diff options
Diffstat (limited to 'gn/packages/bioinformatics.scm')
| -rw-r--r-- | gn/packages/bioinformatics.scm | 290 |
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 |