diff options
Diffstat (limited to 'gn/packages/bioinformatics.scm')
| -rw-r--r-- | gn/packages/bioinformatics.scm | 131 |
1 files changed, 1 insertions, 130 deletions
diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm index 5ee126e..e5914c2 100644 --- a/gn/packages/bioinformatics.scm +++ b/gn/packages/bioinformatics.scm @@ -431,7 +431,7 @@ automatically handles index file generation and use.") ;; A part of the program is licensed GPLv2. (license (list license:non-copyleft license:gpl2))))) -(define-public vcflib ; guix duplicat, see below? +(define-public vcflib (let ((commit "3ce827d8ebf89bb3bdc097ee0fe7f46f9f30d5fb")) (package (name "vcflib") @@ -808,135 +808,6 @@ integration with gPLINK and Haploview, there is some support for the subsequent visualization, annotation and storage of results.") (license license:gpl3+)))) - -(define-public vcflib ; duplicate? See above - (let ((commit "3ce827d8ebf89bb3bdc097ee0fe7f46f9f30d5fb")) - (package - (name "vcflib") - (version (string-append "v1.0.2-" (string-take commit 7))) - (source - (origin - (method url-fetch) - (uri (string-append "https://github.com/vcflib/vcflib/archive/" - "5ac091365fdc716cc47cc5410bb97ee5dc2a2c92" ".tar.gz")) - (file-name "vcflib-5ac0913.tar.gz") - (sha256 - (base32 "0ywshwpif059z5h0g7zzrdfzzdj2gr8xvwlwcsdxrms3p9iy35h8")))) - (build-system gnu-build-system) - (native-inputs - `(("htslib" ,htslib) - ("zlib" ,zlib) - ("python" ,python-2) - ("perl" ,perl) - ("tabixpp-src" - ,(origin - (method url-fetch) - (uri (string-append "https://github.com/ekg/tabixpp/archive/" - "bbc63a49acc52212199f92e9e3b8fba0a593e3f7" ".tar.gz")) - (file-name "tabixpp-src.tar.gz") - (sha256 - (base32 "1s06wmpgj4my4pik5kp2lc42hzzazbp5ism2y4i2ajp2y1c68g77")))) - ("intervaltree-src" - ,(origin - (method url-fetch) - (uri (string-append - "https://github.com/ekg/intervaltree/archive/" - "dbb4c513d1ad3baac516fc1484c995daf9b42838" ".tar.gz")) - (file-name "intervaltree-src.tar.gz") - (sha256 - (base32 "19prwpn2wxsrijp5svfqvfcxl5nj7zdhm3jycd5kqhl9nifpmcks")))) - ("smithwaterman-src" - ,(origin - (method url-fetch) - (uri (string-append "https://github.com/ekg/smithwaterman/archive/" - "203218b47d45ac56ef234716f1bd4c741b289be1" ".tar.gz")) - (file-name "smithwaterman-src.tar.gz") - (sha256 - (base32 "1lkxy4xkjn96l70jdbsrlm687jhisgw4il0xr2dm33qwcclzzm3b")))) - ("multichoose-src" - ,(origin - (method url-fetch) - (uri (string-append "https://github.com/ekg/multichoose/archive/" - "73d35daa18bf35729b9ba758041a9247a72484a5" ".tar.gz")) - (file-name "multichoose-src.tar.gz") - (sha256 - (base32 "07aizwdabmlnjaq4p3v0vsasgz1xzxid8xcxcw3paq8kh9c1099i")))) - ("fsom-src" - ,(origin - (method url-fetch) - (uri (string-append "https://github.com/ekg/fsom/archive/" - "a6ef318fbd347c53189384aef7f670c0e6ce89a3" ".tar.gz")) - (file-name "fsom-src.tar.gz") - (sha256 - (base32 "0q6b57ppxfvsm5cqmmbfmjpn5qvx2zi5pamvp3yh8gpmmz8cfbl3")))) - ("filevercmp-src" - ,(origin - (method url-fetch) - (uri (string-append "https://github.com/ekg/filevercmp/archive/" - "1a9b779b93d0b244040274794d402106907b71b7" ".tar.gz")) - (file-name "filevercmp-src.tar.gz") - (sha256 - (base32 "0yp5jswf5j2pqc6517x277s4s6h1ss99v57kxw9gy0jkfl3yh450")))) - ("fastahack-src" - ,(origin - (method url-fetch) - (uri (string-append "https://github.com/ekg/fastahack/archive/" - "c68cebb4f2e5d5d2b70cf08fbdf1944e9ab2c2dd" ".tar.gz")) - (file-name "fastahack-src.tar.gz") - (sha256 - (base32 "0j25lcl3jk1kls66zzxjfyq5ir6sfcvqrdwfcva61y3ajc9ssay2")))))) - (arguments - `(#:tests? #f - #:phases - (modify-phases %standard-phases - (delete 'configure) - (delete 'check) - (add-after 'unpack 'unpack-submodule-sources - (lambda* (#:key inputs #:allow-other-keys) - (let ((unpack (lambda (source target) - (with-directory-excursion target - (zero? (system* "tar" "xvf" - (assoc-ref inputs source) - "--strip-components=1")))))) - (and - (unpack "intervaltree-src" "intervaltree") - (unpack "fastahack-src" "fastahack") - (unpack "filevercmp-src" "filevercmp") - (unpack "fsom-src" "fsom") - (unpack "intervaltree-src" "intervaltree") - (unpack "multichoose-src" "multichoose") - (unpack "smithwaterman-src" "smithwaterman") - (unpack "tabixpp-src" "tabixpp"))))) - (add-after 'unpack-submodule-sources 'fix-makefile - (lambda* (#:key inputs #:allow-other-keys) - (substitute* '("Makefile") - (("^GIT_VERSION.*") "GIT_VERSION = v1.0.0")))) - (replace - 'build - (lambda* (#:key inputs make-flags #:allow-other-keys) - (with-directory-excursion "tabixpp" - (zero? (system* "make"))) - (zero? (system* "make" "CC=gcc" - (string-append "CFLAGS=\"" "-Itabixpp " - "-I" (assoc-ref inputs "htslib") "/include " "\"") "all")))) - (replace - 'install - (lambda* (#:key outputs #:allow-other-keys) - (let ((bin (string-append (assoc-ref outputs "out") "/bin")) - (lib (string-append (assoc-ref outputs "out") "/lib"))) - (for-each (lambda (file) - (install-file file bin)) - (find-files "bin" ".*")) - (install-file "libvcflib.a" lib))))))) - (home-page "https://github.com/vcflib/vcflib/") - (synopsis "Library for parsing and manipulating VCF files") - (description "Vcflib provides methods to manipulate and interpret -sequence variation as it can be described by VCF. It is both an API for parsing -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 pindel (package (name "pindel") |