diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 459 |
1 files changed, 440 insertions, 19 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 9b0a4314b9..1836939970 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -40,6 +40,7 @@ #:use-module (guix build-system gnu) #:use-module (guix build-system cmake) #:use-module (guix build-system haskell) + #:use-module (guix build-system meson) #:use-module (guix build-system ocaml) #:use-module (guix build-system perl) #:use-module (guix build-system python) @@ -477,6 +478,169 @@ BED, GFF/GTF, VCF.") (base32 "0jhavwifnf7lmkb11h9y7dynr8d699h0rd2l52j1pfgircr2zwv5")))))) +(define-public pbbam + (package + (name "pbbam") + (version "0.23.0") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/PacificBiosciences/pbbam.git") + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0h9gkrpf2lrxklxp72xfl5bi3h5zcm5hprrya9gf0hr3xwlbpp0x")))) + (build-system meson-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'find-googletest + (lambda* (#:key inputs #:allow-other-keys) + ;; It doesn't find gtest_main because there's no pkg-config file + ;; for it. Find it another way. + (substitute* "tests/meson.build" + (("pbbam_gtest_dep = dependency\\('gtest_main'.*") + (format #f "cpp = meson.get_compiler('cpp') +pbbam_gtest_dep = cpp.find_library('gtest_main', dirs : '~a')\n" + (assoc-ref inputs "googletest")))) + #t))) + ;; TODO: tests/pbbam_test cannot be linked + ;; ld: tests/59830eb@@pbbam_test@exe/src_test_Accuracy.cpp.o: + ;; undefined reference to symbol '_ZTIN7testing4TestE' + ;; ld: /gnu/store/...-googletest-1.8.0/lib/libgtest.so: + ;; error adding symbols: DSO missing from command line + #:tests? #f + #:configure-flags '("-Dtests=false"))) + ;; These libraries are listed as "Required" in the pkg-config file. + (propagated-inputs + `(("htslib" ,htslib) + ("zlib" ,zlib))) + (inputs + `(("boost" ,boost) + ("samtools" ,samtools))) + (native-inputs + `(("googletest" ,googletest) + ("pkg-config" ,pkg-config) + ("python" ,python-wrapper))) ; for tests + (home-page "https://github.com/PacificBiosciences/pbbam") + (synopsis "Work with PacBio BAM files") + (description + "The pbbam software package provides components to create, query, and +edit PacBio BAM files and associated indices. These components include a core +C++ library, bindings for additional languages, and command-line utilities. +This library is not intended to be used as a general-purpose BAM utility - all +input and output BAMs must adhere to the PacBio BAM format specification. +Non-PacBio BAMs will cause exceptions to be thrown.") + (license license:bsd-3))) + +(define-public blasr-libcpp + (package + (name "blasr-libcpp") + (version "5.3.3") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/PacificBiosciences/blasr_libcpp.git") + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0cn5l42zyq67sj0g2imqkhayz2iqvv0a1pgpbmlq0qynjmsrbfd2")))) + (build-system meson-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'link-with-hdf5 + (lambda* (#:key inputs #:allow-other-keys) + (let ((hdf5 (assoc-ref inputs "hdf5"))) + (substitute* "meson.build" + (("libblasr_deps = \\[" m) + (string-append + m + (format #f "cpp.find_library('hdf5', dirs : '~a'), \ +cpp.find_library('hdf5_cpp', dirs : '~a'), " + hdf5 hdf5))))) + #t)) + (add-after 'unpack 'find-googletest + (lambda* (#:key inputs #:allow-other-keys) + ;; It doesn't find gtest_main because there's no pkg-config file + ;; for it. Find it another way. + (substitute* "unittest/meson.build" + (("libblasr_gtest_dep = dependency\\('gtest_main'.*") + (format #f "cpp = meson.get_compiler('cpp') +libblasr_gtest_dep = cpp.find_library('gtest_main', dirs : '~a')\n" + (assoc-ref inputs "googletest")))) + #t))) + ;; TODO: unittest/libblasr_unittest cannot be linked + ;; ld: ;; unittest/df08227@@libblasr_unittest@exe/alignment_utils_FileUtils_gtest.cpp.o: + ;; undefined reference to symbol + ;; '_ZN7testing8internal9DeathTest6CreateEPKcPKNS0_2REES3_iPPS1_' + ;; ld: /gnu/store/...-googletest-1.8.0/lib/libgtest.so: + ;; error adding symbols: DSO missing from command line + #:tests? #f + #:configure-flags '("-Dtests=false"))) + (inputs + `(("boost" ,boost) + ("hdf5" ,hdf5) + ("pbbam" ,pbbam) + ("zlib" ,zlib))) + (native-inputs + `(("googletest" ,googletest) + ("pkg-config" ,pkg-config))) + (home-page "https://github.com/PacificBiosciences/blasr_libcpp") + (synopsis "Library for analyzing PacBio genomic sequences") + (description + "This package provides three libraries used by applications for analyzing +PacBio genomic sequences. This library contains three sub-libraries: pbdata, +hdf and alignment.") + (license license:bsd-3))) + +(define-public blasr + (package + (name "blasr") + (version "5.3.3") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/PacificBiosciences/blasr.git") + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1skgy2mvz8gsgfh1gc2nfgwvpyzb1hpmp2cf2773h5wsj8nw22kl")))) + (build-system meson-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'link-with-hdf5 + (lambda* (#:key inputs #:allow-other-keys) + (let ((hdf5 (assoc-ref inputs "hdf5"))) + (substitute* "meson.build" + (("blasr_deps = \\[" m) + (string-append + m + (format #f "cpp.find_library('hdf5', dirs : '~a'), \ +cpp.find_library('hdf5_cpp', dirs : '~a'), " + hdf5 hdf5))))) + #t))) + ;; Tests require "cram" executable, which is not packaged. + #:tests? #f + #:configure-flags '("-Dtests=false"))) + (inputs + `(("boost" ,boost) + ("blasr-libcpp" ,blasr-libcpp) + ("hdf5" ,hdf5) + ("pbbam" ,pbbam) + ("zlib" ,zlib))) + (native-inputs + `(("pkg-config" ,pkg-config))) + (home-page "https://github.com/PacificBiosciences/blasr") + (synopsis "PacBio long read aligner") + (description + "Blasr is a genomic sequence aligner for processing PacBio long reads.") + (license license:bsd-3))) + (define-public ribotaper (package (name "ribotaper") @@ -732,20 +896,30 @@ Python.") (file-name (git-file-name name version)) (sha256 (base32 - "1rna16lyk5aqhnv0dp77wwaplias93f1vw28ad3jmyw6hwkai05v")))) + "1rna16lyk5aqhnv0dp77wwaplias93f1vw28ad3jmyw6hwkai05v")) + (modules '((guix build utils))) + (snippet '(begin + ;; Delete generated C files. + (for-each delete-file (find-files "." "\\.c")) + #t)))) (build-system python-build-system) (arguments `(#:phases (modify-phases %standard-phases (add-after 'unpack 'use-cython (lambda _ (setenv "USE_CYTHON" "1") #t)) - (add-after 'unpack 'disable-broken-test + (add-after 'unpack 'disable-broken-tests (lambda _ (substitute* "biom/tests/test_cli/test_validate_table.py" (("^(.+)def test_invalid_hdf5" m indent) (string-append indent "@npt.dec.skipif(True, msg='Guix')\n" m))) + (substitute* "biom/tests/test_table.py" + (("^(.+)def test_from_hdf5_issue_731" m indent) + (string-append indent + "@npt.dec.skipif(True, msg='Guix')\n" + m))) #t)) (add-before 'reset-gzip-timestamps 'make-files-writable (lambda* (#:key outputs #:allow-other-keys) @@ -1570,6 +1744,47 @@ the original BWA alignment program and shares the genome index structure as well as many of the command line options.") (license license:gpl3+))) +(define-public bwa-meth + (package + (name "bwa-meth") + (version "0.2.2") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/brentp/bwa-meth.git") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "17j31i7zws5j7mhsq9x3qgkxly6mlmrgwhfq0qbflgxrmx04yaiz")))) + (build-system python-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'keep-references-to-bwa + (lambda* (#:key inputs #:allow-other-keys) + (substitute* "bwameth.py" + (("bwa mem") + (string-append (which "bwa") " mem")) + ;; There's an ill-advised check for "samtools" on PATH. + (("^checkX.*") "")) + #t))))) + (inputs + `(("bwa" ,bwa))) + (native-inputs + `(("python-toolshed" ,python-toolshed))) + (home-page "https://github.com/brentp/bwa-meth") + (synopsis "Fast and accurante alignment of BS-Seq reads") + (description + "BWA-Meth works for single-end reads and for paired-end reads from the +directional protocol (most common). It uses the method employed by +methylcoder and Bismark of in silico conversion of all C's to T's in both +reference and reads. It recovers the original read (needed to tabulate +methylation) by attaching it as a comment which BWA appends as a tag to the +read. It performs favorably to existing aligners gauged by number of on and +off-target reads for a capture method that targets CpG-rich region.") + (license license:expat))) + (define-public python-bx-python (package (name "python-bx-python") @@ -6132,6 +6347,28 @@ sequences.") ;; STAR is licensed under GPLv3 or later; htslib is MIT-licensed. (license license:gpl3+))) +(define-public starlong + (package (inherit star) + (name "starlong") + (arguments + (substitute-keyword-arguments (package-arguments star) + ((#:make-flags flags) + `(list "STARlong")) + ((#:phases phases) + `(modify-phases ,phases + ;; Allow extra long sequence reads. + (add-after 'unpack 'make-extra-long + (lambda _ + (substitute* "source/IncludeDefine.h" + (("(#define DEF_readNameLengthMax ).*" _ match) + (string-append match "900000\n"))) + #t)) + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let ((bin (string-append (assoc-ref outputs "out") "/bin/"))) + (install-file "STARlong" bin)) + #t)))))))) + (define-public subread (package (name "subread") @@ -6482,14 +6719,14 @@ distribution.") (define-public r-dexseq (package (name "r-dexseq") - (version "1.28.2") + (version "1.28.3") (source (origin (method url-fetch) (uri (bioconductor-uri "DEXSeq" version)) (sha256 (base32 - "134znafy7hn38rp4nia4pglz56fz6nbkxrf7z2k1sajfsgxa1hs6")))) + "1wsj1kqfrakmjnlplxmrv17r2spzcdkmwdkhggyjbf8mdhqs3w16")))) (properties `((upstream-name . "DEXSeq"))) (build-system r-build-system) (propagated-inputs @@ -6603,14 +6840,14 @@ Enrichment Analysis} (GSEA).") (define-public r-category (package (name "r-category") - (version "2.48.0") + (version "2.48.1") (source (origin (method url-fetch) (uri (bioconductor-uri "Category" version)) (sha256 (base32 - "1jdm83bwdfhpfm1y6hwgvxzj6l83h1bdkqv23799kzywnwm016kv")))) + "18rsxlwa1l06i635cnznb9b2zssqcgb71pihky29gl2gwp7a654b")))) (properties `((upstream-name . "Category"))) (build-system r-build-system) (propagated-inputs @@ -7361,13 +7598,13 @@ CAGE.") (define-public r-variantannotation (package (name "r-variantannotation") - (version "1.28.11") + (version "1.28.13") (source (origin (method url-fetch) (uri (bioconductor-uri "VariantAnnotation" version)) (sha256 (base32 - "19bxi5b9fzqdjadb8bfm8xsgi6nvrwbgn1xcpk59bnmv9vzjkwrh")))) + "1a7b0bg579ynpbfh5dk87fdgl62r9cwk4zmrl61m6zil7881p3gh")))) (properties `((upstream-name . "VariantAnnotation"))) (inputs @@ -7802,13 +8039,13 @@ as well as query and modify the browser state, such as the current viewport.") (define-public r-genomicfeatures (package (name "r-genomicfeatures") - (version "1.34.4") + (version "1.34.6") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicFeatures" version)) (sha256 (base32 - "09gc1vbqszrr3ixv4hsfan2l18fcf3gg58783mrfwjv6ci9c4w0d")))) + "1cz7qx324dmsrkzyhm956cfgr08gpily5rpym7hc8zz5kbl6i3ra")))) (properties `((upstream-name . "GenomicFeatures"))) (build-system r-build-system) @@ -9068,14 +9305,14 @@ trait.") (define-public r-maldiquant (package (name "r-maldiquant") - (version "1.18") + (version "1.19.2") (source (origin (method url-fetch) (uri (cran-uri "MALDIquant" version)) (sha256 (base32 - "18nl214xjsxkcpbg79jkmw0yznwm5szyh2qb84n7ip46mm779ha6")))) + "11zbvm1vw8zn2vmymvydgdczvwj961s2knvrn1q4gbziwi5gqvlc")))) (properties `((upstream-name . "MALDIquant"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/MALDIquant") @@ -9579,14 +9816,14 @@ Shiny-based display methods for Bioconductor objects.") (define-public r-annotationhub (package (name "r-annotationhub") - (version "2.14.4") + (version "2.14.5") (source (origin (method url-fetch) (uri (bioconductor-uri "AnnotationHub" version)) (sha256 (base32 - "18v2mk395svq3c19wzi6bjwjfnmrvjqkzmj7cmaji7rx4xdgz6ck")))) + "0iyrxaijl4614iz5c1j53227xy2g756p3bx7hcwglcybh0k30nki")))) (properties `((upstream-name . "AnnotationHub"))) (build-system r-build-system) (propagated-inputs @@ -12899,14 +13136,14 @@ analyses in addition to large-scale sequence-level searches.") (define-public r-diversitree (package (name "r-diversitree") - (version "0.9-10") + (version "0.9-11") (source (origin (method url-fetch) (uri (cran-uri "diversitree" version)) (sha256 (base32 - "0gh4rcrp0an3jh8915i1fsxlgyfk7njywgbd5ln5r2jhr085kpz7")))) + "1jqfjmmaigq581l4zxysmkhld0xv6izlbr1hihf9zplkix36majc")))) (build-system r-build-system) (native-inputs `(("gfortran" ,gfortran))) @@ -12915,7 +13152,7 @@ analyses in addition to large-scale sequence-level searches.") `(("r-ape" ,r-ape) ("r-desolve" ,r-desolve) ("r-rcpp" ,r-rcpp) - ("r-suplex" ,r-subplex))) + ("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\" @@ -14031,7 +14268,12 @@ choosing which reads pass the filter.") (recursive? #t))) (file-name (git-file-name name version)) (sha256 - (base32 "09j5gz57yr9i34a27vbl72i4g8syv2zzgmsfyjq02yshmnrvkjs6")))) + (base32 "09j5gz57yr9i34a27vbl72i4g8syv2zzgmsfyjq02yshmnrvkjs6")) + (modules '((guix build utils))) + (snippet + '(begin + (delete-file-recursively "htslib") + #t)))) (build-system gnu-build-system) (arguments `(#:make-flags @@ -14070,7 +14312,7 @@ choosing which reads pass the filter.") ("hdf5" ,hdf5) ("htslib" ,htslib) ("perl" ,perl) - ("python" ,python) + ("python" ,python-wrapper) ("python-biopython" ,python-biopython) ("python-numpy" ,python-numpy) ("python-pysam" ,python-pysam) @@ -14152,6 +14394,82 @@ approximate the gradient at each iteration of gradient descent. This package is a Cython wrapper for FIt-SNE.") (license license:bsd-4))) +(define-public bbmap + (package + (name "bbmap") + (version "35.82") + (source (origin + (method url-fetch) + (uri (string-append + "mirror://sourceforge/bbmap/BBMap_" version ".tar.gz")) + (sha256 + (base32 + "1q4rfhxcb6z3gm8zg2davjz98w22lkf4hm9ikxz9kdl93pil3wkd")))) + (build-system ant-build-system) + (arguments + `(#:build-target "dist" + #:tests? #f ; there are none + #:make-flags + (list (string-append "-Dmpijar=" + (assoc-ref %build-inputs "java-openmpi") + "/lib/mpi.jar")) + #:modules ((guix build ant-build-system) + (guix build utils) + (guix build java-utils)) + #:phases + (modify-phases %standard-phases + (add-after 'build 'build-jni-library + (lambda _ + (with-directory-excursion "jni" + (invoke "make" "-f" "makefile.linux")))) + ;; There is no install target + (replace 'install (install-jars "dist")) + (add-after 'install 'install-scripts-and-documentation + (lambda* (#:key outputs #:allow-other-keys) + (substitute* "calcmem.sh" + (("\\| awk ") (string-append "| " (which "awk") " "))) + (let* ((scripts (find-files "." "\\.sh$")) + (out (assoc-ref outputs "out")) + (bin (string-append out "/bin")) + (doc (string-append out "/share/doc/bbmap")) + (jni (string-append out "/lib/jni"))) + (substitute* scripts + (("\\$DIR\"\"docs") doc) + (("^CP=.*") + (string-append "CP=" out "/share/java/BBTools.jar\n")) + (("^NATIVELIBDIR.*") + (string-append "NATIVELIBDIR=" jni "\n")) + (("CMD=\"java") + (string-append "CMD=\"" (which "java")))) + (for-each (lambda (script) (install-file script bin)) scripts) + + ;; Install JNI library + (install-file "jni/libbbtoolsjni.so" jni) + + ;; Install documentation + (install-file "docs/readme.txt" doc) + (copy-recursively "docs/guides" doc)) + #t))) + #:jdk ,openjdk11)) + (inputs + `(("gawk" ,gawk) + ("java-eclipse-jdt-core" ,java-eclipse-jdt-core) + ("java-eclipse-jdt-compiler-apt" ,java-eclipse-jdt-compiler-apt) + ("java-openmpi" ,java-openmpi))) + (home-page "http://sourceforge.net/projects/bbmap/") + (synopsis "Aligner and other tools for short sequencing reads") + (description + "This package provides bioinformatic tools to align, deduplicate, +reformat, filter and normalize DNA and RNA-seq data. It includes the +following tools: BBMap, a short read aligner for DNA and RNA-seq data; BBNorm, +a kmer-based error-correction and normalization tool; Dedupe, a tool to +simplify assemblies by removing duplicate or contained subsequences that share +a target percent identity; Reformat, to convert reads between +fasta/fastq/scarf/fasta+qual/sam, interleaved/paired, and ASCII-33/64, at over +500 MB/s; and BBDuk, a tool to filter, trim, or mask reads with kmer matches +to an artifact/contaminant file.") + (license license:bsd-3))) + (define-public velvet (package (name "velvet") @@ -14240,3 +14558,106 @@ repeated areas between contigs.") "Velocyto is a library for the analysis of RNA velocity. Velocyto includes a command line tool and an analysis pipeline.") (license license:bsd-2))) + +(define-public arriba + (package + (name "arriba") + (version "1.0.1") + (source + (origin + (method url-fetch) + (uri (string-append "https://github.com/suhrig/arriba/releases/" + "download/v" version "/arriba_v" version ".tar.gz")) + (sha256 + (base32 + "0jx9656ry766vb8z08m1c3im87b0c82qpnjby9wz4kcz8vn87dx2")))) + (build-system gnu-build-system) + (arguments + `(#:tests? #f ; there are none + #:phases + (modify-phases %standard-phases + (replace 'configure + (lambda* (#:key inputs #:allow-other-keys) + (let ((htslib (assoc-ref inputs "htslib"))) + (substitute* "Makefile" + (("-I\\$\\(HTSLIB\\)/htslib") + (string-append "-I" htslib "/include/htslib")) + ((" \\$\\(HTSLIB\\)/libhts.a") + (string-append " " htslib "/lib/libhts.so")))) + (substitute* "run_arriba.sh" + (("^STAR ") (string-append (which "STAR") " ")) + (("samtools --version-only") + (string-append (which "samtools") " --version-only")) + (("samtools index") + (string-append (which "samtools") " index")) + (("samtools sort") + (string-append (which "samtools") " sort"))) + #t)) + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let ((bin (string-append (assoc-ref outputs "out") "/bin"))) + (install-file "arriba" bin) + (install-file "run_arriba.sh" bin) + (install-file "draw_fusions.R" bin) + (wrap-program (string-append bin "/draw_fusions.R") + `("R_LIBS_SITE" ":" prefix (,(getenv "R_LIBS_SITE"))))) + #t))))) + (inputs + `(("htslib" ,htslib) + ("r-minimal" ,r-minimal) + ("r-circlize" ,r-circlize) + ("r-genomicalignments" ,r-genomicalignments) + ("r-genomicranges" ,r-genomicranges) + ("samtools" ,samtools) + ("star" ,star) + ("zlib" ,zlib))) + (home-page "https://github.com/suhrig/arriba") + (synopsis "Gene fusion detection from RNA-Seq data ") + (description + "Arriba is a command-line tool for the detection of gene fusions from +RNA-Seq data. It was developed for the use in a clinical research setting. +Therefore, short runtimes and high sensitivity were important design criteria. +It is based on the fast STAR aligner and the post-alignment runtime is +typically just around two minutes. In contrast to many other fusion detection +tools which build on STAR, Arriba does not require to reduce the +@code{alignIntronMax} parameter of STAR to detect small deletions.") + ;; All code is under the Expat license with the exception of + ;; "draw_fusions.R", which is under GPLv3. + (license (list license:expat license:gpl3)))) + +(define-public adapterremoval + (package + (name "adapterremoval") + (version "2.3.0") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/MikkelSchubert/adapterremoval.git") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1nf3ki5pfzalhrx2fr1y6pfqfi133yj2m7q4fj9irf5fb94bapwr")))) + (build-system gnu-build-system) + (arguments + `(#:make-flags (list "COLOR_BUILD=no" + (string-append "PREFIX=" + (assoc-ref %outputs "out"))) + #:test-target "test" + #:phases + (modify-phases %standard-phases + (delete 'configure)))) + (inputs + `(("zlib" ,zlib))) + (home-page "https://adapterremoval.readthedocs.io/") + (synopsis "Rapid sequence adapter trimming, identification, and read merging") + (description + "This program searches for and removes remnant adapter sequences from +@dfn{High-Throughput Sequencing} (HTS) data and (optionally) trims low quality +bases from the 3' end of reads following adapter removal. AdapterRemoval can +analyze both single end and paired end data, and can be used to merge +overlapping paired-ended reads into (longer) consensus sequences. +Additionally, the AdapterRemoval may be used to recover a consensus adapter +sequence for paired-ended data, for which this information is not available.") + (license license:gpl3+))) |