diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 143 |
1 files changed, 116 insertions, 27 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index a573ef682f..07c70fb82c 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -1443,8 +1443,7 @@ confidence to have in an alignment.") "-lboost_system" "-lboost_iostreams" "-lz" - "-fopenmp" - "-std=c++11")))) + "-fopenmp")))) #:phases (modify-phases %standard-phases (add-after 'unpack 'do-not-build-bundled-pigz @@ -1556,14 +1555,14 @@ gapped, local, and paired-end alignment modes.") (define-public bowtie1 (package (name "bowtie1") - (version "1.2.2") + (version "1.2.3") (source (origin (method url-fetch) (uri (string-append "mirror://sourceforge/bowtie-bio/bowtie/" - version "/bowtie-" version "-src.zip")) + version "/bowtie-src-x86_64.zip")) (sha256 (base32 - "1jl2cj9bz8lwz8dwnxbycn8yp8g4kky62fkcxifyf1ri0y6n2vc0")) + "0vmiqdhc9dzyfy9sh6vgi7k9xy2hiw8g87vbamnc6cgpm179zsa4")) (modules '((guix build utils))) (snippet '(substitute* "Makefile" @@ -7731,13 +7730,13 @@ biological sequences or sets of sequences.") (define-public r-rsamtools (package (name "r-rsamtools") - (version "2.0.2") + (version "2.0.3") (source (origin (method url-fetch) (uri (bioconductor-uri "Rsamtools" version)) (sha256 (base32 - "188k5g40lbli7dxr96hldyvg9r9hmlbh2fp0qs5nnd12b8zbf338")))) + "03qfpaqbffirpnby88mv6h45njfapli28crdvg35h2zi2jkkmhvp")))) (properties `((upstream-name . "Rsamtools"))) (build-system r-build-system) @@ -8283,14 +8282,14 @@ secondary structure and comparative analysis in R.") (define-public r-rhtslib (package (name "r-rhtslib") - (version "1.16.2") + (version "1.16.3") (source (origin (method url-fetch) (uri (bioconductor-uri "Rhtslib" version)) (sha256 (base32 - "07qaqj2hypmrg40m3pci082bzar6wi10dh77r4a8x74dfppcwdzf")))) + "1lmrfr32nrz36abn440kvzzck53y2320xjxqzs2jw7m2a9h3ryak")))) (properties `((upstream-name . "Rhtslib"))) (build-system r-build-system) ;; Without this a temporary directory ends up in the Rhtslib.so binary, @@ -8571,13 +8570,13 @@ of gene-level counts.") (define-public r-rhdf5 (package (name "r-rhdf5") - (version "2.28.0") + (version "2.28.1") (source (origin (method url-fetch) (uri (bioconductor-uri "rhdf5" version)) (sha256 (base32 - "0y1w3cs7wg2b3jlkd6wyyz6626xg011nrg36si8gg371iqck9a1i")))) + "027cv1kh3xl66lrrahv2jgfmvgcwfpcj9dpgdj5fd9ybf5nyjcwb")))) (build-system r-build-system) (propagated-inputs `(("r-rhdf5lib" ,r-rhdf5lib))) @@ -9705,14 +9704,14 @@ microarrays or GRanges for sequencing data.") (define-public r-keggrest (package (name "r-keggrest") - (version "1.24.0") + (version "1.24.1") (source (origin (method url-fetch) (uri (bioconductor-uri "KEGGREST" version)) (sha256 (base32 - "1yjrpbm5zfg0h3nb5gg06q2f19ydbhjqwi0jb6q3p8dyrgww9mqp")))) + "0yxp3iajdy61q6mjgp1nxdgmf2yb58cvqmdgab7lqxr0ky1wkfkr")))) (properties `((upstream-name . "KEGGREST"))) (build-system r-build-system) (propagated-inputs @@ -9852,14 +9851,14 @@ originally made available by Holmes, Harris, and Quince, 2012, PLoS ONE 7(2): (define-public r-ensembldb (package (name "r-ensembldb") - (version "2.8.0") + (version "2.8.1") (source (origin (method url-fetch) (uri (bioconductor-uri "ensembldb" version)) (sha256 (base32 - "09s5g9xm9m8mqvzk6pkp9fyhx3zyb4p8yziz49mhfji5n35nydjr")))) + "103z902104ljdp6s9y2dmgrl5wkdz8vvlbbqgk8r4drkg7m3d4lj")))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) @@ -10032,14 +10031,14 @@ interval to data view, mismatch pileup, and several splicing summaries.") (define-public r-gprofiler (package (name "r-gprofiler") - (version "0.6.8") + (version "0.7.0") (source (origin (method url-fetch) (uri (cran-uri "gProfileR" version)) (sha256 (base32 - "05d6y6b7vkkzp2qhs1cwlvp02djij1b28dbwxnrms08f8qi35iaj")))) + "1h1v0kgpsn04ald2izznh7fr2riwisj5hcgz4k7h3qc931rf0r4k")))) (properties `((upstream-name . "gProfileR"))) (build-system r-build-system) (propagated-inputs @@ -10188,14 +10187,14 @@ by Ernst and Kellis.") (define-public r-ldblock (package (name "r-ldblock") - (version "1.14.2") + (version "1.14.3") (source (origin (method url-fetch) (uri (bioconductor-uri "ldblock" version)) (sha256 (base32 - "0xx04cghx6ads1ackwnw3z0gf72qv461nznzmcnkgmp7w5n9m2af")))) + "154yvrvs8ik7ifcny1681cmqra0i163j00k4vbvkvl701p5gsp5q")))) (build-system r-build-system) (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics) @@ -10322,14 +10321,14 @@ with your data.") (define-public r-gwascat (package (name "r-gwascat") - (version "2.16.0") + (version "2.16.1") (source (origin (method url-fetch) (uri (bioconductor-uri "gwascat" version)) (sha256 (base32 - "0akb36mrybmxbb1bc9kgxbnj3cdypfylj3yzrmhjwqxml03mg61i")))) + "0d4krqx8zjniwp6k2vzwqgfws39w03x51kqiwd5dks1fp05sw4xh")))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) @@ -10428,14 +10427,14 @@ provided.") (define-public r-hdf5array (package (name "r-hdf5array") - (version "1.12.2") + (version "1.12.3") (source (origin (method url-fetch) (uri (bioconductor-uri "HDF5Array" version)) (sha256 (base32 - "0afradisrr5gn0lf2kxjw55vdm3lm9mlgx53qlr9r40c1hrydpf5")))) + "1037j6f0yyw4cf6p051810qamxi1sji5w4d0fgq5lyzyl5d36fm6")))) (properties `((upstream-name . "HDF5Array"))) (build-system r-build-system) (inputs @@ -10457,14 +10456,14 @@ block processing.") (define-public r-rhdf5lib (package (name "r-rhdf5lib") - (version "1.6.1") + (version "1.6.3") (source (origin (method url-fetch) (uri (bioconductor-uri "Rhdf5lib" version)) (sha256 (base32 - "0niz9dh66fcwbvqpkpsdlz9d06kwi3kfh45dhk3qz9g9qqyiakr1")) + "0q68n5jm7w99paibj8vkxbdksbyrxilzwc9dkp3zf8zrdc5qfxzy")) (modules '((guix build utils))) (snippet '(begin @@ -10510,8 +10509,8 @@ block processing.") (("HDF5_CXX_INCLUDE=.*") "HDF5_CXX_INCLUDE=./hdf5/c++/src\n") (("HDF5_INCLUDE=.*") "HDF5_INCLUDE=./hdf5/src\n") ;; szip is non-free software - (("cp \\$\\{SZIP_LIB\\}.*") "") - (("\\$\\{USER_LIB_DIR\\}libsz.a") ""))) + (("cp \"\\$\\{SZIP_LIB\\}.*") "") + (("PKG_LIBS =.*") "PKG_LIBS = -lz -lhdf5\n"))) #t))))) (inputs `(("zlib" ,zlib))) @@ -12850,6 +12849,7 @@ HTML reports with interesting findings about your samples.") (uri (git-reference (url "https://github.com/jsh58/Genrich.git") (commit (string-append "v" version)))) + (file-name (git-file-name name version)) (sha256 (base32 "0x0q6z0208n3cxzqjla4rgjqpyqgwpmz27852lcvzkzaigymq4zp")))) @@ -14799,6 +14799,7 @@ and reflect the fast5 file schema, and tools to convert between (uri (git-reference (url "https://github.com/phoenixding/tbsp.git") (commit commit))) + (file-name (git-file-name name version)) (sha256 (base32 "025ym14x8gbd6hb55lsinqj6f5qzw36i10klgs7ldzxxd7s39ki1")))) @@ -15260,3 +15261,91 @@ and/or unmapped/clipped reads to a separate FASTQ file. When marking duplicates, samblaster will require approximately 20MB of memory per 1M read pairs.") (license license:expat))) + +(define-public r-velocyto + (let ((commit "d7790346cb99f49ab9c2b23ba70dcf9d2c9fc350") + (revision "1")) + (package + (name "r-velocyto") + (version (git-version "0.6" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/velocyto-team/velocyto.R.git") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "16wqf70j7rd7pay2q513iyz12i8n9vrpg1bisah4lddbcpx5dz1n")))) + (build-system r-build-system) + (inputs + `(("boost" ,boost))) + (propagated-inputs + `(("r-hdf5r" ,r-hdf5r) + ("r-mass" ,r-mass) + ("r-mgcv" ,r-mgcv) + ("r-pcamethods" ,r-pcamethods) + ("r-rcpp" ,r-rcpp) + ("r-rcpparmadillo" ,r-rcpparmadillo) + ;; Suggested packages + ("r-rtsne" ,r-rtsne) + ("r-cluster" ,r-cluster) + ("r-abind" ,r-abind) + ("r-h5" ,r-h5) + ("r-biocgenerics" ,r-biocgenerics) + ("r-genomicalignments" ,r-genomicalignments) + ("r-rsamtools" ,r-rsamtools) + ("r-edger" ,r-edger) + ("r-igraph" ,r-igraph))) + (home-page "http://velocyto.org") + (synopsis "RNA velocity estimation in R") + (description + "This package provides basic routines for estimation of gene-specific +transcriptional derivatives and visualization of the resulting velocity +patterns.") + (license license:gpl3)))) + +(define-public methyldackel + (package + (name "methyldackel") + (version "0.4.0") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/dpryan79/MethylDackel.git") + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "10gh8k0ca92kywnrw5pkacq3g6r8s976s12k8jhp8g3g49q9a97g")))) + (build-system gnu-build-system) + (arguments + `(#:test-target "test" + #:make-flags + (list "CC=gcc" + (string-append "prefix=" + (assoc-ref %outputs "out") "/bin/")) + #:phases + (modify-phases %standard-phases + (replace 'configure + (lambda* (#:key outputs #:allow-other-keys) + (substitute* "Makefile" + (("install MethylDackel \\$\\(prefix\\)" match) + (string-append "install -d $(prefix); " match))) + #t))))) + (inputs + `(("htslib" ,htslib) + ("zlib" ,zlib))) + ;; Needed for tests + (native-inputs + `(("python" ,python-wrapper))) + (home-page "https://github.com/dpryan79/MethylDackel") + (synopsis "Universal methylation extractor for BS-seq experiments") + (description + "MethylDackel will process a coordinate-sorted and indexed BAM or CRAM +file containing some form of BS-seq alignments and extract per-base +methylation metrics from them. MethylDackel requires an indexed fasta file +containing the reference genome as well.") + ;; See https://github.com/dpryan79/MethylDackel/issues/85 + (license license:expat))) |