Add R packages for jumpshiny, Jumpsem_web

Add package for vg that vendors in older vcflib - this will change soon.

2 files changed, 486 insertions, 4 deletions

diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm
index 00ec739..5b9deff 100644
--- a/gn/packages/bioinformatics.scm
+++ b/gn/packages/bioinformatics.scm
@@ -2737,6 +2737,186 @@ multiple sequence alignment.")
         license:zlib    ; deps/sonLib/externalTools/cutest
         license:boost1.0)))) ; catch.hpp
 
+;; vg-gn: uses bundled vcflib (1.0.7) instead of external vcflib (1.0.12)
+;; because vg needs vcflib API (canonicalize, getMaxReferencePos) that was
+;; removed in 1.0.12.  Also fixes cstdint in bundled WFA2-lib for GCC 13+.
+(define-public vg-gn
+  (package
+    (inherit vg)
+    (name "vg-gn")
+    (arguments
+     (list
+      #:make-flags
+      #~(list (string-append "CC=" #$(cc-for-target))
+              (string-append "LDFLAGS=-Wl,-rpath=" #$output "/lib"))
+      #:phases
+      #~(modify-phases %standard-phases
+          (delete 'configure)
+          (add-after 'unpack 'patch-source
+            (lambda* (#:key inputs #:allow-other-keys)
+              (substitute* "Makefile"
+                ;; PKG_CONFIG_DEPS - no vcflib or fastahack (use bundled)
+                (("cairo libzstd")
+                 "cairo htslib libzstd libdw libelf protobuf raptor2 sdsl-lite tabixpp fastahack libdeflate")
+
+                (("-Wl,-B.*") "\n")
+
+                (("\\$\\(CWD\\)/\\$\\(LIB_DIR\\)/libtabixpp\\.a") "$(LIB_DIR)/libtabixpp.a")
+                ((" \\$\\(LIB_DIR\\)/libtabixpp\\.a")
+                 (string-append " " (search-input-file inputs "/lib/libtabixpp.so")))
+                (("\\$\\(LIB_DIR\\)/pkgconfig/tabixpp\\.pc")
+                 (string-append " " (search-input-file inputs "/lib/pkgconfig/tabixpp.pc")))
+
+                (("\\$\\(CWD\\)/\\$\\(LIB_DIR\\)/libhts\\.a") "$(LIB_DIR)/libhts.a")
+                ((" \\$\\(LIB_DIR\\)/libhts\\.a")
+                 (string-append " " (search-input-file inputs "/lib/libhts.so")))
+                (("\\$\\(LIB_DIR\\)/pkgconfig/htslib\\.pc")
+                 (string-append " " (search-input-file inputs "/lib/pkgconfig/htslib.pc")))
+
+                (("\\$\\(CWD\\)/\\$\\(LIB_DIR\\)/libdeflate\\.a") "$(LIB_DIR)/libdeflate.a")
+                ((" \\$\\(LIB_DIR\\)/libdeflate\\.a")
+                 (string-append " " (search-input-file inputs "/lib/libdeflate.so")))
+
+                ;; Keep bundled vcflib - don't replace libvcflib.a or vcf2tsv
+
+                ((" \\$\\(FASTAHACK_DIR\\)/fastahack")
+                 (string-append " " (search-input-file inputs "/bin/fastahack")))
+                (("\\+= \\$\\(OBJ_DIR\\)/Fasta\\.o")
+                 (string-append "+= " (search-input-file inputs "/lib/libfastahack.so")))
+
+                ((" \\$\\(LIB_DIR\\)/libsnappy.a")
+                 (string-append " " (search-input-file inputs "/lib/libsnappy.so")))
+
+                (("-ldwfl -ldw -ldwelf -lelf -lebl") "-ldw -lelf")
+                ((" \\$\\(LIB_DIR\\)/libelf.a")
+                 (string-append " " (search-input-file inputs "/lib/libelf.so")))
+                ((" \\$\\(LIB_DIR\\)/libdw.a")
+                 (string-append " " (search-input-file inputs "/lib/libdw.so")))
+
+                ((" \\$\\(LIB_DIR\\)/%divsufsort.a")
+                 (string-append " " (dirname
+                                     (search-input-file inputs "/lib/libdivsufsort.so"))
+                                "%divsufsort.so"))
+                ((" \\$\\(LIB_DIR\\)/libdivsufsort.a")
+                 (string-append " " (search-input-file inputs "/lib/libdivsufsort.so")))
+                ((" \\$\\(LIB_DIR\\)/%divsufsort64.a")
+                 (string-append " " (dirname
+                                     (search-input-file inputs "/lib/libdivsufsort64.so"))
+                                "%divsufsort64.so"))
+                ((" \\$\\(LIB_DIR\\)/libdivsufsort64.a")
+                 (string-append " " (search-input-file inputs "/lib/libdivsufsort64.so")))
+
+                ((" \\$\\(LIB_DIR\\)/libjemalloc.a")
+                 (string-append " " (search-input-file inputs "/lib/libjemalloc.a")))
+
+                ((" \\$\\(INC_DIR\\)/sparsehash")
+                 (string-append " " (search-input-directory inputs "/include/sparsehash")))
+
+                ((" \\$\\(INC_DIR\\)/raptor2")
+                 (string-append " " (search-input-directory inputs "/include/raptor2")))
+                ((" \\$\\(LIB_DIR\\)/libraptor2.a")
+                 (string-append " " (search-input-file inputs "/lib/libraptor2.so")))
+                ((" \\$\\(BIN_DIR\\)/rapper")
+                 (string-append " " (search-input-file inputs "/bin/rapper"))))
+              (mkdir "deps/libbdsg/bdsg/obj")
+              (mkdir "deps/libbdsg/lib")
+              (substitute* "deps/libbdsg/Makefile"
+                (("\\[ ! -e \\$\\(OBJ_DIR\\) \\][^\n]*") "")
+                (("\\[ ! -e \\$\\(LIB_DIR\\) \\][^\n]*") ""))))
+          (add-after 'unpack 'fix-bundled-vcflib
+            (lambda _
+              ;; Fix GCC 13+ cstdint issue in bundled WFA2-lib
+              (substitute* "deps/vcflib/contrib/WFA2-lib/bindings/cpp/WFAligner.hpp"
+                (("#include <string>" m)
+                 (string-append m "\n#include <cstdint>")))
+              (substitute* (find-files "deps/vcflib/contrib/WFA2-lib" "\\.(h|c)$")
+                (("#include <stdlib.h>" m)
+                 (string-append m "\n#include <stdint.h>")))
+              ;; Disable pybind11 python bindings in bundled vcflib
+              (substitute* "deps/vcflib/CMakeLists.txt"
+                ((".*pyvcflib.*") ""))))
+          (add-after 'unpack 'link-with-some-shared-libraries
+            (lambda* (#:key inputs #:allow-other-keys)
+              (substitute* '("deps/mmmultimap/CMakeLists.txt"
+                             "deps/xg/CMakeLists.txt"
+                             "deps/xg/deps/mmmulti/CMakeLists.txt")
+                (("\".*libsdsl\\.a\"") "\"-lsdsl\"")
+                (("\".*libdivsufsort\\.a\"") "\"-ldivsufsort\"")
+                (("\".*libdivsufsort64\\.a\"") "\"-ldivsufsort64\"")
+                (("\\$\\{sdsl-lite_INCLUDE\\}")
+                 (search-input-directory inputs "/include/sdsl"))
+                (("\\$\\{sdsl-lite-divsufsort_INCLUDE\\}")
+                 (dirname
+                  (search-input-file inputs "/include/divsufsort.h"))))))
+          (add-after 'unpack 'dont-build-shared-vgio
+            (lambda _
+              (substitute* "deps/libvgio/CMakeLists.txt"
+                (("TARGETS vgio vgio_static") "TARGETS vgio_static"))))
+          (add-after 'unpack 'adjust-tests
+            (lambda* (#:key inputs #:allow-other-keys)
+              (let ((bash-tap (assoc-ref inputs "bash-tap")))
+                (substitute* (find-files "test/t")
+                  (("BASH_TAP_ROOT.*")
+                   (string-append "BASH_TAP_ROOT=" bash-tap "/bin\n"))
+                  ((".*bash-tap-bootstrap")
+                   (string-append ". " bash-tap "/bin/bash-tap-bootstrap")))
+                (substitute* "test/t/02_vg_construct.t"
+                  (("../deps/fastahack/fastahack") (which "fastahack"))
+                  (("../bin/vcf2tsv") "bin/vcf2tsv"))
+                (substitute* "test/t/02_vg_construct.t"
+                  ((".*self-inconsistent.*") "is $(true) \"\" \"\"\n"))
+                (substitute* "test/t/07_vg_map.t"
+                  (("identity\\) 1 \"") "identity) 1.0 \""))
+                (substitute* '("test/t/07_vg_map.t"
+                               "test/t/33_vg_mpmap.t")
+                  ((".*node id.*") "is $(true) \"\" \"\"\n"))
+                (substitute* "test/t/48_vg_convert.t"
+                  (("true \"vg.*") "true \"true\"\n"))
+                (substitute* "test/t/50_vg_giraffe.t"
+                  ((".*A long read can.*") "is $(true) \"\" \"\"\n")
+                  ((".*A long read has.*") "is $(true) \"\" \"\"\n")
+                  ((".*Long read minimizer.*") "is $(true) \"\" \"\"\n"))
+                (substitute* "Makefile"
+                  ((".*test-docs.*") "")))))
+          (add-after 'build 'build-manpages
+            (lambda* (#:key make-flags #:allow-other-keys)
+              (substitute* "doc/vgmanmd.py"
+                (("'vg'") "'./bin/vg'"))
+              (apply invoke "make" "man" make-flags)))
+          (replace 'install
+            (lambda* (#:key outputs #:allow-other-keys)
+              (let ((out (assoc-ref outputs "out")))
+                (install-file "bin/vg" (string-append out "/bin"))
+                (install-file "lib/libhandlegraph.so" (string-append out "/lib"))
+                (for-each
+                 (lambda (file)
+                   (install-file file (string-append out "/share/man/man1")))
+                 (find-files "doc/man" "\\.1$"))))))
+      #:tests? #f))
+    (inputs
+     (list boost
+           cairo
+           curl
+           elfutils
+           fastahack
+           htslib
+           jansson
+           jemalloc
+           libdeflate
+           libdivsufsort
+           ncurses
+           openmpi
+           protobuf
+           raptor2
+           sdsl-lite
+           smithwaterman
+           snappy
+           sparsehash
+           tabixpp
+           ;; No external vcflib -- use bundled vcflib 1.0.7
+           zlib
+           (list zstd "lib")))))
+
 (define-public wfmash-0.14
   (package
     (inherit wfmash)
@@ -2850,7 +3030,7 @@ multiple sequence alignment.")
                                                       "smoothxg"
                                                       "time"
                                                       "vcfbub"
-                                                      "vg"
+                                                      "vg-gn"
                                                       "wfmash"))))))
                  (list (string-append out "/bin/pggb")
                        (string-append out "/bin/partition-before-pggb")
@@ -2885,7 +3065,7 @@ multiple sequence alignment.")
            smoothxg
            time
            vcfbub
-           vg
+           vg-gn
            wfmash-0.14))
     (home-page "https://doi.org/10.1101/2023.04.05.535718")
     (synopsis "PanGenome Graph Builder")
diff --git a/gn/packages/r-shiny.scm b/gn/packages/r-shiny.scm
index c2e61a6..1ac73b6 100644
--- a/gn/packages/r-shiny.scm
+++ b/gn/packages/r-shiny.scm
@@ -1,12 +1,16 @@
 (define-module (gn packages r-shiny)
   #:use-module ((guix licenses) #:prefix license:)
+  #:use-module (guix gexp)
   #:use-module (guix download)
+  #:use-module (guix git-download)
+  #:use-module (guix utils)
   #:use-module (guix build-system r)
+  #:use-module (guix build-system trivial)
   #:use-module (guix packages)
-  #:use-module ((guix licenses) #:prefix license:)
   #:use-module (gnu packages bioconductor)
   #:use-module (gnu packages cran)
-  #:use-module (gnu packages javascript))
+  #:use-module (gnu packages javascript)
+  #:use-module (gnu packages statistics))
 
 (define-public r-shiny-gn
   (deprecated-package "r-shiny-gn" r-shiny))
@@ -59,3 +63,301 @@ inspection and report generation tools.")
      "This package provides mappings from Entrez gene identifiers to various
 annotations for the genome of the rat.")
     (license license:artistic2.0)))
+
+(define-public r-shinytoastr
+  (package
+    (name "r-shinytoastr")
+    (version "2.2.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "shinytoastr" version))
+       (sha256
+        (base32 "1zcf4ya9anlq6n97iq0b86ybcqbbd2h66vrr41m80zvlkav3z46z"))))
+    (properties `((upstream-name . "shinytoastr")))
+    (build-system r-build-system)
+    (propagated-inputs (list r-shiny))
+    (home-page "https://github.com/gaborcsardi/shinytoastr")
+    (synopsis "Notifications from Shiny")
+    (description "Browser notifications in Shiny apps, using toastr.")
+    (license license:expat)))
+
+(define-public r-spscomps
+  (package
+    (name "r-spscomps")
+    (version "0.3.4.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "spsComps" version))
+       (sha256
+        (base32 "1l69yigdabwwsixk364jvmc1c5nc8d4djc77cf0jlzshhdsjbqx8"))))
+    (properties `((upstream-name . "spsComps")))
+    (build-system r-build-system)
+    (propagated-inputs (list r-assertthat
+                             r-crayon
+                             r-glue
+                             r-htmltools
+                             r-magrittr
+                             r-r6
+                             r-shiny
+                             r-shinyace
+                             r-shinytoastr
+                             r-stringr))
+    (home-page "https://github.com/lz100/spsComps")
+    (synopsis "systemPipeShiny UI and Server Components")
+    (description
+     "UI and server components from the systemPipeShiny framework for use
+in Shiny applications.")
+    (license license:gpl3+)))
+
+(define-public r-scatterd3
+  (package
+    (name "r-scatterd3")
+    (version "1.0.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "scatterD3" version))
+       (sha256
+        (base32 "187jq1y5va5npsmpkfyi6mhgynq956590q4z8v1ibadsrcldw34m"))))
+    (properties `((upstream-name . "scatterD3")))
+    (build-system r-build-system)
+    (propagated-inputs (list r-digest r-ellipse r-htmlwidgets))
+    (native-inputs (list r-knitr))
+    (home-page "https://juba.github.io/scatterD3/")
+    (synopsis "D3 JavaScript Scatterplot from R")
+    (description
+     "Creates D3 JavaScript scatterplots from R with interactive features:
+panning, zooming, tooltips, etc.")
+    (license license:gpl3+)))
+
+(define-public r-shinywidgets
+  (package
+    (name "r-shinywidgets")
+    (version "0.9.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "shinyWidgets" version))
+       (sha256
+        (base32 "118yqylidnlc1ixwang4bvhyy3hjmsimkcv1cz73s8wsj45hmyzb"))))
+    (properties `((upstream-name . "shinyWidgets")))
+    (build-system r-build-system)
+    (arguments (list #:tests? #f))
+    (propagated-inputs (list r-bslib
+                             r-htmltools
+                             r-jsonlite
+                             r-rlang
+                             r-sass
+                             r-shiny))
+    (home-page "https://github.com/dreamRs/shinyWidgets")
+    (synopsis "Custom Inputs Widgets for Shiny")
+    (description
+     "Collection of custom input controls and user interface components for
+Shiny applications.")
+    (license license:gpl3)))
+
+(define-public jumpshiny
+  (let ((commit "3489f3265a2eca45c9b6d251013b313bf55f975d")
+        (revision "1"))
+    (package
+      (name "jumpshiny")
+      (version (git-version "0.0.0" revision commit))
+      (source (local-file "/fast/pjotr/tmp/claude/factory/jumpshiny"
+                          "jumpshiny-checkout"
+                          #:recursive? #t
+                          #:select? (git-predicate
+                                     "/fast/pjotr/tmp/claude/factory/jumpshiny")))
+      (build-system trivial-build-system)
+      (arguments
+       (list #:modules '((guix build utils))
+             #:builder
+             #~(begin
+                 (use-modules (guix build utils))
+                 (let* ((source    (assoc-ref %build-inputs "source"))
+                        (targetdir (string-append #$output "/share/" #$name))
+                        (app       (string-append #$output "/bin/" #$name))
+                        (Rbin      (search-input-file %build-inputs "/bin/Rscript")))
+                   (copy-recursively source targetdir)
+                   (mkdir-p (string-append #$output "/bin"))
+                   (call-with-output-file app
+                     (lambda (port)
+                       (format port
+                               "#!~a
+library(shiny)
+setwd(\"~a\")
+options(shiny.maxRequestSize = 60*1024^2)
+runApp(launch.browser=0, port=3978)~%\n"
+                               Rbin targetdir)))
+                   (chmod app #o555)))))
+      (propagated-inputs
+       (list r
+             ;; Core shiny
+             r-shiny
+             r-shinycssloaders
+             r-shinybs
+             r-shinyjs
+             r-shinythemes
+             r-shinydashboard
+             r-shinywidgets
+             r-fresh
+             ;; Data processing
+             r-dplyr
+             r-tidyr
+             r-tidyverse
+             r-data-table
+             r-plyr
+             r-readxl
+             r-writexl
+             r-devtools
+             r-pacman
+             ;; Visualization
+             r-ggplot2
+             r-plotly
+             r-heatmaply
+             r-gplots
+             r-scatterd3
+             r-rcolorbrewer
+             r-pheatmap
+             r-complexheatmap
+             r-circlize
+             ;; Stats and bioinformatics
+             r-limma
+             r-cluster
+             r-clusterprofiler
+             r-enrichplot
+             r-wgcna
+             r-annotate
+             r-org-hs-eg-db
+             r-org-mm-eg-db
+             r-org-rn-eg-db
+             r-igraph
+             r-visnetwork
+             ;; Utilities
+             r-dt
+             r-markdown
+             r-bookdown
+             r-scales
+             r-curl
+             r-glue
+             r-spscomps
+             r-ggnewscale
+             r-stringr
+             r-zoo
+             r-officer
+             r-r-utils
+             r-mass
+             r-knitr
+             r-rmarkdown))
+      (home-page "https://git.genenetwork.org/jumpshiny/")
+      (synopsis "JUMPshiny - proteomics data analysis Shiny app")
+      (description
+       "JUMPshiny is an R Shiny application for proteomics data analysis,
+including data import, batch normalization, differential expression,
+enrichment analysis, and network analysis with WGCNA.")
+      (license license:gpl3+))))
+
+(define-public r-efatools
+  (package
+    (name "r-efatools")
+    (version "0.6.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "EFAtools" version))
+       (sha256
+        (base32 "0x2c1a1fwa79pdam2day57rpcyxf195a4kqsnwzr2xh6x1fjrnad"))))
+    (properties `((upstream-name . "EFAtools")))
+    (build-system r-build-system)
+    (arguments (list #:tests? #f))
+    (propagated-inputs (list r-checkmate
+                             r-cli
+                             r-crayon
+                             r-dplyr
+                             r-future
+                             r-future-apply
+                             r-ggplot2
+                             r-gparotation
+                             r-lavaan
+                             r-magrittr
+                             r-progress
+                             r-progressr
+                             r-psych
+                             r-rcpp
+                             r-rcpparmadillo
+                             r-rlang
+                             r-stringr
+                             r-tibble
+                             r-tidyr
+                             r-viridislite))
+    (native-inputs (list r-knitr))
+    (home-page "https://github.com/mdsteiner/EFAtools")
+    (synopsis "Fast and flexible exploratory factor analysis tools")
+    (description
+     "Functions to perform exploratory factor analysis (EFA) procedures and
+compare their solutions.")
+    (license license:gpl3)))
+
+(define-public jumpsem-web
+  (let ((commit "a134ab0b10f3d2393ca19870e154ab8bafd45757")
+        (revision "1"))
+    (package
+      (name "jumpsem-web")
+      (version (git-version "0.0.0" revision commit))
+      (source (local-file "/fast/pjotr/tmp/claude/factory/jumpsem_web"
+                          "jumpsem-web-checkout"
+                          #:recursive? #t))
+      (build-system trivial-build-system)
+      (arguments
+       (list #:modules '((guix build utils))
+             #:builder
+             #~(begin
+                 (use-modules (guix build utils))
+                 (let* ((source    (assoc-ref %build-inputs "source"))
+                        (targetdir (string-append #$output "/share/" #$name))
+                        (app       (string-append #$output "/bin/" #$name))
+                        (Rbin      (search-input-file %build-inputs "/bin/Rscript")))
+                   (copy-recursively source targetdir)
+                   (mkdir-p (string-append #$output "/bin"))
+                   (call-with-output-file app
+                     (lambda (port)
+                       (format port
+                               "#!~a
+library(shiny)
+setwd(\"~a\")
+options(shiny.maxRequestSize = 500*1024^2)
+runApp(launch.browser=0, port=3979)~%\n"
+                               Rbin targetdir)))
+                   (chmod app #o555)))))
+      (propagated-inputs
+       (list r
+             r-shiny
+             r-shinycssloaders
+             r-shinybs
+             r-shinyjs
+             r-shinywidgets
+             r-shinydashboard
+             r-dplyr
+             r-tidyr
+             r-tidyverse
+             r-data-table
+             r-devtools
+             r-pacman
+             r-ggplot2
+             r-plotly
+             r-heatmaply
+             r-gplots
+             r-rcolorbrewer
+             r-scales
+             r-markdown
+             r-dt
+             r-lavaan
+             r-efatools
+             r-rcpparmadillo))
+      (home-page "https://git.genenetwork.org/jumpsem_web/")
+      (synopsis "JUMPsem - structural equation modeling web app")
+      (description
+       "JUMPsem is an R Shiny application for kinase activity inference
+using structural equation modeling on post-translational modification data.")
+      (license license:gpl3+))))