diff options
Diffstat (limited to 'gn/packages/bioinformatics.scm')
| -rw-r--r-- | gn/packages/bioinformatics.scm | 317 |
1 files changed, 215 insertions, 102 deletions
diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm index 8897752..056bc3f 100644 --- a/gn/packages/bioinformatics.scm +++ b/gn/packages/bioinformatics.scm @@ -14,6 +14,8 @@ #:use-module (guix build-system trivial) #:use-module (guix build-system waf) #:use-module (gnu packages) + #:use-module (gn packages python) + #:use-module (gnu packages bioconductor) #:use-module (gnu packages bioinformatics) #:use-module (gnu packages boost) #:use-module (gnu packages check) @@ -22,6 +24,7 @@ #:use-module (gnu packages datastructures) #:use-module (gnu packages fontutils) #:use-module (gnu packages gcc) + #:use-module (gnu packages graphviz) #:use-module (gnu packages imagemagick) #:use-module (gnu packages jemalloc) #:use-module (gnu packages maths) @@ -31,9 +34,13 @@ #:use-module (gnu packages protobuf) #:use-module (gnu packages python) #:use-module (gnu packages python-science) + #:use-module (gnu packages python-web) #:use-module (gnu packages python-xyz) + #:use-module (gnu packages rdf) #:use-module (gnu packages readline) - #:use-module (gnu packages statistics)) + #:use-module (gnu packages serialization) + #:use-module (gnu packages statistics) + #:use-module (gnu packages time)) (define-public contra (package @@ -415,92 +422,7 @@ reads.") (license license:non-copyleft))) (define-public edirect-gn - (package - (inherit edirect) - (name "edirect-gn") - (arguments - (substitute-keyword-arguments (package-arguments edirect) - ((#:phases phases) - `(modify-phases ,phases - ; (replace 'build - ; (lambda* (#:key inputs #:allow-other-keys) - ; (let ((go (string-append (assoc-ref inputs "go") "/bin/go"))) - ; (invoke go "build" "xtract.go")))) - (add-after 'unpack 'patch-programs - (lambda* (#:key inputs #:allow-other-keys) - (let ((gzip (assoc-ref inputs "gzip"))) - (substitute* '("index-bioc" - "pm-index" - "pm-invert" - "pm-stash" - "rchive.go" - "run-ncbi-converter") - (("gunzip") (string-append gzip "/bin/gunzip"))) - (substitute* (find-files "." "^e") - (("exec perl") "exec")) - (substitute* '("xtract" "rchive") - ;; or add current directory to PATH - ((".*PATH.*") ""))) - #t)) - (replace 'install - (lambda* (#:key inputs outputs #:allow-other-keys) - (let ((bin (string-append (assoc-ref outputs "out") "/bin")) - (xtract.linux (assoc-ref inputs "xtract.Linux")) - (rchive.linux (assoc-ref inputs "rchive.Linux"))) - (for-each - (lambda (file) - (install-file file bin)) - '("archive-pubmed" "asp-cp" "asp-ls" "download-pubmed" - "edirect.pl" "efetch" "epost" "esearch" "fetch-pubmed" - "ftp-cp" "ftp-ls" "has-asp" "pm-prepare" "pm-refresh" - "pm-stash" "rchive" "xtract")) - (copy-file xtract.linux (string-append bin "/xtract.Linux")) - (copy-file rchive.linux (string-append bin "/rchive.Linux")) - (chmod (string-append bin "/xtract.Linux") #o555) - (chmod (string-append bin "/rchive.Linux") #o555)) - #t)) - (replace 'wrap-program - (lambda* (#:key outputs #:allow-other-keys) - ;; Make sure 'edirect.pl' finds all perl inputs at runtime. - (let ((out (assoc-ref outputs "out")) - (path (getenv "PERL5LIB"))) - (for-each - (lambda (file) - (wrap-program (string-append out "/bin/" file) - `("PERL5LIB" ":" prefix (,path)))) - '("edirect.pl" "asp-ls" "ftp-cp" "ftp-ls"))) - #t)))))) - (inputs - `(("gzip" ,gzip) - ,@(package-inputs edirect))) - (native-inputs - `( - ;("go" ,go) - ("xtract.Linux" - ,(origin - (method url-fetch) - (uri (string-append "ftp://ftp.ncbi.nlm.nih.gov/entrez/entrezdirect/" - "/xtract.Linux")) ;; March 10, 2016 - (sha256 - (base32 - "15yhhh8kfipk12rhzabap81ys8wgj0khn0mp8p7zwqhq028fwj0l")))) - ("rchive.Linux" - ,(origin - (method url-fetch) - (uri (string-append "ftp://ftp.ncbi.nlm.nih.gov/entrez/entrezdirect/" - "/rchive.Linux")) ;; November 14, 2017 - (sha256 - (base32 - "0hl8zj1md9xbmaj0pv99rjyisw8w74rirw97xwqk47dz8v8ml338")))))) - (native-search-paths - ;; Ideally this should be set for LWP somewhere. - (list (search-path-specification - (variable "PERL_LWP_SSL_CA_FILE") - (file-type 'regular) - (separator #f) - (files '("/etc/ssl/certs/ca-certificates.crt"))))) - ;; Due to the precompiled binaries we download: - (supported-systems '("x86_64-linux")))) + (deprecated-package "edirect-gn" edirect)) ;; TODO: Unbundle zlib, bamtools, tclap (define-public sniffles @@ -856,19 +778,19 @@ interest, and this app can provide values and figures for applicants to use.") (license license:gpl3)))) (define-public singlecellrshiny - (let ((commit "8061dcb477ba355de77d3e4fd3a15cf3267b56af") - (revision "1")) + (let ((commit "bdca74f4819d11e8fe7b15d9ab91b853f6542f7a") + (revision "3")) (package (name "singlecellrshiny") (version (git-version "0.0.0" revision commit)) (source (origin (method git-fetch) (uri (git-reference - (url "https://github.com/syousefi/singleCellRshiny.git") + (url "https://github.com/genenetwork/singleCellRshiny") (commit commit))) (file-name (git-file-name name version)) (sha256 - (base32 "1pd8a9jx6ijjggsifvq66madx31h29rah5pmz4kdzfzb4fskpqz1")))) + (base32 "1rxj933s9p9r7358vnp15f7ag6c0j65r4hgr8kyirfhmp1i8xdlw")))) (build-system trivial-build-system) (arguments `(#:modules ((guix build utils)) @@ -880,16 +802,20 @@ interest, and this app can provide values and figures for applicants to use.") (app (string-append out "/bin/" ,name)) (Rbin (string-append (assoc-ref %build-inputs "r-min") "/bin/Rscript")) + (top1001 (assoc-ref %build-inputs "RobTop1001.csv")) + (celltypes (assoc-ref %build-inputs "CellTypes_RGC_Master_08Dec2018.csv")) + (800-H1 (assoc-ref %build-inputs "800-H1-H20-RNA-Seq.csv")) (source (assoc-ref %build-inputs "source"))) (copy-recursively source targetdir) + (substitute* (string-append targetdir "/app.R") + ;; As seen in https://github.com/genenetwork/singleCellRshiny/commit/6b2a344dd0d02f65228ad8c350bac0ced5850d05.patch + (("library\\(DT\\)") "library(DT)\nlibrary(multtest)")) (substitute* (string-append targetdir "/global.R") - (("800-H1-H20-RNA-Seq-SingleCell-Retina-OMRF-03-29-19_FPKM_v2_SiamakPlay.csv") - "shinyRappToyDataset_SiamakPlay.csv") - ;; Comment out the two unreferenced files for now - (("^rgc.*") "") - ;(("CellTypes_RGC_Master_08Dec2018.csv") "") - ;(("RobTop1001.csv") "") - ) + (("800-H1-H20-RNA-Seq-SingleCell-Retina-OMRF-03-29-19_FPKM_v2_SiamakPlay.csv") 800-H1) + (("CellTypes_RGC_Master_08Dec2018.csv") celltypes) + (("RobTop1001.csv") top1001) + ;; As seen in https://github.com/genenetwork/singleCellRshiny/commit/6b2a344dd0d02f65228ad8c350bac0ced5850d05.patch + (("dim\\(sc.object.1") "dim(sc.object")) (mkdir-p (string-append out "/bin")) (call-with-output-file app (lambda (port) @@ -901,20 +827,41 @@ runApp(launch.browser=0, port=4208)~%\n" Rbin targetdir))) (chmod app #o555) #t)))) - (native-inputs `(("source" ,source))) (inputs - `(("r-min" ,r-minimal))) + `(("r-min" ,r-minimal) + ("RobTop1001.csv" + ,(origin + (method url-fetch) + (uri "https://archive.org/download/celltypesrgcmaster08dec2018/RobTop1001.csv") + (file-name "RobTop1001.csv") + (sha256 + (base32 "0pa73kc1p8417sjvvvhp9xsbh2h8g7h85pnmm16mnv4wjalhq0gn")))) + ("CellTypes_RGC_Master_08Dec2018.csv" + ,(origin + (method url-fetch) + (uri "https://archive.org/download/celltypesrgcmaster08dec2018/CellTypes_RGC_Master_08Dec2018.csv") + (file-name "CellTypes_RGC_Master_08Dec2018.csv") + (sha256 + (base32 "0y411968np1f5g21iym9xc9yj5c1jsn94rpkwkxh9pw2z43gvghn")))) + ("800-H1-H20-RNA-Seq.csv" + ,(origin + (method url-fetch) + (uri "https://archive.org/download/celltypesrgcmaster08dec2018/800-H1-H20-RNA-Seq-SingleCell-Retina-OMRF-03-29-19_FPKM_v2_SiamakPlay.csv") + (file-name "800-H1-H20-RNA-Seq-SingleCell-Retina-OMRF-03-29-19_FPKM_v2_SiamakPlay.csv") + (sha256 + (base32 "1b1y4lfs8drypm04i1rypbmk67rdqgs27nfh05pwnv3sja2nanam")))))) (propagated-inputs `(("r" ,r) ("r-dt" ,r-dt) + ("r-multtest" ,r-multtest) ("r-seurat" ,r-seurat) ("r-shiny" ,r-shiny))) - (home-page "http://rn6err.opar.io/") + (home-page "http://singlecell.opar.io/") (synopsis "RNA sequencing data analysis") (description "This is the R-Shiny programs to run some basic single cell RNA sequencing (scRNA-seq) data analysis.") - (license license:gpl3)))) + (license license:agpl3)))) (define-public seqwish (package @@ -1193,3 +1140,169 @@ here}.") (synopsis "Efficient sequence alignment of full genomes") (description "MUMmer is a versatil alignment tool for DNA and protein sequences.") (license license:artistic2.0))) + +(define-public grocsvs + (let ((commit "ecd956a65093a0b2c41849050e4512d46fecea5d") + (revision "1")) + (package + (name "grocsvs") + (version (git-version "0.2.6.1" revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/grocsvs/grocsvs") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 "14505725gr7qxc17cxxf0k6lzcwmgi64pija4mwf29aw70qn35cc")))) + (build-system python-build-system) + (arguments + `(#:python ,python-2)) ; Only python-2 supported. + (inputs + `(("python2-admiral" ,python2-admiral) + ("python2-h5py" ,python2-h5py) + ("python2-ipython-cluster-helper" ,python2-ipython-cluster-helper) + ("python2-networkx" ,python2-networkx) + ("python2-psutil" ,python2-psutil) + ("python2-pandas" ,python2-pandas) + ("python2-pybedtools" ,python2-pybedtools) + ("python2-pyfaidx" ,python2-pyfaidx) + ("python2-pygraphviz" ,python2-pygraphviz) + ("python2-pysam" ,python2-pysam) + ("python2-scipy" ,python2-scipy))) + (home-page "https://github.com/grocsvs/grocsvs") + (synopsis "Genome-wide reconstruction of complex structural variants") + (description + "@dfn{Genome-wide Reconstruction of Complex Structural Variants} +(GROC-SVs), is a software pipeline for identifying large-scale structural +variants, performing sequence assembly at the breakpoints, and reconstructing +the complex structural variants using the long-fragment information from the +10x Genomics platform.") + (license license:expat)))) + +(define-public diagnostic-slider + (let ((commit "514d65d4982133e4869e578c5553fced4c6d506c") + (revision "1")) + (package + (name "diagnostic-slider") + (version (git-version "0.0.0" revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/sens/diagnostic-slider") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 "04g8if32g8syg6v0bd3jjn05i3d394nx8i3ccl0883p8mlmdvlmx")))) + (build-system trivial-build-system) + (arguments + `(#:modules ((guix build utils)) + #:builder + (begin + (use-modules (guix build utils)) + (let* ((out (assoc-ref %outputs "out")) + (targetdir (string-append out "/share/" ,name)) + (app (string-append out "/bin/" ,name)) + (Rbin (string-append (assoc-ref %build-inputs "r-min") + "/bin/Rscript")) + (source (assoc-ref %build-inputs "source"))) + (copy-recursively source targetdir) + (mkdir-p (string-append out "/bin")) + (call-with-output-file app + (lambda (port) + (format port +"#!~a +library(shiny) +setwd(\"~a\") +runApp(launch.browser=0, port=4206)~%\n" + Rbin targetdir))) + (chmod app #o555) + #t)))) + (native-inputs + `(("source" ,source))) + (inputs + `(("r-min" ,r-minimal))) + (propagated-inputs + `(("r" ,r) + ("r-shiny" ,r-shiny))) + (home-page "https://github.com/sens/diagnostic-slider") + (synopsis "") + (description + "") + (license #f)))) + +(define-public bh20-seq-resource + (let ((commit "bbca5ac9b2538e410efe3e09651f87e5573145de") + (revision "2")) + (package + (name "bh20-seq-resource") + (version (git-version "1.0" revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/arvados/bh20-seq-resource") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1kkysjgmhp7kfb17470ik821p9djsidyqmkbjvv37jx2w9pvw31z")))) + (build-system python-build-system) + (inputs + `(("python-arvados-python-client" ,python-arvados-python-client) + ("python-flask" ,python-flask) + ("python-magic" ,python-magic) + ("python-pyyaml" ,python-pyyaml) + ("python-schema-salad" ,python-schema-salad))) + (native-inputs + `(("git" ,(@ (gnu packages version-control) git)) + ("python-oauth2client" ,python-oauth2client) + ("python-pytest" ,python-pytest) + ("python-pytest-runner" ,python-pytest-runner) + ("python-uritemplate" ,python-uritemplate))) + (home-page "https://github.com/arvados/bh20-seq-resource") + (synopsis + "Tool to upload SARS-CoV-19 sequences and service to kick off analysis") + (description "This repository provides a sequence uploader for the +COVID-19 Virtual Biohackathon's Public Sequence Resource project. You can use +it to upload the genomes of SARS-CoV-2 samples to make them publicly and freely +available to other researchers.") + (license license:asl2.0)))) + +(define-public python-scanpy-git + (let ((commit "590d42309f9ed6550d7b887039990edfc1ac7648") ; April 22, 2020 + (revision "1")) + (package + (inherit python-scanpy) + (name "python-scanpy-git") + (version (git-version "1.4.6" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/theislab/scanpy") + (commit commit))) + (file-name (git-file-name "python-scanpy" version)) + (sha256 + (base32 "0z3pk9vh4b7fqq7fs262i6z0pm1dnn6bf49a4r7r73k6gjj6namd")))) + (arguments + (substitute-keyword-arguments (package-arguments python-scanpy) + ((#:phases phases) + `(modify-phases ,phases + (add-before 'build 'fix-build + (lambda* (#:key inputs outputs #:allow-other-keys) + (let ((out (assoc-ref outputs "out")) + (pyv (python-version (assoc-ref inputs "python")))) + (substitute* "setup.py" + (("use_scm_version=True") "use_scm_version=False")) + (substitute* "scanpy/__init__.py" + (("__version__.*") + (string-append "__version__ = '" ,version "'\n"))) + (mkdir-p + (string-append out "/lib/python" pyv "/site-packages")) + (setenv "PYTHONPATH" + (string-append out + "/lib/python" pyv "/site-packages/:" + (getenv "PYTHONPATH")))) + ;; These tests fail on this git revision + (delete-file "scanpy/tests/test_neighbors_key_added.py") + (delete-file "scanpy/tests/test_pca.py") + #t))))))))) |