diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 301 |
1 files changed, 298 insertions, 3 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 7c573e1626..76a1c17737 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -40,6 +40,7 @@ #:use-module (gnu packages compression) #:use-module (gnu packages cpio) #:use-module (gnu packages file) + #:use-module (gnu packages gawk) #:use-module (gnu packages java) #:use-module (gnu packages linux) #:use-module (gnu packages machine-learning) @@ -1354,6 +1355,87 @@ supports next-generation sequencing data in fasta/q and csfasta/q format from Illumina, Roche 454, and the SOLiD platform.") (license license:gpl3))) +(define-public fraggenescan + (package + (name "fraggenescan") + (version "1.20") + (source + (origin + (method url-fetch) + (uri + (string-append "mirror://sourceforge/fraggenescan/" + "FragGeneScan" version ".tar.gz")) + (sha256 + (base32 "1zzigqmvqvjyqv4945kv6nc5ah2xxm1nxgrlsnbzav3f5c0n0pyj")))) + (build-system gnu-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (delete 'configure) + (add-before 'build 'patch-paths + (lambda* (#:key outputs #:allow-other-keys) + (let* ((out (string-append (assoc-ref outputs "out"))) + (share (string-append out "/share/fraggenescan/"))) + (substitute* "run_FragGeneScan.pl" + (("system\\(\"rm") + (string-append "system(\"" (which "rm"))) + (("system\\(\"mv") + (string-append "system(\"" (which "mv"))) + ;; This script and other programs expect the training files + ;; to be in the non-standard location bin/train/XXX. Change + ;; this to be share/fraggenescan/train/XXX instead. + (("^\\$train.file = \\$dir.*") + (string-append "$train_file = \"" + share + "train/\".$FGS_train_file;"))) + (substitute* "run_hmm.c" + (("^ strcat\\(train_dir, \\\"train/\\\"\\);") + (string-append " strcpy(train_dir, \"" share "/train/\");"))) + (substitute* "post_process.pl" + (("^my \\$dir = substr.*") + (string-append "my $dir = \"" share "\";")))) + #t)) + (replace 'build + (lambda _ (and (zero? (system* "make" "clean")) + (zero? (system* "make" "fgs"))))) + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let* ((out (string-append (assoc-ref outputs "out"))) + (bin (string-append out "/bin/")) + (share (string-append out "/share/fraggenescan/train"))) + (install-file "run_FragGeneScan.pl" bin) + (install-file "FragGeneScan" bin) + (install-file "FGS_gff.py" bin) + (install-file "post_process.pl" bin) + (copy-recursively "train" share)))) + (delete 'check) + (add-after 'install 'post-install-check + ;; In lieu of 'make check', run one of the examples and check the + ;; output files gets created. + (lambda* (#:key outputs #:allow-other-keys) + (let* ((out (string-append (assoc-ref outputs "out"))) + (bin (string-append out "/bin/"))) + (and (zero? (system* (string-append bin "run_FragGeneScan.pl") + "-genome=./example/NC_000913.fna" + "-out=./test2" + "-complete=1" + "-train=complete")) + (file-exists? "test2.faa") + (file-exists? "test2.ffn") + (file-exists? "test2.gff") + (file-exists? "test2.out")))))))) + (inputs + `(("perl" ,perl) + ("python" ,python-2))) ;not compatible with python 3. + (home-page "https://sourceforge.net/projects/fraggenescan/") + (synopsis "Finds potentially fragmented genes in short reads") + (description + "FragGeneScan is a program for predicting bacterial and archaeal genes in +short and error-prone DNA sequencing reads. It can also be applied to predict +genes in incomplete assemblies or complete genomes.") + ;; GPL3+ according to private correspondense with the authors. + (license license:gpl3+))) + (define-public grit (package (name "grit") @@ -1690,7 +1772,7 @@ sequencing tag position and orientation.") (define-public mafft (package (name "mafft") - (version "7.221") + (version "7.267") (source (origin (method url-fetch) (uri (string-append @@ -1699,7 +1781,7 @@ sequencing tag position and orientation.") (file-name (string-append name "-" version ".tgz")) (sha256 (base32 - "0xi7klbsgi049vsrk6jiwh9wfj3b770gz3c8c7zwij448v0dr73d")))) + "1xl6xq1rfxkws0svrlhyqxhhwbv6r77jwblsdpcyiwzsscw6wlk0")))) (build-system gnu-build-system) (arguments `(#:tests? #f ; no automated tests, though there are tests in the read me @@ -1720,6 +1802,9 @@ sequencing tag position and orientation.") ;; remove mafft-homologs.rb from SCRIPTS (("^SCRIPTS = mafft mafft-homologs.rb") "SCRIPTS = mafft") + ;; remove mafft-homologs from MANPAGES + (("^MANPAGES = mafft.1 mafft-homologs.1") + "MANPAGES = mafft.1") ;; remove mafft-distance from PROGS (("^PROGS = dvtditr dndfast7 dndblast sextet5 mafft-distance") "PROGS = dvtditr dndfast7 dndblast sextet5") @@ -1732,9 +1817,22 @@ sequencing tag position and orientation.") (("^\t\\$\\(INSTALL\\) -m 644 \\$\\(MANPAGES\\) \ \\$\\(DESTDIR\\)\\$\\(LIBDIR\\)") "#")) #t)) + (add-after 'enter-dir 'patch-paths + (lambda* (#:key inputs #:allow-other-keys) + (substitute* '("pairash.c" + "mafft.tmpl") + (("perl") (which "perl")) + (("([\"`| ])awk" _ prefix) + (string-append prefix (which "awk"))) + (("grep") (which "grep"))) + #t)) (delete 'configure)))) (inputs - `(("perl" ,perl))) + `(("perl" ,perl) + ("gawk" ,gawk) + ("grep" ,grep))) + (propagated-inputs + `(("coreutils" ,coreutils))) (home-page "http://mafft.cbrc.jp/alignment/software/") (synopsis "Multiple sequence alignment program") (description @@ -3123,6 +3221,203 @@ BLAST, KEGG, GenBank, MEDLINE and GO.") ;; (LGPLv2.1+) and scripts in samples (which have GPL2 and GPL2+) (license (list license:ruby license:lgpl2.1+ license:gpl2+ )))) +(define-public r-acsnminer + (package + (name "r-acsnminer") + (version "0.15.11") + (source (origin + (method url-fetch) + (uri (cran-uri "ACSNMineR" version)) + (sha256 + (base32 + "1dl4drhjyazwm9wxlm8yfppwvvj4h6jxwmz8kfw5bxpb3jdnsqvy")))) + (properties `((upstream-name . "ACSNMineR"))) + (build-system r-build-system) + (propagated-inputs + `(("r-ggplot2" ,r-ggplot2) + ("r-gridextra" ,r-gridextra))) + (home-page "http://cran.r-project.org/web/packages/ACSNMineR") + (synopsis "Gene enrichment analysis") + (description + "This package provides tools to compute and represent gene set enrichment +or depletion from your data based on pre-saved maps from the @dfn{Atlas of +Cancer Signalling Networks} (ACSN) or user imported maps. The gene set +enrichment can be run with hypergeometric test or Fisher exact test, and can +use multiple corrections. Visualization of data can be done either by +barplots or heatmaps.") + (license license:gpl2+))) + +(define-public r-biocgenerics + (package + (name "r-biocgenerics") + (version "0.16.1") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "BiocGenerics" version)) + (sha256 + (base32 + "0f16ryy5f012hvksrwlmm33bcl7lw97i2jvhbnwfwl03j4w7nhc1")))) + (properties + `((upstream-name . "BiocGenerics") + (r-repository . bioconductor))) + (build-system r-build-system) + (home-page "http://bioconductor.org/packages/BiocGenerics") + (synopsis "S4 generic functions for Bioconductor") + (description + "This package provides S4 generic functions needed by many Bioconductor +packages.") + (license license:artistic2.0))) + +(define-public r-s4vectors + (package + (name "r-s4vectors") + (version "0.8.5") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "S4Vectors" version)) + (sha256 + (base32 + "10f4jxwlwsiy7zhb3kgp6anid0d7wkvrrljl80r3nhx38yr24l5k")))) + (properties + `((upstream-name . "S4Vectors") + (r-repository . bioconductor))) + (build-system r-build-system) + (propagated-inputs + `(("r-biocgenerics" ,r-biocgenerics))) + (home-page "http://bioconductor.org/packages/S4Vectors") + (synopsis "S4 implementation of vectors and lists") + (description + "The S4Vectors package defines the @code{Vector} and @code{List} virtual +classes and a set of generic functions that extend the semantic of ordinary +vectors and lists in R. Package developers can easily implement vector-like +or list-like objects as concrete subclasses of @code{Vector} or @code{List}. +In addition, a few low-level concrete subclasses of general interest (e.g. +@code{DataFrame}, @code{Rle}, and @code{Hits}) are implemented in the +S4Vectors package itself.") + (license license:artistic2.0))) + +(define-public r-iranges + (package + (name "r-iranges") + (version "2.4.6") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "IRanges" version)) + (sha256 + (base32 + "00x0266sys1fc5ipa639y84p6m6mgspk2xb099vcwmd3w4hypj9d")))) + (properties + `((upstream-name . "IRanges") + (r-repository . bioconductor))) + (build-system r-build-system) + (propagated-inputs + `(("r-biocgenerics" ,r-biocgenerics) + ("r-s4vectors" ,r-s4vectors))) + (home-page "http://bioconductor.org/packages/IRanges") + (synopsis "Infrastructure for manipulating intervals on sequences") + (description + "This package provides efficient low-level and highly reusable S4 classes +for storing ranges of integers, RLE vectors (Run-Length Encoding), and, more +generally, data that can be organized sequentially (formally defined as +@code{Vector} objects), as well as views on these @code{Vector} objects. +Efficient list-like classes are also provided for storing big collections of +instances of the basic classes. All classes in the package use consistent +naming and share the same rich and consistent \"Vector API\" as much as +possible.") + (license license:artistic2.0))) + +(define-public r-genomeinfodb + (package + (name "r-genomeinfodb") + (version "1.6.1") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "GenomeInfoDb" version)) + (sha256 + (base32 + "1j2n1v1mrw1fxn7cyffz112pm76wd6gy9q9qwlsfv3brbsqbvdbf")))) + (properties + `((upstream-name . "GenomeInfoDb") + (r-repository . bioconductor))) + (build-system r-build-system) + (propagated-inputs + `(("r-biocgenerics" ,r-biocgenerics) + ("r-iranges" ,r-iranges) + ("r-s4vectors" ,r-s4vectors))) + (home-page "http://bioconductor.org/packages/GenomeInfoDb") + (synopsis "Utilities for manipulating chromosome identifiers") + (description + "This package contains data and functions that define and allow +translation between different chromosome sequence naming conventions (e.g., +\"chr1\" versus \"1\"), including a function that attempts to place sequence +names in their natural, rather than lexicographic, order.") + (license license:artistic2.0))) + +(define-public r-xvector + (package + (name "r-xvector") + (version "0.10.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "XVector" version)) + (sha256 + (base32 + "0havwyr6xqk7w0rmbwfj9jq1djz7wzdz7w39adhklwzwz9l4ih3a")))) + (properties + `((upstream-name . "XVector") + (r-repository . bioconductor))) + (build-system r-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'use-system-zlib + (lambda _ + (substitute* "DESCRIPTION" + (("zlibbioc, ") "")) + (substitute* "NAMESPACE" + (("import\\(zlibbioc\\)") "")) + #t))))) + (inputs + `(("zlib" ,zlib))) + (propagated-inputs + `(("r-biocgenerics" ,r-biocgenerics) + ("r-iranges" ,r-iranges) + ("r-s4vectors" ,r-s4vectors))) + (home-page "http://bioconductor.org/packages/XVector") + (synopsis "Representation and manpulation of external sequences") + (description + "This package provides memory efficient S4 classes for storing sequences +\"externally\" (behind an R external pointer, or on disk).") + (license license:artistic2.0))) + +(define-public r-genomicranges + (package + (name "r-genomicranges") + (version "1.22.2") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "GenomicRanges" version)) + (sha256 + (base32 + "1jffvcs0jsi7q4l3pvjj6r73vll80csgkljvhqp0g2ixc43jjng9")))) + (properties + `((upstream-name . "GenomicRanges") + (r-repository . bioconductor))) + (build-system r-build-system) + (propagated-inputs + `(("r-biocgenerics" ,r-biocgenerics) + ("r-genomeinfodb" ,r-genomeinfodb) + ("r-xvector" ,r-xvector))) + (home-page "http://bioconductor.org/packages/GenomicRanges") + (synopsis "Representation and manipulation of genomic intervals") + (description + "This package provides tools to efficiently represent and manipulate +genomic annotations and alignments is playing a central role when it comes to +analyzing high-throughput sequencing data (a.k.a. NGS data). The +GenomicRanges package defines general purpose containers for storing and +manipulating genomic intervals and variables defined along a genome.") + (license license:artistic2.0))) + (define-public r-qtl (package (name "r-qtl") |