diff options
Diffstat (limited to 'gn/services/ratspub-container.scm')
| -rw-r--r-- | gn/services/ratspub-container.scm | 47 |
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 |