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-rw-r--r--gn/packages/bioinformatics.scm290
1 files changed, 62 insertions, 228 deletions
diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm
index 3d27a72..ea4bf91 100644
--- a/gn/packages/bioinformatics.scm
+++ b/gn/packages/bioinformatics.scm
@@ -48,201 +48,77 @@
#:use-module (gn packages statistics)
#:use-module (srfi srfi-1))
-(define-public freebayes
- (let ((commit "3ce827d8ebf89bb3bdc097ee0fe7f46f9f30d5fb"))
- (package
- (name "freebayes")
- (version (string-append "v1.0.2-" (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)
- (native-inputs
- `(("cmake" ,cmake)
- ("htslib" ,htslib)
- ;;("openmpi" ,openmpi)
- ("zlib" ,zlib)
- ("python" ,python-2)
- ("perl" ,perl)
- ("bamtools-src"
- ,(origin
- (method url-fetch)
- (uri (string-append "https://github.com/ekg/bamtools/archive/"
- "e77a43f5097ea7eee432ee765049c6b246d49baa" ".tar.gz"))
- (file-name "bamtools-src.tar.gz")
- (sha256
- (base32 "0rqymka21g6lfjfgxzr40pxz4c4fcl77jpy1np1li70pnc7h2cs1"))))
- ("vcflib-src"
- ,(origin
- (method url-fetch)
- (uri "https://github.com/vcflib/vcflib/archive/v1.0.0-rc1.tar.gz")
- (file-name "vcflib-v1.0.0-rc1.tar.gz")
- (sha256
- (base32 "0313cxnf77i74mz4xwkpdablw2a1nn7si9g5ar3kr0ipm02afizx"))))
- ;; These are submodules for the vcflib version used in freebayes
- ("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 "bamtools-src" "bamtools")
- (unpack "vcflib-src" "vcflib")
- (unpack "intervaltree-src" "intervaltree")
- (unpack "fastahack-src" "vcflib/fastahack")
- (unpack "filevercmp-src" "vcflib/filevercmp")
- (unpack "intervaltree-src" "vcflib/intervaltree")
- (unpack "multichoose-src" "vcflib/multichoose")
- (unpack "smithwaterman-src" "vcflib/smithwaterman")
- (unpack "tabixpp-src" "vcflib/tabixpp")))))
- (replace
- 'build
- (lambda* (#:key inputs make-flags #:allow-other-keys)
- (and
- ;; We must compile Bamtools before we can compile the main
- ;; project.
- (with-directory-excursion "bamtools"
- (system* "mkdir" "build")
- (with-directory-excursion "build"
- (and (zero? (system* "cmake" "../"))
- (zero? (system* "make")))))
- ;; We must compile vcflib before we can compile the main
- ;; project.
- (with-directory-excursion "vcflib"
- (with-directory-excursion "tabixpp"
- (zero? (system* "make")))
- (zero? (system* "make" "CC=gcc" "-Itabixpp")))
- (zero? (system* "make" "src/version_git.h"))
- (zero? (system* "make" "vcflib/Makefile")))))
- (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))))
- ;; (replace
- ;; 'check
- ;; (lambda* (#:key outputs #:allow-other-keys)
- ;; (with-directory-excursion "test"
- ;; (zero? (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:non-copyleft))))
+(define-public r-biocpreprocesscore
+ (package
+ (name "r-biocpreprocesscore")
+ (version "1.32.0")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "preprocessCore" version))
+ (sha256
+ (base32
+ "07isghjkqm91rg37l1fzpjrbq36b7w4pbsi95wwh6a8qq7r69z1n"))))
+ (properties
+ `((upstream-name . "BiocpreprocessCore")
+ (r-repository . bioconductor)))
+ (build-system r-build-system)
+ (home-page "http://bioconductor.org/packages/preprocessCore")
+ (synopsis "Preprocess functions for Bioconductor")
+ (description
+ "A library of core preprocessing routines.")
+ (license license:lgpl2.0+)))
(define-public r-wgcna
+ (let ((commit "425bc170cc0873ddbd414675ac40f6d4d724c7cb"))
(package
(name "r-wgcna")
- (version "1.48")
- (source
- (origin
- (method url-fetch)
- (uri (cran-uri "WGCNA" version))
- (sha256
- (base32
- "18yl2v3s279saq318vd5hlwnqfm89rxmjjji778d2d26vviaf6bn"))))
+ (version (string-append "1.49-" commit))
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ ;; (url "https://github.com/genenetwork/WGCNA.git")
+ (url "https://github.com/pjotrp/WGCNA.git")
+ (commit commit)))
+ (file-name (string-append name "-" commit))
+ (sha256
+ (base32
+ "1zqnsb8s3065rq1y2y3l79zi8wmdwjkcjls96ypycrb7pmdil58j"))))
(properties `((upstream-name . "WGCNA")))
(build-system r-build-system)
- ;; (propagated-inputs
- ;; `( ;; ("r-annotationdbi" ,r-annotationdbi)
- ;; ("r-doparallel" ,r-doparallel)
- ;; ("r-dynamictreecut" ,r-dynamictreecut)
- ;; ("r-fastcluster" ,r-fastcluster)
- ;; ("r-foreach" ,r-foreach)
- ;; ("r-go.db" ,r-go.db)
- ;; ("r-grdevices" ,r-grdevices)
- ;; ("r-hmisc" ,r-hmisc)
- ;; ("r-impute" ,r-impute)
- ;; ("r-matrixstats" ,r-matrixstats)
- ;; ("r-parallel" ,r-parallel)
- ;; ("r-preprocesscore" ,r-preprocesscore)
- ;; ("r-splines" ,r-splines)
- ;; ("r-stats" ,r-stats)
- ;; ("r-survival" ,r-survival)
- ;; ("r-utils" ,r-utils)))
+ (propagated-inputs
+ `( ;; ("r-annotationdbi" ,r-annotationdbi)
+ ; ("r-biocparallel" ,r-biocparallel)
+ ("r-dynamictreecut" ,r-dynamictreecut)
+ ("r-doparallel" ,r-doparallel)
+ ("r-fastcluster" ,r-fastcluster)
+ ("r-foreach" ,r-foreach)
+ ("r-go-db" ,r-go-db)
+ ; ("r-grdevices" ,r-grdevices)
+ ("r-hmisc" ,r-hmisc)
+ ("r-impute" ,r-impute)
+ ("r-matrixstats" ,r-matrixstats)
+ ; ("r-parallel" ,r-parallel)
+ ("r-biocpreprocesscore" ,r-biocpreprocesscore)
+ ; ("r-splines" ,r-splines)
+ ; ("r-stats" ,r-stats)
+ ; ("r-survival" ,r-survival)
+ ; ("r-utils" ,r-utils)
+ ))
+ (arguments
+ `(
+ #:tests? #f)) ; no 'setup.py test'
(home-page
"http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/Rpackages/WGCNA/")
(synopsis
- "Weighted Correlation Network Analysis")
+ "Weighted gene correlation network analysis (wgcna)")
(description
- "Functions necessary to perform Weighted Correlation Network Analysis on high-dimensional data. Includes functions for rudimentary data cleaning, construction of correlation networks, module identification, summarization, and relating of variables and modules to sample traits. Also includes a number of utility functions for data manipulation and visualization.")
- (license license:gpl2+)))
+ "Functions necessary to perform Weighted Correlation Network
+Analysis on high-dimensional data. Includes functions for rudimentary
+data cleaning, construction of correlation networks, module
+identification, summarization, and relating of variables and modules
+to sample traits. Also includes a number of utility functions for
+data manipulation and visualization.")
+ (license license:gpl2+))))
(define-public qtlreaper
(package
@@ -277,7 +153,7 @@ test. For the permutation test, it performs only as many permutations
as are necessary to define the empirical P-value to a reasonable
precision. It also performs bootstrap resampling to estimate the
confidence region for the location of a putative QTL.")
- (license license:gpl2)))
+ (license license:gpl2+)))
(define-public plink2
(package
@@ -426,48 +302,6 @@ mixed model and some of its close relatives for genome-wide
association studies (GWAS).")
(license license:gpl3))))
-(define-public rdmd
- (let ((commit "4dba6877c"))
- (package
- (name "rdmd")
- (version "20160217")
- (source (origin
- (method git-fetch)
- (uri (git-reference
- (url "https://github.com/D-Programming-Language/tools.git")
- (commit commit)))
- (file-name (string-append name "-" commit))
- (sha256
- (base32
- "1pcx5lyqzrip86f4vv60x292rpvnwsq2hvl1znm9x9rn68f34m45"))))
- (build-system gnu-build-system)
- (arguments
- '(#:phases
- (modify-phases %standard-phases
- (delete 'configure)
- (delete 'check) ; There is no Makefile, so there's no 'make check'.
- (replace
- 'build
- (lambda _
- (zero? (system* "ldc2" "rdmd.d"))))
- (replace
- 'install
- (lambda* (#:key outputs #:allow-other-keys)
- (let ((bin (string-append (assoc-ref outputs "out") "/bin")))
- (mkdir-p bin)
- (copy-file "rdmd" (string-append bin "/rdmd"))))))))
- (native-inputs
- `(("ldc" ,ldc)))
- (home-page "https://github.com/D-Programming-Language/tools/")
- (synopsis "Tool for the D language which is used for compiling")
- (description
- "rdmd is a companion to the dmd compiler that simplifies the typical
-edit-compile-link-run or edit-make-run cycle to a rapid edit-run cycle. Like
-make and other tools, rdmd uses the relative dates of the files involved to
-minimize the amount of work necessary. Unlike make, rdmd tracks dependencies
-and freshness without requiring additional information from the user.")
- (license license:boost1.0))))
-
(define-public sambamba
(let ((commit "2ca5a2dbac5ab90c3b4c588519edc3edcb71df84"))
(package