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-rw-r--r--gnu/packages/bioinformatics.scm248
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+))))