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Diffstat (limited to 'gnu/packages')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 123 |
1 files changed, 123 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 99648d6b74..f6a3b8422b 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -15101,3 +15101,126 @@ and operating on records of genomic variation as it can be described by the VCF format, and a collection of command-line utilities for executing complex manipulations on VCF files.") (license license:expat)))) + +(define-public freebayes + (let ((commit "3ce827d8ebf89bb3bdc097ee0fe7f46f9f30d5fb") + (revision "1") + (version "1.0.2")) + (package + (name "freebayes") + (version (git-version version revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/ekg/freebayes.git") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1sbzwmcbn78ybymjnhwk7qc5r912azy5vqz2y7y81616yc3ba2a2")))) + (build-system gnu-build-system) + (inputs + `(("zlib" ,zlib) + ("htslib" ,htslib))) + (native-inputs + `(("bc" ,bc) ; Needed for running tests. + ("samtools" ,samtools) ; Needed for running tests. + ("parallel" ,parallel) ; Needed for running tests. + ("perl" ,perl) ; Needed for running tests. + ("procps" ,procps) ; Needed for running tests. + ("python" ,python-2) ; Needed for running tests. + ("bamtools" ,bamtools) + ("vcflib-src" ,(package-source vcflib)) + ;; These are submodules for the vcflib version used in freebayes. + ;; This package builds against the .o files so we need to extract the source. + ("tabixpp-src" ,(package-source tabixpp-freebayes)) + ("smithwaterman-src" ,(package-source smithwaterman)) + ("multichoose-src" ,(package-source multichoose)) + ("fsom-src" ,(package-source fsom)) + ("filevercmp-src" ,(package-source filevercmp)) + ("fastahack-src" ,(package-source fastahack)) + ("intervaltree-src" + ,(origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/ekg/intervaltree/") + (commit "dbb4c513d1ad3baac516fc1484c995daf9b42838"))) + (file-name "intervaltree-src-checkout") + (sha256 + (base32 "1fy5qbj4bg8d2bjysvaa9wfnqn2rj2sk5yra2h4l5pzvy53f23fj")))) + ;; These submodules are needed to run the tests. + ("bash-tap-src" ,(package-source bash-tap)) + ("test-simple-bash-src" + ,(origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/ingydotnet/test-simple-bash/") + (commit "124673ff204b01c8e96b7fc9f9b32ee35d898acc"))) + (file-name "test-simple-bash-src-checkout") + (sha256 + (base32 "043plp6z0x9yf7mdpky1fw7zcpwn1p47px95w9mh16603zqqqpga")))))) + (arguments + `(#:tests? #f ; TODO: Re-enable when we have grep with perl support. + #:test-target "test" + #:phases + (modify-phases %standard-phases + (delete 'configure) + (add-after 'unpack 'unpack-submodule-sources + (lambda* (#:key inputs #:allow-other-keys) + (let ((unpack (lambda (source target) + (with-directory-excursion target + (if (file-is-directory? (assoc-ref inputs source)) + (copy-recursively (assoc-ref inputs source) ".") + (invoke "tar" "xvf" + (assoc-ref inputs source) + "--strip-components=1")))))) + (and + (unpack "vcflib-src" "vcflib") + (unpack "fastahack-src" "vcflib/fastahack") + (unpack "filevercmp-src" "vcflib/filevercmp") + (unpack "fsom-src" "vcflib/fsom") + (unpack "intervaltree-src" "vcflib/intervaltree") + (unpack "multichoose-src" "vcflib/multichoose") + (unpack "smithwaterman-src" "vcflib/smithwaterman") + (unpack "tabixpp-src" "vcflib/tabixpp") + (unpack "test-simple-bash-src" "test/test-simple-bash") + (unpack "bash-tap-src" "test/bash-tap"))))) + (add-after 'unpack-submodule-sources 'fix-makefile + (lambda* (#:key inputs #:allow-other-keys) + ;; We don't have the .git folder to get the version tag from. + (substitute* '("vcflib/Makefile") + (("^GIT_VERSION.*") (string-append "GIT_VERSION = v" ,version))))) + (replace 'build + (lambda* (#:key inputs make-flags #:allow-other-keys) + (with-directory-excursion "vcflib" + (with-directory-excursion "tabixpp" + (pk "Compile tabixpp before compiling the main project.") + (let ((htslib-ref (assoc-ref inputs "htslib"))) + (invoke "make" "HTS_HEADERS=" + (string-append "HTS_LIB=" htslib-ref "/lib/libhts.a") + (string-append "LIBPATH=-L. -L" htslib-ref "/include")))) + (pk "Compile vcflib before compiling the main project.") + (invoke "make" "CC=gcc" + (string-append "CFLAGS=\"" "-Itabixpp " + "-I" (assoc-ref inputs "htslib") "/include " "\"") + "all")) + (pk "Compile the main project.") + (with-directory-excursion "src" + (substitute* "Makefile" + (("-I\\$\\(BAMTOOLS_ROOT\\)/src") "-I$(BAMTOOLS_ROOT)/include/bamtools")) + (invoke "make" + (string-append "BAMTOOLS_ROOT=" + (assoc-ref inputs "bamtools")))))) + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let ((bin (string-append (assoc-ref outputs "out") "/bin"))) + (install-file "bin/freebayes" bin) + (install-file "bin/bamleftalign" bin)) + #t))))) + (home-page "https://github.com/ekg/freebayes") + (synopsis "Haplotype-based variant detector") + (description "FreeBayes is a Bayesian genetic variant detector designed to +find small polymorphisms, specifically SNPs (single-nucleotide polymorphisms), +indels (insertions and deletions), MNPs (multi-nucleotide polymorphisms), and +complex events (composite insertion and substitution events) smaller than the +length of a short-read sequencing alignment.") + (license license:expat)))) |