diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 230 |
1 files changed, 211 insertions, 19 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 314d0ad322..a9df676fc6 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -654,6 +654,73 @@ gapped, local, and paired-end alignment modes.") (supported-systems '("x86_64-linux")) (license license:gpl3+))) +(define-public tophat + (package + (name "tophat") + (version "2.1.0") + (source (origin + (method url-fetch) + (uri (string-append + "http://ccb.jhu.edu/software/tophat/downloads/tophat-" + version ".tar.gz")) + (sha256 + (base32 + "168zlzykq622zbgkh90a90f1bdgsxkscq2zxzbj8brq80hbjpyp7")) + (patches (list (search-patch "tophat-build-with-later-seqan.patch"))) + (modules '((guix build utils))) + (snippet + '(begin + ;; Remove bundled SeqAn and samtools + (delete-file-recursively "src/SeqAn-1.3") + (delete-file-recursively "src/samtools-0.1.18") + #t)))) + (build-system gnu-build-system) + (arguments + '(#:parallel-build? #f ; not supported + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'use-system-samtools + (lambda* (#:key inputs #:allow-other-keys) + (substitute* "src/Makefile.in" + (("(noinst_LIBRARIES = )\\$\\(SAMLIB\\)" _ prefix) prefix) + (("\\$\\(SAMPROG\\): \\$\\(SAMLIB\\)") "") + (("SAMPROG = samtools_0\\.1\\.18") "") + (("\\$\\(samtools_0_1_18_SOURCES\\)") "") + (("am__EXEEXT_1 = samtools_0\\.1\\.18\\$\\(EXEEXT\\)") "")) + (substitute* '("src/common.cpp" + "src/tophat.py") + (("samtools_0.1.18") (which "samtools"))) + (substitute* '("src/common.h" + "src/bam2fastx.cpp") + (("#include \"bam.h\"") "#include <samtools/bam.h>") + (("#include \"sam.h\"") "#include <samtools/sam.h>")) + (substitute* '("src/bwt_map.h" + "src/map2gtf.h" + "src/align_status.h") + (("#include <bam.h>") "#include <samtools/bam.h>") + (("#include <sam.h>") "#include <samtools/sam.h>")) + #t))))) + (inputs + `(("boost" ,boost) + ("bowtie" ,bowtie) + ("samtools" ,samtools-0.1) + ("ncurses" ,ncurses) + ("python" ,python-2) + ("perl" ,perl) + ("zlib" ,zlib) + ("seqan" ,seqan))) + (home-page "http://ccb.jhu.edu/software/tophat/index.shtml") + (synopsis "Spliced read mapper for RNA-Seq data") + (description + "TopHat is a fast splice junction mapper for nucleotide sequence +reads produced by the RNA-Seq method. It aligns RNA-Seq reads to +mammalian-sized genomes using the ultra high-throughput short read +aligner Bowtie, and then analyzes the mapping results to identify +splice junctions between exons.") + ;; TopHat is released under the Boost Software License, Version 1.0 + ;; See https://github.com/infphilo/tophat/issues/11#issuecomment-121589893 + (license license:boost1.0))) + (define-public bwa (package (name "bwa") @@ -915,6 +982,64 @@ files between different genome assemblies. It supports most commonly used file formats including SAM/BAM, Wiggle/BigWig, BED, GFF/GTF, VCF.") (license license:gpl2+))) +(define-public cufflinks + (package + (name "cufflinks") + (version "2.2.1") + (source (origin + (method url-fetch) + (uri (string-append "http://cole-trapnell-lab.github.io/" + "cufflinks/assets/downloads/cufflinks-" + version ".tar.gz")) + (sha256 + (base32 + "1bnm10p8m7zq4qiipjhjqb24csiqdm1pwc8c795z253r2xk6ncg8")))) + (build-system gnu-build-system) + (arguments + `(#:make-flags + (list + ;; The includes for "eigen" are located in a subdirectory. + (string-append "EIGEN_CPPFLAGS=" + "-I" (assoc-ref %build-inputs "eigen") + "/include/eigen3/") + ;; Cufflinks must be linked with various boost libraries. + (string-append "LDFLAGS=" + (string-join '("-lboost_system" + "-lboost_serialization" + "-lboost_thread")))) + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'fix-search-for-bam + (lambda _ + (substitute* '("ax_bam.m4" + "configure" + "src/hits.h") + (("<bam/sam\\.h>") "<samtools/sam.h>") + (("<bam/bam\\.h>") "<samtools/bam.h>") + (("<bam/version\\.hpp>") "<samtools/version.h>")) + #t))) + #:configure-flags + (list (string-append "--with-bam=" + (assoc-ref %build-inputs "samtools"))))) + (inputs + `(("eigen" ,eigen) + ("samtools" ,samtools-0.1) + ("htslib" ,htslib) + ("boost" ,boost) + ("python" ,python-2) + ("zlib" ,zlib))) + (home-page "http://cole-trapnell-lab.github.io/cufflinks/") + (synopsis "Transcriptome assembly and RNA-Seq expression analysis") + (description + "Cufflinks assembles RNA transcripts, estimates their abundances, +and tests for differential expression and regulation in RNA-Seq +samples. It accepts aligned RNA-Seq reads and assembles the +alignments into a parsimonious set of transcripts. Cufflinks then +estimates the relative abundances of these transcripts based on how +many reads support each one, taking into account biases in library +preparation protocols.") + (license license:boost1.0))) + (define-public cutadapt (package (name "cutadapt") @@ -3016,40 +3141,107 @@ optimized for modern read lengths of 100 bases or higher, and takes advantage of these reads to align data quickly through a hash-based indexing scheme.") (license license:asl2.0))) +(define-public sortmerna + (package + (name "sortmerna") + (version "2.0") + (source + (origin + (method url-fetch) + (uri (string-append + "https://github.com/biocore/sortmerna/archive/" + version ".tar.gz")) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "1670a92x1vvkacnvgr2i5xac3ls6lp4pc3n0bccnmllsnymggcf0")))) + (build-system gnu-build-system) + (outputs '("out" ;for binaries + "db")) ;for sequence databases + (arguments + `(#:phases + (modify-phases %standard-phases + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out")) + (bin (string-append out "/bin")) + (db (assoc-ref outputs "db")) + (share + (string-append db "/share/sortmerna/rRNA_databases"))) + (install-file "sortmerna" bin) + (install-file "indexdb_rna" bin) + (for-each (lambda (file) + (install-file file share)) + (find-files "rRNA_databases" ".*fasta")) + #t)))))) + (home-page "http://bioinfo.lifl.fr/RNA/sortmerna") + (synopsis "Biological sequence analysis tool for NGS reads") + (description + "SortMeRNA is a biological sequence analysis tool for filtering, mapping +and operational taxonomic unit (OTU) picking of next generation +sequencing (NGS) reads. The core algorithm is based on approximate seeds and +allows for fast and sensitive analyses of nucleotide sequences. The main +application of SortMeRNA is filtering rRNA from metatranscriptomic data.") + (license license:lgpl3))) + (define-public star (package (name "star") - (version "2.4.2a") + (version "2.5.1b") (source (origin (method url-fetch) - (uri (string-append - "https://github.com/alexdobin/STAR/archive/STAR_" - version ".tar.gz")) + (uri (string-append "https://github.com/alexdobin/STAR/archive/" + version ".tar.gz")) + (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "1c3rnm7r5l0kl3d04gl1g7938xqf1c2l0mla87rlplqg1hcns5mc")) + "0wzcfhkg10apnh0y73xlarfa79xxwxdizicbdl11wb48awk44iq4")) (modules '((guix build utils))) (snippet - '(substitute* "source/Makefile" - (("/bin/rm") "rm"))))) + '(begin + (substitute* "source/Makefile" + (("/bin/rm") "rm")) + ;; Remove pre-built binaries and bundled htslib sources. + (delete-file-recursively "bin/MacOSX_x86_64") + (delete-file-recursively "bin/Linux_x86_64") + (delete-file-recursively "source/htslib") + #t)))) (build-system gnu-build-system) (arguments '(#:tests? #f ;no check target #:make-flags '("STAR") #:phases - (alist-cons-after - 'unpack 'enter-source-dir (lambda _ (chdir "source")) - (alist-replace - 'install - (lambda* (#:key outputs #:allow-other-keys) - (let ((bin (string-append (assoc-ref outputs "out") "/bin/"))) - (install-file "STAR" bin))) - (alist-delete - 'configure %standard-phases))))) + (modify-phases %standard-phases + (add-after 'unpack 'enter-source-dir + (lambda _ (chdir "source") #t)) + (add-after 'enter-source-dir 'do-not-use-bundled-htslib + (lambda _ + (substitute* "Makefile" + (("(Depend.list: \\$\\(SOURCES\\) parametersDefault\\.xxd) htslib" + _ prefix) prefix)) + (substitute* '("BAMfunctions.cpp" + "signalFromBAM.h" + "bam_cat.h" + "bam_cat.c" + "STAR.cpp" + "bamRemoveDuplicates.cpp") + (("#include \"htslib/([^\"]+\\.h)\"" _ header) + (string-append "#include <" header ">"))) + (substitute* "IncludeDefine.h" + (("\"htslib/(htslib/[^\"]+.h)\"" _ header) + (string-append "<" header ">"))) + #t)) + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let ((bin (string-append (assoc-ref outputs "out") "/bin/"))) + (install-file "STAR" bin)) + #t)) + (delete 'configure)))) (native-inputs `(("vim" ,vim))) ; for xxd (inputs - `(("zlib" ,zlib))) + `(("htslib" ,htslib) + ("zlib" ,zlib))) (home-page "https://github.com/alexdobin/STAR") (synopsis "Universal RNA-seq aligner") (description @@ -4002,7 +4194,7 @@ genomic intervals. In addition, it can use BAM or BigWig files as input.") (define-public r-qtl (package (name "r-qtl") - (version "1.37-11") + (version "1.38-4") (source (origin (method url-fetch) @@ -4010,7 +4202,7 @@ genomic intervals. In addition, it can use BAM or BigWig files as input.") version ".tar.gz")) (sha256 (base32 - "0h20d36mww7ljp51pfs66xq33yq4b4fwq9nsh02dpmfhlaxgx1xi")))) + "0rv9xhp8lyldpgwxqirhyjqvg07dr5x4x1x2jpyj37dada9ccyx3")))) (build-system r-build-system) (home-page "http://rqtl.org/") (synopsis "R package for analyzing QTL experiments in genetics") |