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authorArun Isaac2023-10-19 13:32:19 +0100
committerArun Isaac2023-10-19 15:15:52 +0100
commitdab19f78848da9c176238cc1eec486964a54dfca (patch)
tree7309a9d303111587b69ca96c672bbb2ebb4f5e74
parent51931f0b587749d31825cee74d0ff76c5aedf6eb (diff)
downloadguix-bioinformatics-dab19f78848da9c176238cc1eec486964a54dfca.tar.gz
Remove bh20-seq-resource.
The package is broken, some of its inputs have been removed from upstream Guix, and we no longer need this package. * gn/packages/bioinformatics.scm (bh20-seq-resource): Delete variable. * gn/services/bh20-seq-resource-container.scm: Delete file.
-rw-r--r--gn/packages/bioinformatics.scm73
-rw-r--r--gn/services/bh20-seq-resource-container.scm110
2 files changed, 0 insertions, 183 deletions
diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm
index 9de6ad8..2832ea6 100644
--- a/gn/packages/bioinformatics.scm
+++ b/gn/packages/bioinformatics.scm
@@ -2096,79 +2096,6 @@ reads, also called read-based phasing or haplotype assembly. It is especially
suitable for long reads, but works also well with short reads.")
(license license:expat)))
-(define-public bh20-seq-resource
- (let ((commit "2ae71911cd87ce4f2eabdff21e538267b3270d45")
- (revision "4"))
- (package
- (name "bh20-seq-resource")
- (version (git-version "1.0" revision commit))
- (source (origin
- (method git-fetch)
- (uri (git-reference
- (url "https://github.com/pubseq/bh20-seq-resource")
- (commit commit)))
- (file-name (git-file-name name version))
- (sha256
- (base32 "1k6cc88hrcm77jwpdk2084q0zirv2vlbz3c07nmpbhk1lhqk5x0n"))
- (modules '((guix build utils)))
- (snippet
- '(begin
- (delete-file "gittaggers.py")))))
- (build-system python-build-system)
- (arguments
- (list
- #:tests? #f ; Tests can't find pytest
- #:phases
- #~(modify-phases %standard-phases
- (add-after 'unpack 'patch-program-calls
- (lambda* (#:key inputs #:allow-other-keys)
- (substitute* "bh20sequploader/qc_fasta.py"
- (("\"minimap2\"")
- (string-append "\"" (search-input-file
- inputs "/bin/minimap2")
- "\""))))))))
- (propagated-inputs
- (list python-arvados-python-client
- python-schema-salad
- python-magic
- python-pyshex
- python-pyshexc-0.7
- python-py-dateutil
-
- ;; for the web
- python-flask
- python-pyyaml
- python-redis
-
- ;; and for the service
- python
- gunicorn))
- (inputs
- (list minimap2))
- (native-inputs
- (list python-pytest-4 ; < 6
- python-pytest-runner-4)) ; < 5
- (home-page "https://github.com/pubseq/bh20-seq-resource")
- (synopsis
- "Tool to upload SARS-CoV-19 sequences and service to kick off analysis")
- (description "This repository provides a sequence uploader for the
-COVID-19 Virtual Biohackathon's Public Sequence Resource project. You can use
-it to upload the genomes of SARS-CoV-2 samples to make them publicly and freely
-available to other researchers.")
- (license license:asl2.0))))
-
-;; This version has no profile collisions.
-(define-public bh20-seq-resource-for-service
- (package
- ;(inherit (fix-profile-collisions-for-bh20 bh20-seq-resource))
- (inherit
- ((package-input-rewriting/spec
- `(("python-google-api-core" . ,(const python-google-api-core-1))
- ("python-google-auth" . ,(const python-google-auth-1))
- ("python-pyparsing" . ,(const python-pyparsing-2.4.7))))
- bh20-seq-resource))
- (properties `((hidden? . #t)))))
-
(define-public python-scanpy-git
(let ((commit "590d42309f9ed6550d7b887039990edfc1ac7648") ; April 22, 2020
(revision "1"))
diff --git a/gn/services/bh20-seq-resource-container.scm b/gn/services/bh20-seq-resource-container.scm
deleted file mode 100644
index e0eccf7..0000000
--- a/gn/services/bh20-seq-resource-container.scm
+++ /dev/null
@@ -1,110 +0,0 @@
-(define-module (gn services bh20-seq-resource-container))
-
-(use-modules (gnu)
- (gn packages bioinformatics)
- (guix modules)
- ((guix packages) #:select (package-source))
- (guix records)
- (guix build-system python) ; for python-version from guix/build/python-build-system.scm
- (ice-9 match))
-(use-service-modules shepherd)
-(use-package-modules compression python python-web)
-
-(define-record-type* <covid19-pubseq-configuration>
- covid19-pubseq-configuration
- make-covid19-pubseq-configuration
- covid19-pubseq-configuration?
- (package covid19-pubseq-configuration-package ; package
- (default bh20-seq-resource-for-service))
- (deploy-directory covid19-pubseq-deploy-directory ; string
- (default "/srv/http"))
- (port covid19-pubseq-configuration-port ; string
- (default "5000")))
-
-(define covid19-pubseq-activation-service
- (match-lambda
- (($ <covid19-pubseq-configuration> package deploy-directory port)
- #~(begin
- (let ((pkg-src #$(package-source package)))
- (when (file-exists? #$deploy-directory)
- (delete-file-recursively (mkdir-p #$deploy-directory)))
- (mkdir-p #$deploy-directory)
- (if (file-is-directory? pkg-src)
- (copy-recursively pkg-src #$deploy-directory)
- (begin
- (copy-file pkg-src #$(string-append deploy-directory
- "/src.tar.xz"))
- (with-directory-excursion #$deploy-directory
- (invoke #$(file-append xz "/bin/xz") "-d" "src.tar.xz")
- (invoke #$(file-append tar "/bin/tar") "xvf" "src.tar"
- "--strip-components=1")))))))))
-
-(define covid19-pubseq-shepherd-service
- (match-lambda
- (($ <covid19-pubseq-configuration> package deploy-directory port)
- (with-imported-modules (source-module-closure
- '((gnu build shepherd)
- (gnu system file-systems)))
- (list (shepherd-service
- (provision '(covid19-pubseq))
- (requirement '(networking))
- (modules '((gnu build shepherd)
- (gnu system file-systems)))
- ;(start #~(make-forkexec-constructor/container
- (start #~(make-forkexec-constructor
- (list
- #$(file-append gunicorn "/bin/gunicorn")
- (string-append "-blocalhost:" #$port)
- "bh20simplewebuploader.main:app")
- #:directory #$deploy-directory
- #:log-file "/var/log/covid19-pubseq.log"
- #:environment-variables
- ;(let (pyversion (python-version (@ (gnu packages python) python)))
- '("TMPDIR=/export/tmp"
- "PYTHONPATH=/run/current-system/profile/lib/python3.9/site-packages")
- ; (string-append "PYTHONPATH=/run/current-system/profile/lib/python" pyversion "/site-packages")))
- ;#:mappings
- ;(list (file-system-mapping
- ; (source "/export/tmp")
- ; (target source)
- ; (writable? #t))
- ; (file-system-mapping
- ; ;; TODO: Don't hardcode python version!
- ; (source "/run/current-system/profile/lib/python3.9/site-packages")
- ; (target source)))
- ))
- (stop #~(make-kill-destructor))))))))
-
-(define covid19-pubseq-service-type
- (service-type
- (name 'covid19-pubseq)
- (extensions
- (list
- (service-extension shepherd-root-service-type
- covid19-pubseq-shepherd-service)
- (service-extension activation-service-type
- covid19-pubseq-activation-service)
- (service-extension profile-service-type
- (compose list
- covid19-pubseq-configuration-package))))
- (default-value (covid19-pubseq-configuration))
- (description
- "Run a COVID-19 PubSeq: Public SARS-CoV-2 Sequence Resource Webserver.")))
-
-(operating-system
- (host-name "covid19-pubseq")
- (timezone "Etc/UTC")
- (locale "en_US.utf8")
-
- (bootloader (bootloader-configuration
- (bootloader grub-bootloader)
- (targets '("does-not-matter"))))
- (file-systems %base-file-systems)
- ;; No firmware for VMs.
- (firmware '())
- ;; We don't need any packages inside the container.
- (packages '())
-
- (services (list (service covid19-pubseq-service-type))))
-
-;; guix system container /home/shepherd/guix-bioinformatics/gn/services/bh20-seq-resource-container.scm --share=/export/tmp=/export/tmp --network