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authorEfraim Flashner2020-06-16 10:01:40 +0300
committerEfraim Flashner2020-06-16 10:08:15 +0300
commitf4c3abf2b8625e73c8aa945c5be1ee3f4b6715be (patch)
treee5a88f5f22f1f79cec171b1c474e1fb41bd47717 /gn
parent6f3f24b04d2d5d59d466ec74535d2257807c078b (diff)
downloadguix-bioinformatics-f4c3abf2b8625e73c8aa945c5be1ee3f4b6715be.tar.gz
containerize rn6-assembly app
Diffstat (limited to 'gn')
-rw-r--r--gn/packages/bioinformatics.scm11
-rw-r--r--gn/services/rn6-assembly-container.scm24
2 files changed, 32 insertions, 3 deletions
diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm
index 6ae76ae..fca21a9 100644
--- a/gn/packages/bioinformatics.scm
+++ b/gn/packages/bioinformatics.scm
@@ -15,6 +15,7 @@
#:use-module (guix build-system waf)
#:use-module (gnu packages)
#:use-module (gn packages python)
+ #:use-module (gnu packages base)
#:use-module (gnu packages bioconductor)
#:use-module (gnu packages bioinformatics)
#:use-module (gnu packages boost)
@@ -672,13 +673,16 @@ different datasets.
"/bin/Rscript"))
(convert (string-append (assoc-ref %build-inputs "imagemagick")
"/bin/convert"))
+ (cp (string-append (assoc-ref %build-inputs "coreutils")
+ "/bin/cp"))
(source (assoc-ref %build-inputs "source")))
(copy-recursively source targetdir)
(substitute* (string-append targetdir "/server.r")
;; This version is ideal for deploying with the included PNGs.
- ;; But we want all of them, so we use a local copy in gn-rshiny's $HOME.
+ ;; But we want all of them, so we use a local copy in shepherd's $HOME.
;;(("./pngs") (string-append targetdir "/pngs"))
- (("./pngs") "/home/gn-rshiny/hchen/rn6app/pngs")
+ (("./pngs") "/home/shepherd/rn6app/pngs")
+ (("cp") cp)
(("convert") convert))
(mkdir-p (string-append out "/bin"))
(call-with-output-file app
@@ -693,7 +697,8 @@ runApp(launch.browser=0, port=4202)~%\n"
#t))))
(native-inputs `(("source" ,source)))
(inputs
- `(("imagemagick" ,imagemagick)
+ `(("coreutils" ,coreutils-minimal)
+ ("imagemagick" ,imagemagick)
("r-min" ,r-minimal)))
(propagated-inputs
`(("freetype" ,freetype)
diff --git a/gn/services/rn6-assembly-container.scm b/gn/services/rn6-assembly-container.scm
new file mode 100644
index 0000000..44056c3
--- /dev/null
+++ b/gn/services/rn6-assembly-container.scm
@@ -0,0 +1,24 @@
+(define-module (gn services rn6-assembly-container))
+
+(use-modules (gnu)
+ (gn packages bioinformatics)
+ (gn services rshiny))
+
+(operating-system
+ (host-name "rn6-assembly")
+ (timezone "Etc/UTC")
+ (locale "en_US.utf8")
+
+ (bootloader (bootloader-configuration
+ (bootloader grub-bootloader)
+ (target "does-not-matter")))
+ (file-systems %base-file-systems)
+ ;; No firmware for VMs.
+ (firmware '())
+ ;; We only need a few packages inside the container.
+ (packages '())
+
+ (services (list (service rshiny-service-type
+ (rshiny-configuration
+ (package rn6-assembly-error-app)
+ (binary "rn6-assembly-error-app"))))))