record but can also be told to look in the header, +comment or quality sections.") + (license license:expat)))) + (define-public grit (package (name "grit") |