diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 51 |
1 files changed, 42 insertions, 9 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index c0e5a9c638..aa4c1ee8f4 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -10541,7 +10541,6 @@ once. This package provides tools to perform Drop-seq analyses.") ("r-rjson" ,r-rjson) ("salmon" ,salmon) ("pandoc" ,pandoc) - ("pandoc-citeproc" ,pandoc-citeproc) ("python-wrapper" ,python-wrapper) ("python-deeptools" ,python-deeptools) ("python-pyyaml" ,python-pyyaml))) @@ -10614,7 +10613,6 @@ expression report comparing samples in an easily configurable manner.") ("multiqc" ,multiqc) ("perl" ,perl) ("pandoc" ,pandoc) - ("pandoc-citeproc" ,pandoc-citeproc) ("fastqc" ,fastqc) ("bowtie" ,bowtie) ("idr" ,idr) @@ -10682,7 +10680,6 @@ in an easily configurable manner.") ("r-ggplot2" ,r-ggplot2) ("r-ggbio" ,r-ggbio) ("pandoc" ,pandoc) - ("pandoc-citeproc" ,pandoc-citeproc) ("python-wrapper" ,python-wrapper) ("python-pyyaml" ,python-pyyaml) ("snakemake" ,snakemake) @@ -10731,7 +10728,6 @@ methylation and segmentation.") ("python-numpy" ,python-numpy) ("python-loompy" ,python-loompy) ("pandoc" ,pandoc) - ("pandoc-citeproc" ,pandoc-citeproc) ("samtools" ,samtools) ("snakemake" ,snakemake) ("star" ,star-for-pigx) @@ -12461,17 +12457,17 @@ datasets.") (define-public ngless (package (name "ngless") - (version "1.1.0") + (version "1.3.0") (source (origin (method git-fetch) (uri (git-reference - (url "https://gitlab.com/ngless/ngless.git") + (url "https://github.com/ngless-toolkit/ngless.git") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 (base32 - "1wim8wpqyff080dfcazynrmjwqas38m24m0v350w245mmhrapdma")))) + "0pb9f6b0yk9p4cdwiym8r190q1bcdiwvc7i2s6rw54qgi8r3g6pj")))) (build-system haskell-build-system) (arguments `(#:haddock? #f ; The haddock phase fails with: NGLess/CmdArgs.hs:20:1: @@ -12546,7 +12542,7 @@ datasets.") ("ghc-http-conduit" ,ghc-http-conduit) ("ghc-inline-c" ,ghc-inline-c) ("ghc-inline-c-cpp" ,ghc-inline-c-cpp) - ("ghc-intervalmap" ,ghc-intervalmap) + ("ghc-int-interval-map" ,ghc-int-interval-map) ("ghc-missingh" ,ghc-missingh) ("ghc-optparse-applicative" ,ghc-optparse-applicative) ("ghc-regex" ,ghc-regex) @@ -12573,12 +12569,49 @@ datasets.") ("ghc-test-framework-hunit",ghc-test-framework-hunit) ("ghc-test-framework-quickcheck2" ,ghc-test-framework-quickcheck2) ("ghc-test-framework-th" ,ghc-test-framework-th))) - (home-page "https://gitlab.com/ngless/ngless") + (home-page "https://ngless.embl.de/") (synopsis "DSL for processing next-generation sequencing data") (description "Ngless is a domain-specific language for @dfn{next-generation sequencing} (NGS) data processing.") (license license:expat))) +(define-public ghc-int-interval-map + (let ((commit "678763de7fe6d7fa3f1c44b32d18ce58670270f4") + (revision "1")) + (package + (name "ghc-int-interval-map") + (version "0.0.0.0") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/ngless-toolkit/interval-to-int.git") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 (base32 "0fd728b5if89vj5j4f9y7k0b2xv2ycz5a21iy15wbdcf5bhim7i8")))) + (build-system haskell-build-system) + (inputs + `(("ghc-either" ,ghc-either) + ("ghc-primitive" ,ghc-primitive) + ("ghc-vector" ,ghc-vector) + ("ghc-vector-algorithms" ,ghc-vector-algorithms))) + (native-inputs + `(("ghc-hedgehog" ,ghc-hedgehog) + ("ghc-tasty" ,ghc-tasty) + ("ghc-tasty-hedgehog" ,ghc-tasty-hedgehog) + ("ghc-tasty-hunit" ,ghc-tasty-hunit) + ("ghc-tasty-quickcheck" ,ghc-tasty-quickcheck) + ("ghc-tasty-th" ,ghc-tasty-th))) + (home-page "https://github.com/luispedro/interval-to-int#readme") + (synopsis "Interval map structure in Haskell") + (description "An interval map structure that is optimized for low +memory (each interval is represented by about 3 words + whatever the +cargo is) and has semantics that are appropriate for genomic intervals +(namely, intervals can overlap and queries will return all matches +together). It also designed to be used in two phases: a construction +phase + query phase).") + (license license:expat)))) + (define-public filtlong ;; The recommended way to install is to clone the git repository ;; https://github.com/rrwick/Filtlong#installation |