diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 248 |
1 files changed, 197 insertions, 51 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 67f24a6170..e74abf005f 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -2936,18 +2936,15 @@ indexing scheme is called a @dfn{Hierarchical Graph FM index} (HGFM).") (define-public hmmer (package (name "hmmer") - (version "3.1b2") + (version "3.2.1") (source (origin (method url-fetch) (uri (string-append - "http://eddylab.org/software/hmmer" - (version-major version) "/" - version "/hmmer-" version ".tar.gz")) + "http://eddylab.org/software/hmmer/hmmer-" version ".tar.gz")) (sha256 (base32 - "0djmgc0pfli0jilfx8hql1axhwhqxqb8rxg2r5rg07aw73sfs5nx")) - (patches (search-patches "hmmer-remove-cpu-specificity.patch")))) + "171bivy6xhgjsz5nv53n81pc3frnwz29ylblawk2bv46szwjjqd5")))) (build-system gnu-build-system) (native-inputs `(("perl" ,perl))) (home-page "http://hmmer.org/") @@ -2957,12 +2954,10 @@ indexing scheme is called a @dfn{Hierarchical Graph FM index} (HGFM).") sequences, and for making protein sequence alignments. It implements methods using probabilistic models called profile hidden Markov models (profile HMMs).") - (license (list license:gpl3+ - ;; The bundled library 'easel' is distributed - ;; under The Janelia Farm Software License. - (license:non-copyleft - "file://easel/LICENSE" - "See easel/LICENSE in the distribution."))))) + ;; hmmer uses non-portable SSE intrinsics so building fails on other + ;; platforms. + (supported-systems '("x86_64-linux" "i686-linux")) + (license license:bsd-3))) (define-public htseq (package @@ -4800,66 +4795,79 @@ phylogenies.") (define-public rsem (package (name "rsem") - (version "1.2.20") + (version "1.3.1") (source (origin - (method url-fetch) - (uri - (string-append "http://deweylab.biostat.wisc.edu/rsem/src/rsem-" - version ".tar.gz")) + (method git-fetch) + (uri (git-reference + (url "https://github.com/deweylab/RSEM.git") + (commit (string-append "v" version)))) (sha256 - (base32 "0nzdc0j0hjllhsd5f2xli95dafm3nawskigs140xzvjk67xh0r9q")) - (patches (search-patches "rsem-makefile.patch")) + (base32 "1jlq11d1p8qp64w75yj8cnbbd1a93viq10pzsbwal7vdn8fg13j1")) + (file-name (git-file-name name version)) (modules '((guix build utils))) (snippet '(begin - ;; remove bundled copy of boost + ;; remove bundled copy of boost and samtools (delete-file-recursively "boost") + (delete-file-recursively "samtools-1.3") #t)))) (build-system gnu-build-system) (arguments `(#:tests? #f ;no "check" target + #:make-flags + (list (string-append "BOOST=" + (assoc-ref %build-inputs "boost") + "/include/") + (string-append "SAMHEADERS=" + (assoc-ref %build-inputs "htslib") + "/include/htslib/sam.h") + (string-append "SAMLIBS=" + (assoc-ref %build-inputs "htslib") + "/lib/libhts.a")) #:phases (modify-phases %standard-phases ;; No "configure" script. ;; Do not build bundled samtools library. (replace 'configure - (lambda _ - (substitute* "Makefile" - (("^all : sam/libbam.a") "all : ")) - #t)) + (lambda _ + (substitute* "Makefile" + (("^all : \\$\\(PROGRAMS\\).*") "all: $(PROGRAMS)\n") + (("^\\$\\(SAMLIBS\\).*") "")) + #t)) (replace 'install - (lambda* (#:key outputs #:allow-other-keys) - (let* ((out (string-append (assoc-ref outputs "out"))) - (bin (string-append out "/bin/")) - (perl (string-append out "/lib/perl5/site_perl"))) - (mkdir-p bin) - (mkdir-p perl) - (for-each (lambda (file) - (install-file file bin)) - (find-files "." "rsem-.*")) - (install-file "rsem_perl_utils.pm" perl)) - #t)) - (add-after - 'install 'wrap-program - (lambda* (#:key outputs #:allow-other-keys) - (let ((out (assoc-ref outputs "out"))) - (for-each (lambda (prog) - (wrap-program (string-append out "/bin/" prog) - `("PERL5LIB" ":" prefix - (,(string-append out "/lib/perl5/site_perl"))))) - '("rsem-plot-transcript-wiggles" - "rsem-calculate-expression" - "rsem-generate-ngvector" - "rsem-run-ebseq" - "rsem-prepare-reference"))) - #t))))) + (lambda* (#:key outputs #:allow-other-keys) + (let* ((out (string-append (assoc-ref outputs "out"))) + (bin (string-append out "/bin/")) + (perl (string-append out "/lib/perl5/site_perl"))) + (mkdir-p bin) + (mkdir-p perl) + (for-each (lambda (file) + (install-file file bin)) + (find-files "." "rsem-.*")) + (install-file "rsem_perl_utils.pm" perl)) + #t)) + (add-after 'install 'wrap-program + (lambda* (#:key outputs #:allow-other-keys) + (let ((out (assoc-ref outputs "out"))) + (for-each (lambda (prog) + (wrap-program (string-append out "/bin/" prog) + `("PERL5LIB" ":" prefix + (,(string-append out "/lib/perl5/site_perl"))))) + '("rsem-calculate-expression" + "rsem-control-fdr" + "rsem-generate-data-matrix" + "rsem-generate-ngvector" + "rsem-plot-transcript-wiggles" + "rsem-prepare-reference" + "rsem-run-ebseq" + "rsem-run-prsem-testing-procedure"))) + #t))))) (inputs `(("boost" ,boost) - ("ncurses" ,ncurses) ("r-minimal" ,r-minimal) ("perl" ,perl) - ("samtools" ,samtools-0.1) + ("htslib" ,htslib-1.3) ("zlib" ,zlib))) (home-page "http://deweylab.biostat.wisc.edu/rsem/") (synopsis "Estimate gene expression levels from RNA-Seq data") @@ -13723,3 +13731,141 @@ juicer) and single-resolution or multi-resolution @code{.cool} files (for cooler). Both @code{hic} and @code{cool} files describe Hi-C contact matrices.") (license license:expat))) + +(define-public r-pore + (package + (name "r-pore") + (version "0.24") + (source + (origin + (method url-fetch) + (uri + (string-append "mirror://sourceforge/rpore/" version + "/poRe_" version ".tar.gz")) + (sha256 + (base32 "0pih9nljbv8g4x8rkk29i7aqq681b782r5s5ynp4nw9yzqnmmksv")))) + (properties `((upstream-name . "poRe"))) + (build-system r-build-system) + (propagated-inputs + `(("r-bit64" ,r-bit64) + ("r-data-table" ,r-data-table) + ("r-rhdf5" ,r-rhdf5) + ("r-shiny" ,r-shiny) + ("r-svdialogs" ,r-svdialogs))) + (home-page "https://sourceforge.net/projects/rpore/") + (synopsis "Visualize Nanopore sequencing data") + (description + "This package provides graphical user interfaces to organize and visualize Nanopore +sequencing data.") + ;; This is free software but the license variant is unclear: + ;; <https://github.com/mw55309/poRe_docs/issues/10>. + (license license:bsd-3))) + +(define-public r-xbioc + (let ((revision "1") + (commit "f798c187e376fd1ba27abd559f47bbae7e3e466b")) + (package + (name "r-xbioc") + (version (git-version "0.1.15" revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/renozao/xbioc.git") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "03hffh2f6z71y6l6dqpa5cql3hdaw7zigdi8sm2dzgx379k9rgrr")))) + (build-system r-build-system) + (propagated-inputs + `(("r-annotationdbi" ,r-annotationdbi) + ("r-assertthat" ,r-assertthat) + ("r-biobase" ,r-biobase) + ("r-biocinstaller" ,r-biocinstaller) + ("r-digest" ,r-digest) + ("r-pkgmaker" ,r-pkgmaker) + ("r-plyr" ,r-plyr) + ("r-reshape2" ,r-reshape2) + ("r-stringr" ,r-stringr))) + (home-page "https://github.com/renozao/xbioc/") + (synopsis "Extra base functions for Bioconductor") + (description "This package provides extra utility functions to perform +common tasks in the analysis of omics data, leveraging and enhancing features +provided by Bioconductor packages.") + (license license:gpl3+)))) + +(define-public r-cssam + (let ((revision "1") + (commit "9ec58c982fa551af0d80b1a266890d92954833f2")) + (package + (name "r-cssam") + (version (git-version "1.4" revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/shenorrLab/csSAM.git") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "128syf9v39gk0z3ip000qpsjbg6l1siyq6c8b0hz41dzg5achyb3")))) + (build-system r-build-system) + (propagated-inputs + `(("r-formula" ,r-formula) + ("r-ggplot2" ,r-ggplot2) + ("r-pkgmaker" ,r-pkgmaker) + ("r-plyr" ,r-plyr) + ("r-rngtools" ,r-rngtools) + ("r-scales" ,r-scales))) + (home-page "https://github.com/shenorrLab/csSAM/") + (synopsis "Cell type-specific statistical analysis of microarray") + (description "This package implements the method csSAM that computes +cell-specific differential expression from measured cell proportions using +SAM.") + ;; Any version + (license license:lgpl2.1+)))) + +(define-public r-bseqsc + (let ((revision "1") + (commit "fef3f3e38dcf3df37103348b5780937982b43b98")) + (package + (name "r-bseqsc") + (version (git-version "1.0" revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/shenorrLab/bseqsc.git") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1prw13wa20f7wlc3gkkls66n1kxz8d28qrb8icfqdwdnnv8w5qg8")))) + (build-system r-build-system) + (propagated-inputs + `(("r-abind" ,r-abind) + ("r-annotationdbi" ,r-annotationdbi) + ("r-biobase" ,r-biobase) + ("r-cssam" ,r-cssam) + ("r-dplyr" ,r-dplyr) + ("r-e1071" ,r-e1071) + ("r-edger" ,r-edger) + ("r-ggplot2" ,r-ggplot2) + ("r-nmf" ,r-nmf) + ("r-openxlsx" ,r-openxlsx) + ("r-pkgmaker" ,r-pkgmaker) + ("r-plyr" ,r-plyr) + ("r-preprocesscore" ,r-preprocesscore) + ("r-rngtools" ,r-rngtools) + ("r-scales" ,r-scales) + ("r-stringr" ,r-stringr) + ("r-xbioc" ,r-xbioc))) + (home-page "https://github.com/shenorrLab/bseqsc") + (synopsis "Deconvolution of bulk sequencing experiments using single cell data") + (description "BSeq-sc is a bioinformatics analysis pipeline that +leverages single-cell sequencing data to estimate cell type proportion and +cell type-specific gene expression differences from RNA-seq data from bulk +tissue samples. This is a companion package to the publication \"A +single-cell transcriptomic map of the human and mouse pancreas reveals inter- +and intra-cell population structure.\" Baron et al. Cell Systems (2016) +@url{https://www.ncbi.nlm.nih.gov/pubmed/27667365}.") + (license license:gpl2+)))) |