diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 138 |
1 files changed, 93 insertions, 45 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index bb15672d51..f1a73bca7e 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -5516,7 +5516,7 @@ Roche 454, Ion Torrent and Pacific BioSciences SMRT.") (define-public ngs-sdk (package (name "ngs-sdk") - (version "2.9.3") + (version "2.9.6") (source (origin (method git-fetch) (uri (git-reference @@ -5525,7 +5525,7 @@ Roche 454, Ion Torrent and Pacific BioSciences SMRT.") (file-name (git-file-name name version)) (sha256 (base32 - "17c0v1nah3g3d2ib5bbi0vhma1ghd6vb9xycavqsh64lhp840rk3")))) + "0d5k5kabgl15as37kj9x65xc92j4gcqms86hvihw3yb6wag0r0q3")))) (build-system gnu-build-system) (arguments `(#:parallel-build? #f ; not supported @@ -5582,7 +5582,7 @@ simultaneously.") (define-public ncbi-vdb (package (name "ncbi-vdb") - (version "2.9.3") + (version "2.9.6") (source (origin (method git-fetch) (uri (git-reference @@ -5591,11 +5591,12 @@ simultaneously.") (file-name (git-file-name name version)) (sha256 (base32 - "1l4ny67nxwv1lagk9wwjbrgm7ln7adci6dnpc7k1yaln6shj0qpm")))) + "0knkj1sq34hlivgv5qd6jlczqrs3ldmfgn6vbbw7p4mqxvb9mirk")))) (build-system gnu-build-system) (arguments `(#:parallel-build? #f ; not supported #:tests? #f ; no "check" target + #:make-flags '("HAVE_HDF5=1") #:phases (modify-phases %standard-phases (add-after 'unpack 'make-files-writable @@ -5607,6 +5608,13 @@ simultaneously.") (string-append (getcwd) "/setup:" (getenv "PERL5LIB"))) #t)) + ;; See https://github.com/ncbi/ncbi-vdb/issues/14 + (add-after 'unpack 'patch-krypto-flags + (lambda _ + (substitute* "libs/krypto/Makefile" + (("-Wa,-march=generic64\\+aes") "") + (("-Wa,-march=generic64\\+sse4") "")) + #t)) (replace 'configure (lambda* (#:key inputs outputs #:allow-other-keys) (let ((out (assoc-ref outputs "out"))) @@ -5933,7 +5941,7 @@ sequence itself can be retrieved from these databases.") (define-public sra-tools (package (name "sra-tools") - (version "2.9.3") + (version "2.9.6") (source (origin (method git-fetch) @@ -5943,7 +5951,7 @@ sequence itself can be retrieved from these databases.") (file-name (git-file-name name version)) (sha256 (base32 - "0663gcdxkziwsmlznjxysb00621rllpbz6jwsfifq7z3dj3lwm8b")))) + "0vqzap68v81k0zif2mnqfy8pnw2nrhsg87p6mgq8qk3nk2jv2rgy")))) (build-system gnu-build-system) (arguments `(#:parallel-build? #f ; not supported @@ -6946,14 +6954,14 @@ ungapped alignment formats.") (define-public r-systempiper (package (name "r-systempiper") - (version "1.18.0") + (version "1.18.1") (source (origin (method url-fetch) (uri (bioconductor-uri "systemPipeR" version)) (sha256 (base32 - "1063vdf4g2i5xyabwvzkqfxd2j8s4zs6z4zxf8lx2ccjddhkn37a")))) + "1k57zyzagd7g7wl38l3cn9csylykxcllbfvyq7dz8pvihgkn0ssi")))) (properties `((upstream-name . "systemPipeR"))) (build-system r-build-system) (propagated-inputs @@ -8548,13 +8556,13 @@ factors bound at the specific regions.") (define-public r-tximport (package (name "r-tximport") - (version "1.12.0") + (version "1.12.1") (source (origin (method url-fetch) (uri (bioconductor-uri "tximport" version)) (sha256 (base32 - "0nl4imr5klwcd0xnp5y0g61d6mcgd50q60zkl86ymfmc0id368jr")))) + "1nq8v1sgkm2ssmvr2z3qw0zsk7zy0dzb95g1mfs8fkpjqh3nqq5s")))) (build-system r-build-system) (home-page "https://bioconductor.org/packages/tximport") (synopsis "Import and summarize transcript-level estimates for gene-level analysis") @@ -9452,13 +9460,13 @@ and irregular enzymatic cleavages, mass measurement accuracy, etc.") (define-public r-seurat (package (name "r-seurat") - (version "3.0.1") + (version "3.0.2") (source (origin (method url-fetch) (uri (cran-uri "Seurat" version)) (sha256 (base32 - "0mx2fvhdswbcsgqxhfc6d0gr92bkibwpz2bavqdzbbxrzpdpnilc")))) + "016fgcmjz3sjfxdvam5hd7mdxpmpnc7f6p5zqlh97m21dgn5vpqn")))) (properties `((upstream-name . "Seurat"))) (build-system r-build-system) (propagated-inputs @@ -12536,7 +12544,7 @@ once. This package provides tools to perform Drop-seq analyses.") (define-public pigx-rnaseq (package (name "pigx-rnaseq") - (version "0.0.5") + (version "0.0.7") (source (origin (method url-fetch) (uri (string-append "https://github.com/BIMSBbioinfo/pigx_rnaseq/" @@ -12544,7 +12552,7 @@ once. This package provides tools to perform Drop-seq analyses.") "/pigx_rnaseq-" version ".tar.gz")) (sha256 (base32 - "05gn658zpj9xki5dbs728z9zxq1mcm25hkwr5vzwqxsfi15l5f2l")))) + "013inbh22bjvwg2w0kx5i42k66w1zl4310ldip2ax6msgprs2ydj")))) (build-system gnu-build-system) (arguments `(#:parallel-tests? #f ; not supported @@ -12559,7 +12567,9 @@ once. This package provides tools to perform Drop-seq analyses.") (("^ test.sh") "")) #t))))) (inputs - `(("gzip" ,gzip) + `(("coreutils" ,coreutils) + ("sed" ,sed) + ("gzip" ,gzip) ("snakemake" ,snakemake) ("fastqc" ,fastqc) ("multiqc" ,multiqc) @@ -12567,7 +12577,6 @@ once. This package provides tools to perform Drop-seq analyses.") ("trim-galore" ,trim-galore) ("htseq" ,htseq) ("samtools" ,samtools) - ("bedtools" ,bedtools) ("r-minimal" ,r-minimal) ("r-rmarkdown" ,r-rmarkdown) ("r-ggplot2" ,r-ggplot2) @@ -13087,35 +13096,6 @@ known and yet unknown splice junctions. Circular-to-linear ratios of circRNAs can be calculated, and a number of descriptive plots easily generated.") (license license:artistic2.0))) -(define-public r-loomr - (let ((commit "df0144bd2bbceca6fadef9edc1bbc5ca672d4739") - (revision "1")) - (package - (name "r-loomr") - (version (git-version "0.2.0" revision commit)) - (source - (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/mojaveazure/loomR.git") - (commit commit))) - (file-name (git-file-name name version)) - (sha256 - (base32 - "1b1g4dlmfdyhn56bz1mkh9ymirri43wiz7rjhs7py3y7bdw1s3yr")))) - (build-system r-build-system) - (propagated-inputs - `(("r-r6" ,r-r6) - ("r-hdf5r" ,r-hdf5r) - ("r-iterators" ,r-iterators) - ("r-itertools" ,r-itertools) - ("r-matrix" ,r-matrix))) - (home-page "https://github.com/mojaveazure/loomR") - (synopsis "R interface for loom files") - (description "This package provides an R interface to access, create, -and modify loom files. loomR aims to be completely compatible with loompy.") - (license license:gpl3)))) - (define-public gffread ;; We cannot use the tagged release because it is not in sync with gclib. ;; See https://github.com/gpertea/gffread/issues/26 @@ -14755,3 +14735,71 @@ ATAC-seq results. It was written to make it easier to spot differences that might be caused by ATAC-seq library prep or sequencing. The main program, @code{ataqv}, examines aligned reads and reports some basic metrics.") (license license:gpl3+))) + +(define-public r-psiplot + (package + (name "r-psiplot") + (version "2.3.0") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/kcha/psiplot.git") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "08438h16cfry5kqh3y9hs8q1b1a8bxhblsm75knviz5r6q0n1jxh")))) + (build-system r-build-system) + (propagated-inputs + `(("r-mass" ,r-mass) + ("r-dplyr" ,r-dplyr) + ("r-tidyr" ,r-tidyr) + ("r-purrr" ,r-purrr) + ("r-readr" ,r-readr) + ("r-magrittr" ,r-magrittr) + ("r-ggplot2" ,r-ggplot2))) + (home-page "https://github.com/kcha/psiplot") + (synopsis "Plot percent spliced-in values of alternatively-spliced exons") + (description + "PSIplot is an R package for generating plots of @dfn{percent +spliced-in} (PSI) values of alternatively-spliced exons that were computed by +vast-tools, an RNA-Seq pipeline for alternative splicing analysis. The plots +are generated using @code{ggplot2}.") + (license license:expat))) + +(define-public tbsp + (let ((commit "ec8fff4410cfb13a677dbbb95cbbc60217e64907") + (revision "1")) + (package + (name "tbsp") + (version (git-version "1.0.0" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/phoenixding/tbsp.git") + (commit commit))) + (sha256 + (base32 + "025ym14x8gbd6hb55lsinqj6f5qzw36i10klgs7ldzxxd7s39ki1")))) + (build-system python-build-system) + (arguments '(#:tests? #f)) ; no tests included + (inputs + `(("python-matplotlib" ,python-matplotlib) + ("python-networkx" ,python-networkx) + ("python-numpy" ,python-numpy) + ("python-pybigwig" ,python-pybigwig) + ("python-biopython" ,python-biopython) + ("python-scikit-learn" ,python-scikit-learn) + ("python-scipy" ,python-scipy))) + (home-page "https://github.com/phoenixding/tbsp/") + (synopsis "SNP-based trajectory inference") + (description + "Several studies focus on the inference of developmental and response +trajectories from single cell RNA-Seq (scRNA-Seq) data. A number of +computational methods, often referred to as pseudo-time ordering, have been +developed for this task. CRISPR has also been used to reconstruct lineage +trees by inserting random mutations. The tbsp package implements an +alternative method to detect significant, cell type specific sequence +mutations from scRNA-Seq data.") + (license license:expat)))) |