diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 56 |
1 files changed, 31 insertions, 25 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 528b603476..613015c67e 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -11,9 +11,10 @@ ;;; Copyright © 2017 Arun Isaac <arunisaac@systemreboot.net> ;;; Copyright © 2018 Joshua Sierles, Nextjournal <joshua@nextjournal.com> ;;; Copyright © 2018 Gábor Boskovits <boskovits@gmail.com> -;;; Copyright © 2018 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de> +;;; Copyright © 2018, 2019 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de> ;;; Copyright © 2019 Maxim Cournoyer <maxim.cournoyer@gmail.com> ;;; Copyright © 2019 Brian Leung <bkleung89@gmail.com> +;;; Copyright © 2019 Brett Gilio <brettg@gnu.org> ;;; ;;; This file is part of GNU Guix. ;;; @@ -84,10 +85,10 @@ #:use-module (gnu packages imagemagick) #:use-module (gnu packages java) #:use-module (gnu packages java-compression) - #:use-module (gnu packages javascript) #:use-module (gnu packages jemalloc) #:use-module (gnu packages dlang) #:use-module (gnu packages linux) + #:use-module (gnu packages lisp-xyz) #:use-module (gnu packages logging) #:use-module (gnu packages machine-learning) #:use-module (gnu packages man) @@ -1615,7 +1616,7 @@ genome (2.9 GB for paired-end).") #t)))) (build-system gnu-build-system) (arguments - '(#:parallel-build? #f ; not supported + '(#:parallel-build? #f ; not supported #:phases (modify-phases %standard-phases (add-after 'unpack 'use-system-samtools @@ -1639,16 +1640,18 @@ genome (2.9 GB for paired-end).") (("#include <bam.h>") "#include <samtools/bam.h>") (("#include <sam.h>") "#include <samtools/sam.h>")) #t))))) + (native-inputs + `(("gcc" ,gcc-5))) ;; doesn't build with later versions (inputs `(("boost" ,boost) ("bowtie" ,bowtie) - ("samtools" ,samtools-0.1) ("ncurses" ,ncurses) - ("python" ,python-2) ("perl" ,perl) - ("zlib" ,zlib) - ("seqan" ,seqan-1))) - (home-page "http://ccb.jhu.edu/software/tophat/index.shtml") + ("python" ,python-2) + ("samtools" ,samtools-0.1) + ("seqan" ,seqan-1) + ("zlib" ,zlib))) + (home-page "https://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 @@ -2995,7 +2998,8 @@ reasonable amount of time and memory. For large alignments, FastTree is (inputs `(("libgtextutils" ,libgtextutils))) (native-inputs - `(("pkg-config" ,pkg-config))) + `(("gcc" ,gcc-6) ;; doesn't build with later versions + ("pkg-config" ,pkg-config))) (home-page "http://hannonlab.cshl.edu/fastx_toolkit/") (synopsis "Tools for FASTA/FASTQ file preprocessing") (description @@ -6918,14 +6922,14 @@ testing and other simple calculations.") (define-public r-shortread (package (name "r-shortread") - (version "1.44.0") + (version "1.44.1") (source (origin (method url-fetch) (uri (bioconductor-uri "ShortRead" version)) (sha256 (base32 - "18v2khq53za1m8i9va1z4wynah55gccbb42nq769vdcw7bl80wpa")))) + "1dh3q83hmi4l72vpif6dn51dzbi9ljrjgkq2zxg4sqy2jxv4vwza")))) (properties `((upstream-name . "ShortRead"))) (build-system r-build-system) (inputs @@ -7683,13 +7687,13 @@ powerful online queries from gene annotation to database mining.") (define-public r-biocparallel (package (name "r-biocparallel") - (version "1.20.0") + (version "1.20.1") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocParallel" version)) (sha256 (base32 - "1wgnad4089xn8yxl9md7xprgh3vswcbyxg7di0931ik6x54m9zws")))) + "0g0znb4whsvb9hpwx9xaasdi5n4vjqw8cpdyqgrdrjm91rls1h21")))) (properties `((upstream-name . "BiocParallel"))) (build-system r-build-system) @@ -7779,13 +7783,13 @@ tab-delimited (tabix) files.") (define-public r-delayedarray (package (name "r-delayedarray") - (version "0.12.0") + (version "0.12.1") (source (origin (method url-fetch) (uri (bioconductor-uri "DelayedArray" version)) (sha256 (base32 - "0329n1gbg2bq2vjhxfqqgakg75cdzcrcrgcwafjbg5zhkq86lc0q")))) + "1yr4i2x127v814nxg53aibp77p3vg76f3n3hgknpwx3snfhc81xs")))) (properties `((upstream-name . "DelayedArray"))) (build-system r-build-system) @@ -7811,13 +7815,13 @@ array-like objects like @code{DataFrame} objects (typically with Rle columns), (define-public r-summarizedexperiment (package (name "r-summarizedexperiment") - (version "1.16.0") + (version "1.16.1") (source (origin (method url-fetch) (uri (bioconductor-uri "SummarizedExperiment" version)) (sha256 (base32 - "04ljfw49ydgshrjv71qv9xr6y23a9vb8kp5fdjvpa8f6gzlb2a8m")))) + "1z9bdk49dajafkfvv99nv6zyn6v70iyyy2jgdp5w5z8174a2bnn1")))) (properties `((upstream-name . "SummarizedExperiment"))) (build-system r-build-system) @@ -7987,13 +7991,13 @@ information about the latest version of the Gene Ontologies.") (define-public r-topgo (package (name "r-topgo") - (version "2.37.0") + (version "2.38.1") (source (origin (method url-fetch) (uri (bioconductor-uri "topGO" version)) (sha256 (base32 - "1cplr92aq3pa266ilvmg9xfmc95gag89b5jka04a5mh88j24y2ca")))) + "1kw9m2j67895k58lx9msc248pjwblp8clxwgsl01cql7sgi1xzlf")))) (properties `((upstream-name . "topGO"))) (build-system r-build-system) @@ -10623,13 +10627,13 @@ libraries.") (define-public r-scater (package (name "r-scater") - (version "1.14.5") + (version "1.14.6") (source (origin (method url-fetch) (uri (bioconductor-uri "scater" version)) (sha256 (base32 - "1c2p1dqz4lckk657v5g0labxrf0i21l0wa3rvszslmrszn60mkif")))) + "0sxd1s8wdlj9926bagq4crjrk1nnmh3j3bhgrw160zfgc3y8pzck")))) (build-system r-build-system) (propagated-inputs `(("r-beachmat" ,r-beachmat) @@ -13286,21 +13290,23 @@ million cells.") (define-public python-bbknn (package (name "python-bbknn") - (version "1.3.1") + (version "1.3.6") (source (origin (method url-fetch) (uri (pypi-uri "bbknn" version)) (sha256 (base32 - "1qgdganvj3lyxj84v7alm23b9vqhwpn8z0115qndpnpy90qxynwz")))) + "1jbsh01f57zj4bhvjr3jh4532zznqd6nccmgrl3qi9gnhkf7c4y0")))) (build-system python-build-system) + (arguments + `(#:tests? #f)) ; TODO: Enable after migration to scikit-learn. (propagated-inputs `(("python-annoy" ,python-annoy) ("python-cython" ,python-cython) - ("python-faiss" ,python-faiss) ("python-numpy" ,python-numpy) - ("python-scanpy" ,python-scanpy))) + ("python-scipy" ,python-scipy) + ("python-umap-learn" ,python-umap-learn))) (home-page "https://github.com/Teichlab/bbknn") (synopsis "Batch balanced KNN") (description "BBKNN is a batch effect removal tool that can be directly |