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authorEfraim Flashner2021-05-27 02:27:29 -0500
committerEfraim Flashner2021-05-27 02:27:38 -0500
commit2df25a354555437cfe149f4293adb0ad8cbc5160 (patch)
treec19940f46e9dd451a0dd707a440873ee0f41b1b7 /gn/services
parent76a0deb6f1a6898814cb257afc0b6b61c38e63a2 (diff)
downloadguix-bioinformatics-2df25a354555437cfe149f4293adb0ad8cbc5160.tar.gz
gn: genecup testing
Diffstat (limited to 'gn/services')
-rw-r--r--gn/services/genecup-container.scm129
1 files changed, 129 insertions, 0 deletions
diff --git a/gn/services/genecup-container.scm b/gn/services/genecup-container.scm
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+(define-module (gn services genecup-container))
+
+(use-modules (gnu)
+ (gn packages ratspub)
+ (guix download)
+ (guix modules)
+ (guix packages)
+ (guix records)
+ (ice-9 match))
+(use-service-modules shepherd)
+(use-package-modules certs compression)
+
+(define-record-type* <genecup-configuration>
+ genecup-configuration
+ make-genecup-configuration
+ genecup-configuration?
+ (package genecup-configuration-package ; package
+ (default genecup)))
+
+(define %punkt.zip
+ (origin
+ (method url-fetch)
+ (uri "https://github.com/nltk/nltk_data/raw/b63a469d2f83a3cc9a2efcfe36915839d4e11d42/packages/tokenizers/punkt.zip")
+ (sha256
+ (base32 "0i01c5qzn1p8dxyrpx4hry2n6x6b8rgcq1sck091n0jp036f6x4s"))))
+
+(define genecup-activation
+ (match-lambda
+ (($ <genecup-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 #$(file-append package "/userspub.sqlite") data_dir)
+ (chmod (string-append data_dir "/userspub.sqlite") #o554))))))))
+
+(define genecup-shepherd-service
+ (match-lambda
+ (($ <genecup-configuration> package)
+ (with-imported-modules (source-module-closure
+ '((gnu build shepherd)
+ (gnu system file-systems)))
+ (list (shepherd-service
+ (provision '(genecup))
+ (requirement '(networking))
+ (modules '((gnu build shepherd)
+ (gnu system file-systems)))
+ (start #~(make-forkexec-constructor/container
+ (list #$(file-append package "/server.py"))
+ ;; Needs to run from the directory it is located in.
+ #:directory #$package
+ #:log-file "/var/log/genecup.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/nltk_data"
+ "PERL_LWP_SSL_CA_FILE=/etc/ssl/certs/ca-certificates.crt")
+ #:mappings (list (file-system-mapping
+ (source "/export2/PubMed")
+ (target source)
+ (writable? #t))
+ (file-system-mapping
+ (source "/export/ratspub")
+ (target source)
+ (writable? #t))
+ (file-system-mapping
+ (source "/var/cache/nltk_data")
+ (target source))
+ (file-system-mapping
+ (source "/etc/ssl/certs")
+ (target source)))))
+ (stop #~(make-kill-destructor))))))))
+
+(define genecup-service-type
+ (service-type
+ (name 'genecup)
+ (extensions
+ (list
+ (service-extension shepherd-root-service-type
+ genecup-shepherd-service)
+ (service-extension activation-service-type
+ genecup-activation)
+ ;; Make sure we get all the dependencies of RatsPub.
+ (service-extension profile-service-type
+ (compose list genecup-configuration-package))))
+ (default-value (genecup-configuration))
+ (description
+ "Run a GeneCup Webserver.")))
+
+(operating-system
+ (host-name "genecup")
+ (timezone "Etc/UTC")
+ (locale "en_US.utf8")
+
+ (bootloader (bootloader-configuration
+ (bootloader grub-bootloader)
+ (target "does-not-matter")))
+ (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 (cons nss-certs %base-packages)) ;(list nss-certs))
+
+ (services (list (service genecup-service-type
+ (genecup-configuration
+ ;; genecup for docker, genecup-with-tensorflow-native for architecture specific speed optimizations.
+ ;(package genecup))))))
+ (package genecup-with-tensorflow-native))))))
+
+;; guix system container -L /path/to/guix-bioinformatics/ -L /path/to/guix-past/modules/ /path/to/guix-bioinformatics/gn/services/genecup-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/genecup-container.scm --network
+;; Docker instructions:
+;; docker load --input genecup-docker-image.tar.gz
+;; docker run -d --privileged --net=host --name genecup --volume /path/to/PubMed:/export2/PubMed guix