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authorEfraim Flashner2020-09-15 07:27:21 -0500
committerEfraim Flashner2020-09-15 07:27:21 -0500
commit48ffb5f29d7186b6bad131bdf67f9e2ff413f6a9 (patch)
tree9d6d3d74646dcbfe2de61419105186b6fa0a47da /gn
parentcd3531f61594989d80ea11cf8ecd710054d15180 (diff)
downloadguix-bioinformatics-48ffb5f29d7186b6bad131bdf67f9e2ff413f6a9.tar.gz
ratspub: Add support for building docker container
Diffstat (limited to 'gn')
-rw-r--r--gn/services/ratspub-container.scm47
1 files changed, 34 insertions, 13 deletions
diff --git a/gn/services/ratspub-container.scm b/gn/services/ratspub-container.scm
index 4ffb3b8..472dd28 100644
--- a/gn/services/ratspub-container.scm
+++ b/gn/services/ratspub-container.scm
@@ -24,15 +24,25 @@
(sha256
(base32 "0i01c5qzn1p8dxyrpx4hry2n6x6b8rgcq1sck091n0jp036f6x4s"))))
-;; The correct way would be to use python-nltk to download the data
-;; python3 -m nltk.downloader -d /var/cache/ratspub punkt
(define ratspub-activation
- (lambda _
- #~(begin
- (let ((nltk_data "/var/cache/ratspub/tokenizers"))
- (mkdir-p nltk_data)
- (chdir nltk_data)
- (invoke #$(file-append unzip "/bin/unzip") "-q" #$%punkt.zip)))))
+ (match-lambda
+ (($ <ratspub-configuration> package)
+ #~(begin
+ (let ((nltk_data "/var/cache/nltk_data/tokenizers")
+ (data_dir "/export/ratspub"))
+ (unless (file-exists? "/export2/PubMed")
+ (mkdir-p "/export2/PubMed"))
+ (unless (file-exists? nltk_data)
+ (begin
+ ;; The correct way would be to use python-nltk to download the data
+ ;; python3 -m nltk.downloader -d /var/cache/nltk_data punkt
+ (mkdir-p nltk_data)
+ (chdir nltk_data)
+ (invoke #$(file-append unzip "/bin/unzip") "-q" #$%punkt.zip)))
+ (unless (file-exists? (string-append data_dir "/userspub.sqlite"))
+ (begin
+ (install-file #$(file-append package "/userspub.sqlite") data_dir)
+ (chmod (string-append data_dir "/userspub.sqlite") #o554))))))))
(define ratspub-shepherd-service
(match-lambda
@@ -50,9 +60,10 @@
;; Needs to run from the directory it is located in.
#:directory #$package
#:log-file "/var/log/ratspub.log"
+ ;; We don't need to set TMPDIR because we're inside a container.
#:environment-variables
'("EDIRECT_PUBMED_MASTER=/export2/PubMed"
- "NLTK_DATA=/var/cache/ratspub"
+ "NLTK_DATA=/var/cache/nltk_data"
"PERL_LWP_SSL_CA_FILE=/etc/ssl/certs/ca-certificates.crt")
#:mappings (list (file-system-mapping
(source "/export2/PubMed")
@@ -63,7 +74,7 @@
(target source)
(writable? #t))
(file-system-mapping
- (source "/var/cache/ratspub")
+ (source "/var/cache/nltk_data")
(target source))
(file-system-mapping
(source "/etc/ssl/certs")
@@ -77,7 +88,6 @@
(list
(service-extension shepherd-root-service-type
ratspub-shepherd-service)
- ;; Setup the NLTK_DATA data.
(service-extension activation-service-type
ratspub-activation)
;; Make sure we get all the dependencies of RatsPub.
@@ -95,14 +105,25 @@
(bootloader (bootloader-configuration
(bootloader grub-bootloader)
(target "does-not-matter")))
- (file-systems %base-file-systems)
+ (file-systems (list (file-system
+ (device "does-not-matter")
+ (mount-point "/")
+ (type "does-not-matter"))))
+ ;; TODO: A more minimal kernel for use in a docker image
+ ;; (kernel linux-libre-vm)
;; No firmware for VMs.
(firmware '())
(packages (list nss-certs))
(services (list (service ratspub-service-type
(ratspub-configuration
- ;(package ratspub)
+ ;; ratspub for docker, ratspub-with-tensorflow-native for architecture specific speed optimizations.
+ ;(package ratspub))))))
(package ratspub-with-tensorflow-native))))))
;; guix system container -L /path/to/guix-bioinformatics/ -L /path/to/guix-past/modules/ /path/to/guix-bioinformatics/gn/services/ratspub-container.scm --network --share=/export2/PubMed=/export2/PubMed --share=/export/ratspub=/export/ratspub
+;; For docker it isn't necessary to list the shared folders at build time.
+;; guix system docker-image -L /path/to/guix-bioinformatics/ -L /path/to/guix-past/modules/ /path/to/guix-bioinformatics/gn/services/ratspub-container.scm --network
+;; Docker instructions:
+;; docker load --input ratspub-docker-image.tar.gz
+;; docker run -d --privileged --net=host --name ratspub --volume /path/to/PubMed:/export2/PubMed guix