diff options
Diffstat (limited to 'gnu')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 60 |
1 files changed, 60 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 8b38c7ce0d..b258b796f7 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -52,6 +52,7 @@ #:use-module (guix build-system ocaml) #:use-module (guix build-system perl) #:use-module (guix build-system python) + #:use-module (guix build-system qt) #:use-module (guix build-system r) #:use-module (guix build-system ruby) #:use-module (guix build-system scons) @@ -125,6 +126,7 @@ #:use-module (gnu packages python-science) #:use-module (gnu packages python-web) #:use-module (gnu packages python-xyz) + #:use-module (gnu packages qt) #:use-module (gnu packages rdf) #:use-module (gnu packages readline) #:use-module (gnu packages ruby) @@ -13187,6 +13189,64 @@ concatenates pieces of read sequences to generate the final unitig sequences. Thus the per-base error rate is similar to the raw input reads.") (license license:expat))) +(define-public bandage + (package + (name "bandage") + (version "0.8.1") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/rrwick/Bandage") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1bbsn5f5x8wlspg4pbibqz6m5vin8c19nl224f3z3km0pkc97rwv")))) + (build-system qt-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (replace 'configure + (lambda _ + (invoke "qmake" "Bandage.pro"))) + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (substitute* "tests/bandage_command_line_tests.sh" + (("^bandagepath=.*") + (string-append "bandagepath=" (getcwd) "/Bandage\n"))) + (with-directory-excursion "tests" + (setenv "XDG_RUNTIME_DIR" (getcwd)) + (invoke "./bandage_command_line_tests.sh"))) + #t)) + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let ((out (assoc-ref outputs "out"))) + (install-file "Bandage" (string-append out "/bin")) + #t)))))) + (inputs + `(("qtbase" ,qtbase) + ("qtsvg" ,qtsvg))) + (native-inputs + `(("imagemagick" ,imagemagick))) + (home-page "https://rrwick.github.io/Bandage/") + (synopsis + "Bioinformatics Application for Navigating De novo Assembly Graphs Easily") + (description "Bandage is a program for visualising de novo assembly graphs. +It allows users to interact with the assembly graphs made by de novo assemblers +such as Velvet, SPAdes, MEGAHIT and others. De novo assembly graphs contain not +only assembled contigs but also the connections between those contigs, which +were previously not easily accessible. Bandage visualises assembly graphs, with +connections, using graph layout algorithms. Nodes in the drawn graph, which +represent contigs, can be automatically labelled with their ID, length or depth. +Users can interact with the graph by moving, labelling and colouring nodes. +Sequence information can also be extracted directly from the graph viewer. By +displaying connections between contigs, Bandage opens up new possibilities for +analysing and improving de novo assemblies that are not possible by looking at +contigs alone.") + (license (list license:gpl2+ ; bundled ogdf + license:gpl3+)))) + (define-public r-circus (package (name "r-circus") |