diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 449 |
1 files changed, 149 insertions, 300 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index a556354438..ffa2618458 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -2620,7 +2620,7 @@ with Python.") (define-public delly (package (name "delly") - (version "0.7.9") + (version "0.8.3") (source (origin (method git-fetch) (uri (git-reference @@ -2628,7 +2628,7 @@ with Python.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "034jqsxswy9gqdh2zkgc1js99qkv75ks4xvzgmh0284sraagv61z")) + (base32 "1ibnplgfzj96w8glkx17v7sld3pm402fr5ybmf3h0rlcryabxrqy")) (modules '((guix build utils))) (snippet '(begin @@ -2652,9 +2652,9 @@ with Python.") #t)))))) (inputs `(("boost" ,boost) + ("bzip2" ,bzip2) ("htslib" ,htslib) - ("zlib" ,zlib) - ("bzip2" ,bzip2))) + ("zlib" ,zlib))) (home-page "https://github.com/dellytools/delly") (synopsis "Integrated structural variant prediction method") (description "Delly is an integrated structural variant prediction method @@ -6357,14 +6357,14 @@ bioinformatics file formats, sequence alignment, and more.") (define-public seqmagick (package (name "seqmagick") - (version "0.7.0") + (version "0.8.0") (source (origin (method url-fetch) (uri (pypi-uri "seqmagick" version)) (sha256 (base32 - "12bfyp8nqi0hd36rmj450aygafp01qy3hkbvlwn3bk39pyjjkgg5")))) + "0pf98da7i59q47gwrbx0wjk6xlvbybiwphw80w7h4ydjj0579a2b")))) (build-system python-build-system) (inputs `(("python-biopython" ,python-biopython))) @@ -8510,57 +8510,6 @@ Stephens (1990).") throughput genetic sequencing data sets using regression methods.") (license license:artistic2.0))) -(define-public r-qtl - (package - (name "r-qtl") - (version "1.46-2") - (source - (origin - (method url-fetch) - (uri (string-append "mirror://cran/src/contrib/qtl_" - version ".tar.gz")) - (sha256 - (base32 - "0rbwcnvyy96gq1dsgpxx03pv423qya26h6ws5y0blj3blfdmj83a")))) - (build-system r-build-system) - (home-page "https://rqtl.org/") - (synopsis "R package for analyzing QTL experiments in genetics") - (description "R/qtl is an extension library for the R statistics -system. It is used to analyze experimental crosses for identifying -genes contributing to variation in quantitative traits (so-called -quantitative trait loci, QTLs). - -Using a hidden Markov model, R/qtl estimates genetic maps, to -identify genotyping errors, and to perform single-QTL and two-QTL, -two-dimensional genome scans.") - (license license:gpl3))) - -(define-public r-qtl2 - (package - (name "r-qtl2") - (version "0.22-11") - (source (origin - (method url-fetch) - (uri (cran-uri "qtl2" version)) - (sha256 - (base32 "0dfdzjylqzc92dcszawc8cyinxccjm3p36v9vcq9ma818pqcanmr")))) - (build-system r-build-system) - (propagated-inputs - `(("r-data-table" ,r-data-table) - ("r-jsonlite" ,r-jsonlite) - ("r-rcpp" ,r-rcpp) - ("r-rcppeigen" ,r-rcppeigen) - ("r-rsqlite" ,r-rsqlite) - ("r-yaml" ,r-yaml))) - (home-page "https://kbroman.org/qtl2/") - (synopsis "Quantitative Trait Locus Mapping in Experimental Crosses") - (description - "This package provides a set of tools to perform @dfn{Quantitative Trait -Locus} (QTL) analysis in experimental crosses. It is a reimplementation of the -@code{R/qtl} package to better handle high-dimensional data and complex cross -designs. Broman et al. (2018) <doi:10.1534/genetics.118.301595>.") - (license license:gpl3))) - (define-public r-zlibbioc (package (name "r-zlibbioc") @@ -9444,28 +9393,6 @@ imaging data that can be used in subsequent analyses to adjust for unknown, unmodeled, or latent sources of noise.") (license license:artistic2.0))) -(define-public r-seqminer - (package - (name "r-seqminer") - (version "8.0") - (source - (origin - (method url-fetch) - (uri (cran-uri "seqminer" version)) - (sha256 - (base32 - "00jzj8mwb0zaiwlifd41b26mrq9mzigj18nc29dydi0r42hxg16i")))) - (build-system r-build-system) - (inputs - `(("zlib" ,zlib))) - (home-page "http://seqminer.genomic.codes") - (synopsis "Read nucleotide sequence data (VCF, BCF, and METAL formats)") - (description - "This package provides tools to integrate nucleotide sequencing -data (variant call format, e.g. VCF or BCF) or meta-analysis results in R.") - ;; Any version of the GPL is acceptable - (license (list license:gpl2+ license:gpl3+)))) - (define-public r-raremetals2 (package (name "r-raremetals2") @@ -9498,32 +9425,6 @@ for analyzing gene-level association tests in meta-analyses for binary trait.") (license license:gpl3))) -(define-public r-maldiquant - (package - (name "r-maldiquant") - (version "1.19.3") - (source - (origin - (method url-fetch) - (uri (cran-uri "MALDIquant" version)) - (sha256 - (base32 - "0b7kdz3x4sdq413h1q09l1qhcvdnnwv6fqsqwllks1cd3xy34c57")))) - (properties `((upstream-name . "MALDIquant"))) - (build-system r-build-system) - (home-page "https://cran.r-project.org/web/packages/MALDIquant") - (synopsis "Quantitative analysis of mass spectrometry data") - (description - "This package provides a complete analysis pipeline for matrix-assisted -laser desorption/ionization-time-of-flight (MALDI-TOF) and other -two-dimensional mass spectrometry data. In addition to commonly used plotting -and processing methods it includes distinctive features, namely baseline -subtraction methods such as morphological filters (TopHat) or the -statistics-sensitive non-linear iterative peak-clipping algorithm (SNIP), peak -alignment using warping functions, handling of replicated measurements as well -as allowing spectra with different resolutions.") - (license license:gpl3+))) - (define-public r-protgenerics (package (name "r-protgenerics") @@ -9834,71 +9735,6 @@ contains a number of utilities to explore the MS/MS results and assess missed and irregular enzymatic cleavages, mass measurement accuracy, etc.") (license license:artistic2.0))) -(define-public r-seurat - (package - (name "r-seurat") - (version "3.2.0") - (source (origin - (method url-fetch) - (uri (cran-uri "Seurat" version)) - (sha256 - (base32 - "1vj3dlsqakgnn4x1jz9fkl2cy0jzc5s65h1c20fnamr7lk45pnf2")))) - (properties `((upstream-name . "Seurat"))) - (build-system r-build-system) - (propagated-inputs - `(("r-ape" ,r-ape) - ("r-cluster" ,r-cluster) - ("r-cowplot" ,r-cowplot) - ("r-fitdistrplus" ,r-fitdistrplus) - ("r-future" ,r-future) - ("r-future-apply" ,r-future-apply) - ("r-ggplot2" ,r-ggplot2) - ("r-ggrepel" ,r-ggrepel) - ("r-ggridges" ,r-ggridges) - ("r-httr" ,r-httr) - ("r-ica" ,r-ica) - ("r-igraph" ,r-igraph) - ("r-irlba" ,r-irlba) - ("r-jsonlite" ,r-jsonlite) - ("r-kernsmooth" ,r-kernsmooth) - ("r-leiden" ,r-leiden) - ("r-lmtest" ,r-lmtest) - ("r-mass" ,r-mass) - ("r-matrix" ,r-matrix) - ("r-miniui" ,r-miniui) - ("r-patchwork" ,r-patchwork) - ("r-pbapply" ,r-pbapply) - ("r-plotly" ,r-plotly) - ("r-png" ,r-png) - ("r-rann" ,r-rann) - ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-rcpp" ,r-rcpp) - ("r-rcppannoy" ,r-rcppannoy) - ("r-rcppeigen" ,r-rcppeigen) - ("r-rcppprogress" ,r-rcppprogress) - ("r-reticulate" ,r-reticulate) - ("r-rlang" ,r-rlang) - ("r-rocr" ,r-rocr) - ("r-rsvd" ,r-rsvd) - ("r-rtsne" ,r-rtsne) - ("r-scales" ,r-scales) - ("r-sctransform" ,r-sctransform) - ("r-shiny" ,r-shiny) - ("r-spatstat" ,r-spatstat) - ("r-tibble" ,r-tibble) - ("r-uwot" ,r-uwot))) - (home-page "http://www.satijalab.org/seurat") - (synopsis "Seurat is an R toolkit for single cell genomics") - (description - "This package is an R package designed for QC, analysis, and -exploration of single cell RNA-seq data. It easily enables widely-used -analytical techniques, including the identification of highly variable genes, -dimensionality reduction; PCA, ICA, t-SNE, standard unsupervised clustering -algorithms; density clustering, hierarchical clustering, k-means, and the -discovery of differentially expressed genes and markers.") - (license license:gpl3))) - (define-public r-aroma-light (package (name "r-aroma-light") @@ -11100,34 +10936,6 @@ are optimized per data type and for subsetted calculations such that both memory usage and processing time is minimized.") (license license:expat))) -(define-public r-phangorn - (package - (name "r-phangorn") - (version "2.5.5") - (source - (origin - (method url-fetch) - (uri (cran-uri "phangorn" version)) - (sha256 - (base32 - "0ihkaykqjmf80d8wrk3saphxvnv58zma6pd13633bd3cwanc33f5")))) - (build-system r-build-system) - (propagated-inputs - `(("r-ape" ,r-ape) - ("r-fastmatch" ,r-fastmatch) - ("r-igraph" ,r-igraph) - ("r-magrittr" ,r-magrittr) - ("r-matrix" ,r-matrix) - ("r-quadprog" ,r-quadprog) - ("r-rcpp" ,r-rcpp))) - (home-page "https://github.com/KlausVigo/phangorn") - (synopsis "Phylogenetic analysis in R") - (description - "Phangorn is a package for phylogenetic analysis in R. It supports -estimation of phylogenetic trees and networks using Maximum Likelihood, -Maximum Parsimony, distance methods and Hadamard conjugation.") - (license license:gpl2+))) - (define-public r-dropbead (let ((commit "d746c6f3b32110428ea56d6a0001ce52a251c247") (revision "2")) @@ -13276,37 +13084,6 @@ analyses in addition to large-scale sequence-level searches.") (supported-systems '("x86_64-linux")) (license license:bsd-3)))) -(define-public r-diversitree - (package - (name "r-diversitree") - (version "0.9-13") - (source - (origin - (method url-fetch) - (uri (cran-uri "diversitree" version)) - (sha256 - (base32 - "00vi4klywi35hd170ksjv3xja3hqqbkcidcnrrlpgv4179k0azix")))) - (build-system r-build-system) - (native-inputs - `(("gfortran" ,gfortran))) - (inputs `(("fftw" ,fftw) ("gsl" ,gsl))) - (propagated-inputs - `(("r-ape" ,r-ape) - ("r-desolve" ,r-desolve) - ("r-rcpp" ,r-rcpp) - ("r-subplex" ,r-subplex))) - (home-page "https://www.zoology.ubc.ca/prog/diversitree") - (synopsis "Comparative 'phylogenetic' analyses of diversification") - (description "This package contains a number of comparative \"phylogenetic\" -methods, mostly focusing on analysing diversification and character evolution. -Contains implementations of \"BiSSE\" (Binary State Speciation and Extinction) -and its unresolved tree extensions, \"MuSSE\" (Multiple State Speciation and -Extinction), \"QuaSSE\", \"GeoSSE\", and \"BiSSE-ness\" Other included methods -include Markov models of discrete and continuous trait evolution and constant -rate speciation and extinction.") - (license license:gpl2+))) - (define-public sjcount ;; There is no tag for version 3.2, nor is there a release archive. (let ((commit "292d3917cadb3f6834c81e509c30e61cd7ead6e5") @@ -14306,33 +14083,6 @@ downstream analysis. Poretools operates directly on the native FAST5, a variant of the Hierarchical Data Format (HDF5) standard.") (license license:expat)))) -(define-public r-absfiltergsea - (package - (name "r-absfiltergsea") - (version "1.5.1") - (source - (origin - (method url-fetch) - (uri (cran-uri "AbsFilterGSEA" version)) - (sha256 - (base32 "15srxkxsvn38kd5frdrwfdf0ad8gskrd0h01wmdf9hglq8fjrp7w")))) - (properties `((upstream-name . "AbsFilterGSEA"))) - (build-system r-build-system) - (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-deseq" ,r-deseq) - ("r-limma" ,r-limma) - ("r-rcpp" ,r-rcpp) - ("r-rcpparmadillo" ,r-rcpparmadillo))) - (home-page "https://cran.r-project.org/web/packages/AbsFilterGSEA/") - (synopsis "Improved false positive control of gene-permuting with absolute filtering") - (description - "This package provides a function that performs gene-permuting of a gene-set -enrichment analysis (GSEA) calculation with or without the absolute filtering. - Without filtering, users can perform (original) two-tailed or one-tailed -absolute GSEA.") - (license license:gpl2))) - (define-public jamm (package (name "jamm") @@ -15400,12 +15150,34 @@ mutations from scRNA-Seq data.") (string-append "HTS_LIB=" htslib-ref "/lib/libhts.a") (string-append "INCLUDES= -I" htslib-ref "/include/htslib") "HTS_HEADERS=" ; No need to check for headers here. - (string-append "LIBPATH=-L. -L" htslib-ref "/include"))))) + (string-append "LIBPATH=-L. -L" htslib-ref "/include")) + (invoke "g++" "-shared" "-o" "libtabixpp.so" "tabix.o" "-lhts") + (invoke "ar" "rcs" "libtabixpp.a" "tabix.o")))) (replace 'install (lambda* (#:key outputs #:allow-other-keys) - (let ((bin (string-append (assoc-ref outputs "out") "/bin"))) - (install-file "tabix++" bin)) - #t))))) + (let* ((out (assoc-ref outputs "out")) + (lib (string-append out "/lib")) + (bin (string-append out "/bin"))) + (install-file "tabix++" bin) + (install-file "libtabixpp.so" lib) + (install-file "libtabixpp.a" lib) + (install-file "tabix.hpp" (string-append out "/include")) + (mkdir-p (string-append lib "/pkgconfig")) + (with-output-to-file (string-append lib "/pkgconfig/tabixpp.pc") + (lambda _ + (format #t "prefix=~a~@ + exec_prefix=${prefix}~@ + libdir=${exec_prefix}/lib~@ + includedir=${prefix}/include~@ + ~@ + ~@ + Name: libtabixpp~@ + Version: ~a~@ + Description: C++ wrapper around tabix project~@ + Libs: -L${libdir} -ltabixpp~@ + Cflags: -I${includedir}~%" + out ,version))) + #t)))))) (home-page "https://github.com/ekg/tabixpp") (synopsis "C++ wrapper around tabix project") (description "This is a C++ wrapper around the Tabix project which abstracts @@ -15432,13 +15204,45 @@ some of the details of opening and jumping in tabix-indexed files.") #:phases (modify-phases %standard-phases (delete 'configure) ; There is no configure phase. + (add-after 'unpack 'patch-source + (lambda _ + (substitute* "Makefile" + (("-c ") "-c -fPIC ")) + #t)) + (add-after 'build 'build-dynamic + (lambda _ + (invoke "g++" + "-shared" "-o" "libsmithwaterman.so" + "smithwaterman.o" "SmithWatermanGotoh.o" + "disorder.o" "BandedSmithWaterman.o" + "LeftAlign.o" "Repeats.o" "IndelAllele.o"))) (replace 'install (lambda* (#:key outputs #:allow-other-keys) (let* ((out (assoc-ref outputs "out")) (bin (string-append out "/bin")) (lib (string-append out "/lib"))) (install-file "smithwaterman" bin) - (install-file "libsw.a" lib)) + (for-each + (lambda (file) + (install-file file (string-append out "/include/smithwaterman"))) + (find-files "." "\\.h$")) + (install-file "libsmithwaterman.so" lib) + (install-file "libsw.a" lib) + (mkdir-p (string-append lib "/pkgconfig")) + (with-output-to-file (string-append lib "/pkgconfig/smithwaterman.pc") + (lambda _ + (format #t "prefix=~a~@ + exec_prefix=${prefix}~@ + libdir=${exec_prefix}/lib~@ + includedir=${prefix}/include/smithwaterman~@ + ~@ + ~@ + Name: smithwaterman~@ + Version: ~a~@ + Description: smith-waterman-gotoh alignment algorithm~@ + Libs: -L${libdir} -lsmithwaterman~@ + Cflags: -I${includedir}~%" + out ,version)))) #t))))) (home-page "https://github.com/ekg/smithwaterman") (synopsis "Implementation of the Smith-Waterman algorithm") @@ -15528,10 +15332,43 @@ neural networks.") #:phases (modify-phases %standard-phases (delete 'configure) ; There is no configure phase. + (add-after 'unpack 'patch-source + (lambda _ + (substitute* "Makefile" + (("-c ") "-c -fPIC ")) + #t)) + (add-after 'build 'build-dynamic + (lambda _ + (invoke "g++" + "-shared" "-o" "libfastahack.so" + "Fasta.o" "FastaHack.o" "split.o" "disorder.o"))) (replace 'install (lambda* (#:key outputs #:allow-other-keys) - (let ((bin (string-append (assoc-ref outputs "out") "/bin"))) - (install-file "fastahack" bin)) + (let* ((out (assoc-ref outputs "out")) + (lib (string-append out "/lib")) + (bin (string-append out "/bin"))) + (mkdir-p (string-append out "/include/fastahack")) + (for-each + (lambda (file) + (install-file file (string-append out "/include/fastahack"))) + (find-files "." "\\.h$")) + (install-file "fastahack" bin) + (install-file "libfastahack.so" lib) + (mkdir-p (string-append lib "/pkgconfig")) + (with-output-to-file (string-append lib "/pkgconfig/fastahack.pc") + (lambda _ + (format #t "prefix=~a~@ + exec_prefix=${prefix}~@ + libdir=${exec_prefix}/lib~@ + includedir=${prefix}/include/fastahack~@ + ~@ + ~@ + Name: fastahack~@ + Version: ~a~@ + Description: Indexing and sequence extraction from FASTA files~@ + Libs: -L${libdir} -lfastahack~@ + Cflags: -I${includedir}~%" + out ,version)))) #t))))) (home-page "https://github.com/ekg/fastahack") (synopsis "Indexing and sequence extraction from FASTA files") @@ -15554,9 +15391,16 @@ library automatically handles index file generation and use.") "/vcflib-" version "-src.tar.gz")) (sha256 (base32 "14zzrg8hg8cq9cvq2wdvp21j7nmxxkjrbagw2apd2yqv2kyx42lm")) + (patches (search-patches "vcflib-use-shared-libraries.patch")) (modules '((guix build utils))) (snippet `(begin + (substitute* (find-files "." "\\.(h|c)(pp)?$") + (("\"SmithWatermanGotoh.h\"") "<smithwaterman/SmithWatermanGotoh.h>") + (("\"convert.h\"") "<smithwaterman/convert.h>") + (("\"disorder.h\"") "<smithwaterman/disorder.h>") + (("\"tabix.hpp\"") "<tabix.hpp>") + (("\"Fasta.h\"") "<fastahack/Fasta.h>")) (for-each delete-file-recursively '("fastahack" "filevercmp" "fsom" "googletest" "intervaltree" "libVCFH" "multichoose" "smithwaterman" "tabixpp")) @@ -15564,34 +15408,34 @@ library automatically handles index file generation and use.") (build-system gnu-build-system) (inputs `(("htslib" ,htslib) + ("fastahack" ,fastahack) ("perl" ,perl) ("python" ,python) + ("smithwaterman" ,smithwaterman) + ("tabixpp" ,tabixpp) + ("xz" ,xz) ("zlib" ,zlib))) (native-inputs - `(;; Submodules. + `(("pkg-config" ,pkg-config) + ;; Submodules. ;; This package builds against the .o files so we need to extract the source. - ("fastahack-src" ,(package-source fastahack)) ("filevercmp-src" ,(package-source filevercmp)) - ("fsom-src" ,(package-source fsom)) ("intervaltree-src" ,(package-source intervaltree)) - ("multichoose-src" ,(package-source multichoose)) - ("smithwaterman-src" ,(package-source smithwaterman)) - ("tabixpp-src" ,(package-source tabixpp)))) + ("multichoose-src" ,(package-source multichoose)))) (arguments `(#:tests? #f ; no tests - #:make-flags (list (string-append "HTS_LIB=" - (assoc-ref %build-inputs "htslib") - "/lib/libhts.a") - (string-append "HTS_INCLUDES= -I" - (assoc-ref %build-inputs "htslib") - "/include/htslib") - (string-append "HTS_LDFLAGS= -L" - (assoc-ref %build-inputs "htslib") - "/include/htslib" " -lhts")) #:phases (modify-phases %standard-phases + (add-after 'unpack 'set-flags + (lambda* (#:key outputs #:allow-other-keys) + (substitute* "Makefile" + (("LDFLAGS =") + (string-append "LDFLAGS = -Wl,-rpath=" + (assoc-ref outputs "out") "/lib "))) + (substitute* "filevercmp/Makefile" + (("-c") "-c -fPIC")) + #t)) (delete 'configure) - (delete 'check) (add-after 'unpack 'unpack-submodule-sources (lambda* (#:key inputs #:allow-other-keys) (let ((unpack (lambda (source target) @@ -15603,34 +15447,39 @@ library automatically handles index file generation and use.") (assoc-ref inputs source) "--strip-components=1")))))) (and - (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"))))) - (replace 'build - (lambda* (#:key inputs make-flags #:allow-other-keys) - (let ((htslib (assoc-ref inputs "htslib"))) - (with-directory-excursion "tabixpp" - (substitute* "Makefile" - (("-Ihtslib") (string-append "-I" htslib "/include/htslib")) - (("-Lhtslib") (string-append "-L" htslib "/lib/htslib")) - (("htslib/htslib") (string-append htslib "/include/htslib"))) - (invoke "make" - (string-append "HTS_LIB=" htslib "/lib/libhts.a"))) - (apply invoke "make" "CC=gcc" "CFLAGS=-Itabixpp" make-flags)))) + (unpack "multichoose-src" "multichoose"))))) (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"))) + (let* ((out (assoc-ref outputs "out")) + (bin (string-append out "/bin")) + (lib (string-append out "/lib"))) (for-each (lambda (file) (install-file file bin)) (find-files "bin" ".*")) - ;; The header files in src/ do not interface libvcflib, - ;; therefore they are left out. - (install-file "libvcflib.a" lib)) + (install-file "libvcflib.so" lib) + (install-file "libvcflib.a" lib) + (for-each + (lambda (file) + (install-file file (string-append out "/include"))) + (find-files "include" "\\.h(pp)?$")) + (mkdir-p (string-append lib "/pkgconfig")) + (with-output-to-file (string-append lib "/pkgconfig/vcflib.pc") + (lambda _ + (format #t "prefix=~a~@ + exec_prefix=${prefix}~@ + libdir=${exec_prefix}/lib~@ + includedir=${prefix}/include~@ + ~@ + ~@ + Name: libvcflib~@ + Version: ~a~@ + Requires: smithwaterman, fastahack~@ + Description: C++ library for parsing and manipulating VCF files~@ + Libs: -L${libdir} -lvcflib~@ + Cflags: -I${includedir}~%" + out ,version)))) #t))))) (home-page "https://github.com/vcflib/vcflib/") (synopsis "Library for parsing and manipulating VCF files") |