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authorShepherd on Tux022024-06-21 04:51:09 -0500
committerShepherd on Tux022024-06-21 04:51:17 -0500
commitd5aa746d3f7ecf46fcab2c527fb2d033a77c5143 (patch)
tree3b122d45d1ca6c5ba62ea8a05c2270c6e27996f2 /gn/services
parentfe579ad20464adae86939345c214cc41028825f3 (diff)
downloadguix-bioinformatics-d5aa746d3f7ecf46fcab2c527fb2d033a77c5143.tar.gz
ratspub: remove definitions as they are replaced by genecup
Diffstat (limited to 'gn/services')
-rw-r--r--gn/services/ratspub-container.scm129
1 files changed, 0 insertions, 129 deletions
diff --git a/gn/services/ratspub-container.scm b/gn/services/ratspub-container.scm
deleted file mode 100644
index 1bf9fc6..0000000
--- a/gn/services/ratspub-container.scm
+++ /dev/null
@@ -1,129 +0,0 @@
-(define-module (gn services ratspub-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* <ratspub-configuration>
- ratspub-configuration
- make-ratspub-configuration
- ratspub-configuration?
- (package ratspub-configuration-package ; package
- (default ratspub)))
-
-(define %punkt.zip
- (origin
- (method url-fetch)
- (uri "https://github.com/nltk/nltk_data/raw/b63a469d2f83a3cc9a2efcfe36915839d4e11d42/packages/tokenizers/punkt.zip")
- (sha256
- (base32 "0i01c5qzn1p8dxyrpx4hry2n6x6b8rgcq1sck091n0jp036f6x4s"))))
-
-(define ratspub-activation
- (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 #$(file-append package "/userspub.sqlite") data_dir)
- (chmod (string-append data_dir "/userspub.sqlite") #o554))))))))
-
-(define ratspub-shepherd-service
- (match-lambda
- (($ <ratspub-configuration> package)
- (with-imported-modules (source-module-closure
- '((gnu build shepherd)
- (gnu system file-systems)))
- (list (shepherd-service
- (provision '(ratspub))
- (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/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/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 ratspub-service-type
- (service-type
- (name 'ratspub)
- (extensions
- (list
- (service-extension shepherd-root-service-type
- ratspub-shepherd-service)
- (service-extension activation-service-type
- ratspub-activation)
- ;; Make sure we get all the dependencies of RatsPub.
- (service-extension profile-service-type
- (compose list ratspub-configuration-package))))
- (default-value (ratspub-configuration))
- (description
- "Run a RatsPub Webserver.")))
-
-(operating-system
- (host-name "ratspub")
- (timezone "Etc/UTC")
- (locale "en_US.utf8")
-
- (bootloader (bootloader-configuration
- (bootloader grub-bootloader)
- (targets '("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 (list nss-certs))
-
- (services (list (service ratspub-service-type
- (ratspub-configuration
- ;; 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