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| 1 | +;; To use this file to build HEAD of freebayes: |
| 2 | +;; |
| 3 | +;; guix build -f guix.scm |
| 4 | +;; |
| 5 | +;; To get a development container (emacs shell will work) |
| 6 | +;; |
| 7 | +;; guix environment -C -l guix.scm |
| 8 | + |
| 9 | +(use-modules |
| 10 | + ((guix licenses) #:prefix license:) |
| 11 | + (guix gexp) |
| 12 | + (guix packages) |
| 13 | + (guix git-download) |
| 14 | + (guix build-system cmake) |
| 15 | + (gnu packages algebra) |
| 16 | + (gnu packages base) |
| 17 | + (gnu packages compression) |
| 18 | + (gnu packages bioinformatics) |
| 19 | + (gnu packages build-tools) |
| 20 | + (gnu packages curl) |
| 21 | + (gnu packages llvm) |
| 22 | + (gnu packages python) |
| 23 | + ;; (gnu packages ninja) |
| 24 | + (gnu packages parallel) |
| 25 | + (gnu packages perl) |
| 26 | + (gnu packages perl6) |
| 27 | + (gnu packages pkg-config) |
| 28 | + (srfi srfi-1) |
| 29 | + (ice-9 popen) |
| 30 | + (ice-9 rdelim)) |
| 31 | + |
| 32 | +;; (substitute* (find-files "." "\\.(h|c)(pp)?$") |
| 33 | +;; (("\"SmithWatermanGotoh.h\"") "<smithwaterman/SmithWatermanGotoh.h>") |
| 34 | +;; (("\"convert.h\"") "<smithwaterman/convert.h>") |
| 35 | +;; (("\"disorder.h\"") "<smithwaterman/disorder.h>") |
| 36 | +;; (("\"tabix.hpp\"") "<tabix.hpp>") |
| 37 | +;; (("\"Fasta.h\"") "<fastahack/Fasta.h>")) |
| 38 | +;; (for-each delete-file-recursively |
| 39 | +;; '("fastahack" "filevercmp" "fsom" "googletest" "intervaltree" |
| 40 | +;; "libVCFH" "multichoose" "smithwaterman" "tabixpp")) |
| 41 | + |
| 42 | +(define %source-dir (dirname (current-filename))) |
| 43 | + |
| 44 | +(define %git-commit |
| 45 | + (read-string (open-pipe "git show HEAD | head -1 | cut -d ' ' -f 2" OPEN_READ))) |
| 46 | + |
| 47 | +(define-public vcflib-git |
| 48 | + (package |
| 49 | + (name "vcflib-git") |
| 50 | + (version (git-version "1.0.2" "HEAD" %git-commit)) |
| 51 | + (source (local-file %source-dir #:recursive? #t)) |
| 52 | + (build-system cmake-build-system) |
| 53 | + (inputs |
| 54 | + `(("curl" ,curl) |
| 55 | + ("fastahack" ,fastahack) |
| 56 | + ("htslib" ,htslib) |
| 57 | + ("perl" ,perl) |
| 58 | + ("python" ,python) |
| 59 | + ("smithwaterman" ,smithwaterman) |
| 60 | + ("tabixpp" ,tabixpp) |
| 61 | + ("xz" ,xz) |
| 62 | + ("zlib" ,zlib))) |
| 63 | + (native-inputs |
| 64 | + `(("pkg-config" ,pkg-config))) |
| 65 | + (home-page "https://github.com/vcflib/vcflib/") |
| 66 | + (synopsis "Library for parsing and manipulating VCF files") |
| 67 | + (description "Vcflib provides methods to manipulate and interpret |
| 68 | +sequence variation as it can be described by VCF. It is both an API for parsing |
| 69 | +and operating on records of genomic variation as it can be described by the VCF |
| 70 | +format, and a collection of command-line utilities for executing complex |
| 71 | +manipulations on VCF files.") |
| 72 | + (license license:expat))) |
| 73 | + |
| 74 | +vcflib-git |
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