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.

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