diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 108 |
1 files changed, 104 insertions, 4 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index cb3c4bc1fd..f60fc4c84c 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -11,6 +11,7 @@ ;;; 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> ;;; ;;; This file is part of GNU Guix. ;;; @@ -3601,7 +3602,7 @@ experiments and provide highly stable thresholds based on reproducibility.") (define-public jellyfish (package (name "jellyfish") - (version "2.2.7") + (version "2.2.10") (source (origin (method url-fetch) (uri (string-append "https://github.com/gmarcais/Jellyfish/" @@ -3609,7 +3610,7 @@ experiments and provide highly stable thresholds based on reproducibility.") "/jellyfish-" version ".tar.gz")) (sha256 (base32 - "1a1iwq9pq54k2m9ypvwl5s0bqfl64gwh9dx5af9i382ajas2016q")))) + "1k4pc3fvv6w1km2yph4m5sd78fbxp21d6xyzgmy0gjihzc6mb249")))) (build-system gnu-build-system) (outputs '("out" ;for library "ruby" ;for Ruby bindings @@ -3646,8 +3647,8 @@ DNA sequences. It outputs its k-mer counts in a binary format, which can be translated into a human-readable text format using the @code{jellyfish dump} command, or queried for specific k-mers with @code{jellyfish query}.") (home-page "http://www.genome.umd.edu/jellyfish.html") - ;; From their website: JELLYFISH runs on 64-bit Intel-compatible processors - (supported-systems '("x86_64-linux")) + ;; JELLYFISH seems to be 64-bit only. + (supported-systems '("x86_64-linux" "aarch64-linux" "mips64el-linux")) ;; The combined work is published under the GPLv3 or later. Individual ;; files such as lib/jsoncpp.cpp are released under the Expat license. (license (list license:gpl3+ license:expat)))) @@ -13458,3 +13459,102 @@ conversions, region filtering, FASTA sequence extraction and more.") spliced (back-spliced) sequencing reads, indicative of circular RNA (circRNA) in RNA-seq data.") (license license:gpl3)))) + +(define-public python-scanpy + (package + (name "python-scanpy") + (version "1.2.2") + (source + (origin + (method url-fetch) + (uri (pypi-uri "scanpy" version)) + (sha256 + (base32 + "1ak7bxms5a0yvf65prppq2g38clkv7c7jnjbnfpkh3xxv7q512jz")))) + (build-system python-build-system) + (propagated-inputs + `(("python-anndata" ,python-anndata) + ("python-igraph" ,python-igraph) + ("python-numba" ,python-numba) + ("python-joblib" ,python-joblib) + ("python-natsort" ,python-natsort) + ("python-networkx" ,python-networkx) + ("python-statsmodels" ,python-statsmodels) + ("python-scikit-learn" ,python-scikit-learn) + ("python-matplotlib" ,python-matplotlib) + ("python-pandas" ,python-pandas) + ("python-scipy" ,python-scipy) + ("python-seaborn" ,python-seaborn) + ("python-h5py" ,python-h5py) + ("python-tables" ,python-tables))) + (home-page "http://github.com/theislab/scanpy") + (synopsis "Single-Cell Analysis in Python.") + (description "Scanpy is a scalable toolkit for analyzing single-cell gene +expression data. It includes preprocessing, visualization, clustering, +pseudotime and trajectory inference and differential expression testing. The +Python-based implementation efficiently deals with datasets of more than one +million cells.") + (license license:bsd-3))) + +(define-public gffcompare + (let ((commit "be56ef4349ea3966c12c6397f85e49e047361c41") + (revision "1")) + (package + (name "gffcompare") + (version (git-version "0.10.15" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/gpertea/gffcompare/") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0cp5qpxdhw4mxpya5dld8wi3jk00zyklm6rcri426wydinrnfmkg")))) + (build-system gnu-build-system) + (arguments + `(#:tests? #f ; no check target + #:phases + (modify-phases %standard-phases + (delete 'configure) + (add-before 'build 'copy-gclib-source + (lambda* (#:key inputs #:allow-other-keys) + (mkdir "../gclib") + (copy-recursively + (assoc-ref inputs "gclib-source") "../gclib") + #t)) + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let ((bin (string-append (assoc-ref outputs "out") "/bin"))) + (install-file "gffcompare" bin) + #t)))))) + (native-inputs + `(("gclib-source" ; see 'README.md' of gffcompare + ,(let ((commit "54917d0849c1e83cfb057b5f712e5cb6a35d948f") + (revision "1") + (name "gclib") + (version (git-version "0.10.3" revision commit))) + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/gpertea/gclib/") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0b51lc0b8syrv7186fd7n8f15rwnf264qgfmm2palrwks1px24mr"))))))) + (home-page "https://github.com/gpertea/gffcompare/") + (synopsis "Tool for comparing or classifing transcripts of RNA-Seq") + (description + "@code{gffcompare} is a tool that can: +@enumerate +@item compare and evaluate the accuracy of RNA-Seq transcript assemblers +(Cufflinks, Stringtie); +@item collapse (merge) duplicate transcripts from multiple GTF/GFF3 files (e.g. +resulted from assembly of different samples); +@item classify transcripts from one or multiple GTF/GFF3 files as they relate to +reference transcripts provided in a annotation file (also in GTF/GFF3 format). +@end enumerate") + (license + (list + license:expat ;license for gffcompare + license:artistic2.0))))) ;license for gclib |