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-rw-r--r--gn/packages/bioinformatics.scm91
1 files changed, 91 insertions, 0 deletions
diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm
index c899615..76406db 100644
--- a/gn/packages/bioinformatics.scm
+++ b/gn/packages/bioinformatics.scm
@@ -33,6 +33,7 @@
#:use-module (gnu packages fontutils)
#:use-module (gnu packages gcc)
#:use-module (gnu packages gtk)
+ #:use-module (gnu packages image)
#:use-module (gnu packages imagemagick)
#:use-module (gnu packages jemalloc)
#:use-module (gnu packages linux)
@@ -49,9 +50,12 @@
#:use-module (gnu packages python-xyz)
#:use-module (gnu packages rdf)
#:use-module (gnu packages readline)
+ #:use-module (gnu packages rsync)
#:use-module (gnu packages ruby)
+ #:use-module (gnu packages shells)
#:use-module (gnu packages statistics)
#:use-module (gnu packages time)
+ #:use-module (gnu packages tls)
#:use-module (gnu packages vim)
#:use-module (gnu packages web))
@@ -1563,3 +1567,90 @@ multiple sequence alignment.")
license:gpl3+ ; all sdsl-lite copies
license:zlib ; deps/sonLib/externalTools/cutest
license:boost1.0)))) ; catch.hpp
+
+(define-public ucsc-genome-browser
+ (package
+ (name "ucsc-genome-browser")
+ (version "413")
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://genome-source.gi.ucsc.edu/kent.git/")
+ (commit (string-append "v" version "_base"))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "1qcjhd4wcajik71z5347fw2sfhfkv0p6y7yldrrkmycw2qhqmpzn"))))
+ (build-system gnu-build-system)
+ (arguments
+ `(#:tests? #f ; fix later
+ #:phases
+ (modify-phases %standard-phases
+ (delete 'configure) ; There is no configure phase.
+ (add-before 'build 'pre-build
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let ((out (assoc-ref outputs "out")))
+ ;; Start by setting some variables.
+ (chdir "src")
+ (setenv "CC" ,(cc-for-target))
+ (setenv "HOME" (getcwd))
+
+ ;; And here we set the output directories
+ (setenv "CGI_BIN" (string-append out "/cgi-bin"))
+ (setenv "CGI_BIN_USER" (string-append out "/cgi-bin"))
+ (setenv "DOCUMENTROOT" (string-append out "/html"))
+ (setenv "DOCUMENTROOT_USER" (string-append out "/html"))
+ (setenv "BINDIR" (string-append out "/bin"))
+
+ ;; Now let's fix some errors
+ (mkdir-p (string-append out "/cgi-bin"))
+ (substitute* "inc/cgi_build_rules.mk"
+ (("rm -f.*") ""))
+ (substitute* (cons* "inc/cgi_build_rules.mk"
+ (find-files "." "makefile"))
+ (("CGI_BIN\\}-\\$\\{USER") "CGI_BIN_USER"))
+
+ #t)))
+ ;; Install happens during the 'build phase.
+ ;; Install the website files too
+ ;; rsync -avzP rsync://hgdownload.cse.ucsc.edu/htdocs/ /var/www/html/
+ (replace 'install
+ (lambda _
+ (invoke "make" "doc-install")
+ #t)))))
+ (inputs
+ `(("libpng" ,libpng)
+ ("mysql:dev" ,mariadb "dev")
+ ("mysql:lib" ,mariadb "lib")
+ ("openssl" ,openssl)
+ ("perl" ,perl)
+ ("python2" ,python-2)
+ ("zlib" ,zlib)))
+ (native-inputs
+ `(;("python" ,python)
+ ("rsync" ,rsync) ; For installing js files from the source checkout
+ ;("tcl" ,tcl)
+ ;("tcsh" ,tcsh)
+ ("util-linux:lib" ,util-linux "lib")
+ ("which" ,(@ (gnu packages base) which))))
+ (home-page "https://www.genome.ucsc.edu/")
+ (synopsis "Structural variants detector for next-gen sequencing data")
+ (description
+ "The UCSC Genome Browser provides a rapid and reliable display of any
+requested portion of genomes at any scale, together with dozens of aligned
+annotation tracks (known genes, predicted genes, ESTs, mRNAs, CpG islands,
+assembly gaps and coverage, chromosomal bands, mouse homologies, and more).
+Half of the annotation tracks are computed at UCSC from publicly available
+sequence data. The remaining tracks are provided by collaborators worldwide.
+Users can also add their own custom tracks to the browser for educational or
+research purposes.
+The Genome Browser stacks annotation tracks beneath genome coordinate positions,
+allowing rapid visual correlation of different types of information. The user
+can look at a whole chromosome to get a feel for gene density, open a specific
+cytogenetic band to see a positionally mapped disease gene candidate, or zoom in
+to a particular gene to view its spliced ESTs and possible alternative splicing.
+The Genome Browser itself does not draw conclusions; rather, it collates all
+relevant information in one location, leaving the exploration and interpretation
+to the user.")
+ (license (license:non-copyleft
+ "https://www.genome.ucsc.edu/conditions.html"
+ "Free for academic/non-profit/personal use only."))))