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-rw-r--r--gn/packages/bioinformatics.scm480
1 files changed, 0 insertions, 480 deletions
diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm
index 040373c..00eab03 100644
--- a/gn/packages/bioinformatics.scm
+++ b/gn/packages/bioinformatics.scm
@@ -222,486 +222,6 @@ data. For whole genome sequencing data analysis, the program can also use
mappability data (files created by GEM). ")
(license license:gpl2+)))
-(define-public tabixpp
- (package
- (name "tabixpp")
- (version "1.0.0")
- (source (origin
- (method url-fetch)
- (uri (string-append "https://github.com/ekg/tabixpp/archive/v"
- version ".tar.gz"))
- (file-name (string-append name "-" version ".tar.gz"))
- (sha256
- (base32 "1s0lgks7qlvlhvcjhi2wm18nnza1bwcnic44ij7z8wfg88h4ivwn"))))
- (build-system gnu-build-system)
- (inputs
- `(("htslib" ,htslib)
- ("zlib" ,zlib)))
- (arguments
- `(#:tests? #f ; There are no tests to run.
- #:phases
- (modify-phases %standard-phases
- (delete 'configure) ; There is no configure phase.
- ;; The build phase needs overriding the location of htslib.
- (replace 'build
- (lambda* (#:key inputs #:allow-other-keys)
- (let ((htslib-ref (assoc-ref inputs "htslib")))
- (zero?
- (system* "make"
- (string-append "HTS_LIB=" htslib-ref "/lib/libhts.a")
- "HTS_HEADERS=" ; No need to check for headers here.
- (string-append "LIBPATH=-L. -L" htslib-ref "/include"))))))
- (replace 'install
- (lambda* (#:key outputs #:allow-other-keys)
- (let ((bin (string-append (assoc-ref outputs "out") "/bin")))
- (install-file "tabix++" bin)))))))
- (home-page "https://github.com/ekg/tabixpp")
- (synopsis "C++ wrapper around tabix project")
- (description "This is a C++ wrapper around the Tabix project which abstracts
-some of the details of opening and jumping in tabix-indexed files.")
- (license license:expat)))
-
-;; This version works with FreeBayes while the released version doesn't. The
-;; released creates a variable with the name "vcf" somewhere, which is also the
-;; name of a namespace in vcflib.
-(define-public tabixpp-freebayes
- (let ((commit "bbc63a49acc52212199f92e9e3b8fba0a593e3f7"))
- (package (inherit tabixpp)
- (name "tabixpp-freebayes")
- (version (string-append "0-1." (string-take commit 7)))
- (source (origin
- (method url-fetch)
- (uri (string-append "https://github.com/ekg/tabixpp/archive/"
- commit ".tar.gz"))
- (file-name (string-append name "-" version "-checkout.tar.gz"))
- (sha256
- (base32 "1s06wmpgj4my4pik5kp2lc42hzzazbp5ism2y4i2ajp2y1c68g77")))))))
-
-(define-public smithwaterman
- ;; TODO: Upgrading smithwaterman breaks FreeBayes.
- (let ((commit "203218b47d45ac56ef234716f1bd4c741b289be1"))
- (package
- (name "smithwaterman")
- (version (string-append "0-1." (string-take commit 7)))
- (source (origin
- (method url-fetch)
- (uri (string-append "https://github.com/ekg/smithwaterman/archive/"
- commit ".tar.gz"))
- (file-name (string-append name "-" version "-checkout.tar.gz"))
- (sha256
- (base32 "1lkxy4xkjn96l70jdbsrlm687jhisgw4il0xr2dm33qwcclzzm3b"))))
- (build-system gnu-build-system)
- (arguments
- `(#:tests? #f ; There are no tests to run.
- #:phases
- (modify-phases %standard-phases
- (delete 'configure) ; There is no configure phase.
- (replace 'install
- (lambda* (#:key outputs #:allow-other-keys)
- (let ((bin (string-append (assoc-ref outputs "out") "/bin")))
- (install-file "smithwaterman" bin)))))))
- (home-page "https://github.com/ekg/smithwaterman")
- (synopsis "Implementation of the Smith-Waterman algorithm")
- (description "Implementation of the Smith-Waterman algorithm.")
- ;; The project contains a license file for the GPLv2. The source files
- ;; do not contain a license notice, so GPLv2-only is assumed here.
- (license license:gpl2))))
-
-(define-public multichoose
- (package
- (name "multichoose")
- (version "1.0.3")
- (source (origin
- (method url-fetch)
- (uri (string-append "https://github.com/ekg/multichoose/archive/v"
- version ".tar.gz"))
- (file-name (string-append name "-" version ".tar.gz"))
- (sha256
- (base32 "0xy86vvr3qrs4l81qis7ia1q2hnqv0xcb4a1n60smxbhqqis5w3l"))))
- (build-system gnu-build-system)
- (native-inputs
- `(("python" ,python-2)
- ("node" ,node)))
- (arguments
- `(#:tests? #f ; There are no tests to run.
- #:phases
- (modify-phases %standard-phases
- (delete 'configure) ; There is no configure phase.
- (replace 'install
- (lambda* (#:key outputs #:allow-other-keys)
- (let ((bin (string-append (assoc-ref outputs "out") "/bin")))
- ;; TODO: There are Python modules for these programs too.
- (install-file "multichoose" bin)
- (install-file "multipermute" bin)))))))
- (home-page "https://github.com/ekg/multichoose")
- (synopsis "Library for efficient loopless multiset combination generation
-algorithm")
- (description "A library implements an efficient loopless multiset
-combination generation algorithm which is (approximately) described in
-\"Loopless algorithms for generating permutations, combinations, and other
-combinatorial configurations.\" G Ehrlich - Journal of the ACM (JACM),
-1973. (Algorithm 7.)")
- (license license:expat)))
-
-(define-public fsom
- (let ((commit "a6ef318fbd347c53189384aef7f670c0e6ce89a3"))
- (package
- (name "fsom")
- (version (string-append "0-1." (string-take commit 7)))
- (source (origin
- (method url-fetch)
- (uri (string-append "https://github.com/ekg/fsom/archive/"
- "a6ef318fbd347c53189384aef7f670c0e6ce89a3" ".tar.gz"))
- (file-name (string-append name "-" version "-checkout.tar.gz"))
- (sha256
- (base32 "0q6b57ppxfvsm5cqmmbfmjpn5qvx2zi5pamvp3yh8gpmmz8cfbl3"))))
- (build-system gnu-build-system)
- (arguments
- `(#:tests? #f ; There are no tests to run.
- #:phases
- (modify-phases %standard-phases
- (delete 'configure) ; There is no configure phase.
- (replace 'install
- (lambda* (#:key outputs #:allow-other-keys)
- (let ((bin (string-append (assoc-ref outputs "out") "/bin")))
- (install-file "fsom" bin)))))))
- (home-page "https://github.com/ekg/fsom")
- (synopsis "Program for managing SOM (Self-Organizing Maps) neural networks")
- (description "Program for managing SOM (Self-Organizing Maps) neural networks.")
- (license license:gpl3))))
-
-(define-public filevercmp
- (let ((commit "1a9b779b93d0b244040274794d402106907b71b7"))
- (package
- (name "filevercmp")
- (version (string-append "0-1." (string-take commit 7)))
- (source (origin
- (method url-fetch)
- (uri (string-append "https://github.com/ekg/filevercmp/archive/"
- commit ".tar.gz"))
- (file-name "filevercmp-src.tar.gz")
- (sha256
- (base32 "0yp5jswf5j2pqc6517x277s4s6h1ss99v57kxw9gy0jkfl3yh450"))))
- (build-system gnu-build-system)
- (arguments
- `(#:tests? #f ; There are no tests to run.
- #:phases
- (modify-phases %standard-phases
- (delete 'configure) ; There is no configure phase.
- (replace 'install
- (lambda* (#:key outputs #:allow-other-keys)
- (let ((bin (string-append (assoc-ref outputs "out") "/bin")))
- (install-file "filevercmp" bin)))))))
- (home-page "https://github.com/ekg/filevercmp")
- (synopsis "Program to compare version strings")
- (description "A program to compare version strings. It intends to be a
-replacement for strverscmp.")
- (license license:gpl3+))))
-
-(define-public fastahack ; guix ready
- (let ((commit "c68cebb4f2e5d5d2b70cf08fbdf1944e9ab2c2dd"))
- (package
- (name "fastahack")
- (version (string-append "0-1." (string-take commit 7)))
- (source (origin
- (method url-fetch)
- (uri (string-append "https://github.com/ekg/fastahack/archive/"
- commit ".tar.gz"))
- (file-name (string-append name "-" version "-checkout.tar.gz"))
- (sha256
- (base32 "0j25lcl3jk1kls66zzxjfyq5ir6sfcvqrdwfcva61y3ajc9ssay2"))))
- (build-system gnu-build-system)
- (arguments
- `(#:tests? #f ; There are no tests to run.
- #:phases
- (modify-phases %standard-phases
- (delete 'configure) ; There is no configure phase.
- (replace 'install
- (lambda* (#:key outputs #:allow-other-keys)
- (let ((bin (string-append (assoc-ref outputs "out") "/bin")))
- (install-file "fastahack" bin)))))))
- (home-page "https://github.com/ekg/fastahack")
- (synopsis "Program for indexing and sequence extraction from FASTA files")
- (description "Fastahack is a small application for indexing and extracting
-sequences and subsequences from FASTA files. The included Fasta.cpp library
-provides a FASTA reader and indexer that can be embeddedinto applications which
-would benefit from directly reading subsequences from FASTA files. The library
-automatically handles index file generation and use.")
- ;; There is no specific license for fastahack.
- ;; A part of the program is licensed GPLv2.
- (license (list license:non-copyleft license:gpl2)))))
-
-(define-public vcflib
- (let ((commit "3ce827d8ebf89bb3bdc097ee0fe7f46f9f30d5fb"))
- (package
- (name "vcflib")
- (version (string-append "1.0.2-1." (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)
- ("r" ,r)
- ("node" ,node)
- ("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 url-fetch)
- (uri (string-append
- "https://github.com/ekg/intervaltree/archive/"
- "dbb4c513d1ad3baac516fc1484c995daf9b42838" ".tar.gz"))
- (file-name "intervaltree-src.tar.gz")
- (sha256
- (base32 "19prwpn2wxsrijp5svfqvfcxl5nj7zdhm3jycd5kqhl9nifpmcks"))))))
- (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 "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"))
- ;;(include (string-append (assoc-ref outputs "out") "/include"))
- (lib (string-append (assoc-ref outputs "out") "/lib")))
- (for-each (lambda (file)
- (install-file file bin))
- (find-files "bin" ".*"))
- ;; The header files do not correspond to libvcflib.a, therefore
- ;; I left them out.
- ;;(for-each (lambda (file)
- ;; (install-file file include))
- ;; (find-files "src" "\\.h$"))
- (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 bash-tap ; guix license issue
- (package
- (name "bash-tap")
- (version "1.0.2")
- (source (origin
- (method url-fetch)
- (uri (string-append "https://github.com/illusori/bash-tap/archive/"
- version ".tar.gz"))
- (file-name (string-append name "-" version ".tar.gz"))
- (sha256
- (base32 "0qs1qi38bl3ns4mpagcawv618dsk2q1lgrbddgvs0wl3ia12cyz5"))))
- (build-system trivial-build-system)
- (native-inputs `(("source" ,source)
- ("tar" ,tar)
- ("gzip" ,gzip)))
- (arguments
- `(#:modules ((guix build utils))
- #:builder (begin
- (use-modules (guix build utils))
- (let ((tar (string-append (assoc-ref %build-inputs "tar") "/bin/tar"))
- (path (string-append (assoc-ref %build-inputs "gzip") "/bin"))
- (bin (string-append %output "/bin"))
- (source (string-append (assoc-ref %build-inputs "source"))))
- (setenv "PATH" path)
- (mkdir-p bin)
- (with-directory-excursion bin
- (zero? (system* tar "xvf" source
- "--strip-components=1"
- "--no-anchored"
- "bash-tap"
- "bash-tap-bootstrap"
- "bash-tap-mock")))))))
- (home-page "http://www.illusori.co.uk/projects/bash-tap/")
- (synopsis "Bash port of a Test::More/Test::Builder-style TAP-compliant
-test library")
- (description "Bash TAP is a TAP-compliant Test::More-style testing library
-for Bash shell scripts and functions. Along with the Test::More-style testing
-helpers it provides helper functions for mocking commands and functions and
-in-process output capturing.")
- ;; The author didn't specify a license.
- (license license:public-domain)))
-
-(define-public freebayes ; guix dependent package issues
- (let ((commit "3ce827d8ebf89bb3bdc097ee0fe7f46f9f30d5fb")
- (revision "1"))
- (package
- (name "freebayes")
- (version (string-append "1.0.2-" revision "." (string-take commit 7)))
- (source (origin
- (method git-fetch)
- (uri (git-reference
- (url "https://github.com/ekg/freebayes.git")
- (commit commit)))
- (file-name (string-append name "-" version "-checkout"))
- (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.
- ("procps" ,procps) ; Needed for running tests.
- ("bamtools" ,bamtools)
- ("cmake" ,cmake)
- ("python" ,python-2)
- ("node" ,node)
- ("r" ,r)
- ("perl" ,perl)
- ("bamtools-src" ,(package-source bamtools))
- ("vcflib-src" ,(package-source vcflib))
- ;; These are submodules for the vcflib version used in freebayes
- ("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 url-fetch)
- (uri (string-append
- "https://github.com/ekg/intervaltree/archive/"
- "dbb4c513d1ad3baac516fc1484c995daf9b42838" ".tar.gz"))
- (file-name "intervaltree-src.tar.gz")
- (sha256
- (base32 "19prwpn2wxsrijp5svfqvfcxl5nj7zdhm3jycd5kqhl9nifpmcks"))))
- ;; These submodules are needed to run the tests.
- ("bash-tap-src" ,(package-source bash-tap))
- ;; ,(origin
- ;; (method url-fetch)
- ;; (uri (string-append "https://github.com/illusori/bash-tap/archive/"
- ;; "c38fbfa401600cc81ccda66bfc0da3ea56288d03" ".tar.gz"))
- ;; (file-name "bash-tap-src.tar.gz")
- ;; (sha256
- ;; (base32 "07ijb1p0aa65ajpg9nkghc183iha6lwiydkckay8pghapa01j6nz"))))
- ("test-simple-bash-src"
- ,(origin
- (method url-fetch)
- (uri (string-append "https://github.com/ingydotnet/test-simple-bash/archive/"
- "124673ff204b01c8e96b7fc9f9b32ee35d898acc" ".tar.gz"))
- (file-name "test-simple-bash-src.tar.gz")
- (sha256
- (base32 "016xf3wbgqbav9dncvfdx5k0f10z5xwq8jdszajzmcvnhz5wis14"))))))
- (arguments
- `(#: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
- (zero? (system* "tar" "xvf"
- (assoc-ref inputs source)
- "--strip-components=1"))))))
- (and
- (unpack "bamtools-src" "bamtools")
- (unpack "vcflib-src" "vcflib")
- ;;(unpack "intervaltree-src" "intervaltree")
- (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.
- ;; For this checkout of the code, it's v1.0.0.
- (substitute* '("vcflib/Makefile")
- (("^GIT_VERSION.*") "GIT_VERSION = v1.0.0"))))
- (replace 'build
- (lambda* (#:key inputs make-flags #:allow-other-keys)
- (and
- ;; Compile Bamtools before compiling the main project.
- (with-directory-excursion "bamtools"
- (system* "mkdir" "build")
- (with-directory-excursion "build"
- (and (zero? (system* "cmake" "../"))
- (zero? (system* "make")))))
- ;; Compile vcflib before we compiling the main project.
- (with-directory-excursion "vcflib"
- (with-directory-excursion "tabixpp"
- (let ((htslib-ref (assoc-ref inputs "htslib")))
- (zero?
- (system* "make" "HTS_HEADERS="
- (string-append "HTS_LIB=" htslib-ref "/lib/libhts.a")
- (string-append "LIBPATH=-L. -L" htslib-ref "/include")))))
- (zero? (system* "make" "CC=gcc"
- (string-append "CFLAGS=\"" "-Itabixpp "
- "-I" (assoc-ref inputs "htslib") "/include " "\"") "all")))
- (with-directory-excursion "src"
- (zero? (system* "make"))))))
- (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))))
- ;; There are three tests that fail. All because of the -P
- ;; (--perl-regexp) option in grep, which is not compiled into the
- ;; version of grep in Guix.
- (replace 'check
- (lambda* (#:key inputs #:allow-other-keys)
- (system* "make" "test"))))))
- (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))))
-
(define-public plink2
(package
(name "plink2")