From da02d64280a03fbba4b2f93923e2479728ba2033 Mon Sep 17 00:00:00 2001
From: Efraim Flashner
Date: Sun, 22 Jan 2023 02:10:04 -0600
Subject: general service updates

---
 shepherd/disabled/covid19-pubseq.scm | 12 ++++++++++++
 shepherd/disabled/genenetwork1.scm   | 12 ++++++++++++
 shepherd/disabled/gitea.scm          | 12 ++++++++++++
 shepherd/disabled/hrdp-project.scm   | 14 ++++++++++++++
 shepherd/disabled/ipfs.scm           | 12 ++++++++++++
 shepherd/disabled/mcron.scm          | 12 ++++++++++++
 shepherd/disabled/ratspub.scm        | 19 +++++++++++++++++++
 shepherd/disabled/test-upgrade.scm   | 27 +++++++++++++++++++++++++++
 shepherd/disabled/virtuoso.scm       | 13 +++++++++++++
 9 files changed, 133 insertions(+)
 create mode 100644 shepherd/disabled/covid19-pubseq.scm
 create mode 100644 shepherd/disabled/genenetwork1.scm
 create mode 100644 shepherd/disabled/gitea.scm
 create mode 100644 shepherd/disabled/hrdp-project.scm
 create mode 100644 shepherd/disabled/ipfs.scm
 create mode 100644 shepherd/disabled/mcron.scm
 create mode 100644 shepherd/disabled/ratspub.scm
 create mode 100644 shepherd/disabled/test-upgrade.scm
 create mode 100644 shepherd/disabled/virtuoso.scm

(limited to 'shepherd/disabled')

diff --git a/shepherd/disabled/covid19-pubseq.scm b/shepherd/disabled/covid19-pubseq.scm
new file mode 100644
index 0000000..0d1709d
--- /dev/null
+++ b/shepherd/disabled/covid19-pubseq.scm
@@ -0,0 +1,12 @@
+(define covid19-pubseq
+  (make <service>
+	#:provides '(covid19-pubseq)
+	#:docstring "Run the COVID-19 PubSeq: Public SARS-CoV-2 Sequence Resource Webserver"
+	#:start (make-forkexec-constructor
+		  '("/usr/bin/sudo" "/home/shepherd/run_covid19-pubseq.sh")
+		  #:log-file "/home/shepherd/logs/covid19-pubseq.log")
+	#:stop (make-kill-destructor)
+	#:respawn? #t))
+(register-services covid19-pubseq)
+
+(start covid19-pubseq)
diff --git a/shepherd/disabled/genenetwork1.scm b/shepherd/disabled/genenetwork1.scm
new file mode 100644
index 0000000..31f1bb0
--- /dev/null
+++ b/shepherd/disabled/genenetwork1.scm
@@ -0,0 +1,12 @@
+(define genenetwork1
+  (make <service>
+	#:provides '(genenetwork1)
+	#:docstring "Run the Legacy Genenetwork webserver"
+	#:start (make-forkexec-constructor
+		  '("/usr/bin/sudo" "/home/shepherd/run_genenetwork1.sh")
+		  #:log-file "/home/shepherd/logs/genenetwork1.log")
+	#:stop (make-kill-destructor)
+	#:respawn? #t))
+(register-services genenetwork1)
+
+(start genenetwork1)
diff --git a/shepherd/disabled/gitea.scm b/shepherd/disabled/gitea.scm
new file mode 100644
index 0000000..b5d77f0
--- /dev/null
+++ b/shepherd/disabled/gitea.scm
@@ -0,0 +1,12 @@
+(define gitea
+  (make <service>
+	#:provides '(gitea)
+	#:docstring "Run a Gitea instance"
+	#:start (make-forkexec-constructor
+		  '("/usr/bin/sudo" "/home/shepherd/run_gitea.sh")
+		  #:log-file "/home/shepherd/logs/gitea.log")
+	#:stop (make-kill-destructor)
+	#:respawn? #t))
+(register-services gitea)
+
+(start gitea)
diff --git a/shepherd/disabled/hrdp-project.scm b/shepherd/disabled/hrdp-project.scm
new file mode 100644
index 0000000..54ad53a
--- /dev/null
+++ b/shepherd/disabled/hrdp-project.scm
@@ -0,0 +1,14 @@
+(define hrdp-project
+  (make <service>
+	#:provides '(hrdp-project)
+	#:docstring "Run the hrdp-project web server"
+	#:start (make-forkexec-constructor
+		  '("/var/guix/profiles/per-user/shepherd/current-guix/bin/guix"
+		    "environment" "--ad-hoc" "hrdp-project" "--"
+		    "sh" "-c" "$GUIX_ENVIRONMENT/main.py")
+		  #:log-file "/home/shepherd/logs/hrdp-project.log")
+	#:stop (make-kill-destructor)
+	#:respawn? #t))
+(register-services hrdp-project)
+
+(start hrdp-project)
diff --git a/shepherd/disabled/ipfs.scm b/shepherd/disabled/ipfs.scm
new file mode 100644
index 0000000..1b8d21a
--- /dev/null
+++ b/shepherd/disabled/ipfs.scm
@@ -0,0 +1,12 @@
+(define ipfs
+  (make <service>
+	#:provides '(ipfs)
+	#:docstring "Run the IPFS daemon"
+	#:start (make-forkexec-constructor
+		  '("/usr/bin/sudo" "/home/shepherd/run_ipfs.sh")
+		  #:log-file "/home/shepherd/logs/ipfs.log")
+	#:stop (make-kill-destructor)
+	#:respawn? #t))
+(register-services ipfs)
+
+(start ipfs)
diff --git a/shepherd/disabled/mcron.scm b/shepherd/disabled/mcron.scm
new file mode 100644
index 0000000..415e1f0
--- /dev/null
+++ b/shepherd/disabled/mcron.scm
@@ -0,0 +1,12 @@
+(define mcron
+  (make <service>
+	#:provides '(mcron)
+	#:docstring "Run the mcron daemon"
+	#:start (make-forkexec-constructor
+		  '("/var/guix/profiles/per-user/shepherd/guix-profile/bin/mcron")
+		  #:log-file "/home/shepherd/logs/mcron.log")
+	#:stop (make-kill-destructor)
+	#:respawn? #t))
+(register-services mcron)
+
+(start mcron)
diff --git a/shepherd/disabled/ratspub.scm b/shepherd/disabled/ratspub.scm
new file mode 100644
index 0000000..c1d552a
--- /dev/null
+++ b/shepherd/disabled/ratspub.scm
@@ -0,0 +1,19 @@
+(define ratspub
+  (make <service>
+	#:provides '(ratspub)
+	#:docstring "Run the rats.pub web server"
+	#:start (make-forkexec-constructor
+		  ;(system* "/var/guix/profiles/per-user/shepherd/current-guix/bin/guix" "environment" "--ad-hoc" "ratspub" "--" "./server.py")
+		  '("/home/shepherd/run_ratspub.sh")
+		  ;#:directory (system* "/var/guix/profiles/per-user/shepherd/current-guix/bin/guix" "build" "ratspub") ; returns 0
+		  #:environment-variables
+		  (list "EDIRECT_PUBMED_MASTER=/export2/PubMed"
+			"NLTK_DATA=/home/hchen/nltk_data"
+			"PERL_LWP_SSL_CA_FILE=/etc/ssl/certs/ca-certificates.crt"
+			"TMPDIR=/export/ratspub/tmp")
+		  #:log-file "/home/shepherd/logs/ratspub.log")
+	#:stop (make-kill-destructor)
+	#:respawn? #t))
+(register-services ratspub)
+
+(start ratspub)
diff --git a/shepherd/disabled/test-upgrade.scm b/shepherd/disabled/test-upgrade.scm
new file mode 100644
index 0000000..6750ede
--- /dev/null
+++ b/shepherd/disabled/test-upgrade.scm
@@ -0,0 +1,27 @@
+(define test-upgrade
+  (make <service>
+	#:provides '(test-upgrade)
+	#:docstring "Build all the services to make sure they work on an upgrade"
+	#:start (make-forkexec-constructor
+		  ;; First attempt to build all the packages and only afterward attempt to build the containers.
+		  ;(when (zero? (system*
+		  '("guix" "build"
+		    "-L" "/home/shepherd/guix-bioinformatics"
+		    "-L" "/home/shepherd/guix-past/modules"
+		    "genenetwork1" "httpd22-with-mod-python"
+		    ;"bnw" octave-3.4.3 FTBFS
+		    "gitea"
+		    "go-ipfs"
+		    "edirect"
+		    "bxd-power-calculator-app"
+		    "rn6-assembly-error-app"
+		    "singlecellrshiny"
+		    "virtuoso-ose"
+		    "hrdp-project"
+		    "bh20-seq-resource")
+		    ;(zero? (system* "guix" "system" "-L" "/home/shepherd/guix-bioinformatics"
+		    ;		    "container" "/home/shepherd/guix-bioinformatics/gn/services/bnw-container.scm"
+		    ;		    "--share=/home/shepherd/logs/bnw-server=/var/log" "--network")))
+		  #:log-file "/home/shepherd/logs/test-upgrade.log")
+	#:one-shot? #t))
+(register-services test-upgrade)
diff --git a/shepherd/disabled/virtuoso.scm b/shepherd/disabled/virtuoso.scm
new file mode 100644
index 0000000..241fe23
--- /dev/null
+++ b/shepherd/disabled/virtuoso.scm
@@ -0,0 +1,13 @@
+(define virtuoso
+  (make <service>
+	#:provides '(virtuoso)
+	#:docstring "Run the virtuoso web server"
+	#:start (make-forkexec-constructor
+		  '("/var/guix/profiles/per-user/shepherd/current-guix/bin/guix" "environment" "--ad-hoc" "virtuoso-ose" "--" "virtuoso-t" "-f")
+		  #:directory "/export/virtuoso/var/lib/virtuoso/db"
+		  #:log-file "/home/shepherd/logs/virtuoso.log")
+	#:stop (make-kill-destructor)
+	#:respawn? #t))
+(register-services virtuoso)
+
+(start virtuoso)
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