initial commit

10 files changed, 123 insertions, 0 deletions

diff --git a/README b/README
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+This repo contains the files used to run shepherd services.
+
+The `shepherd` and `cron` directories go in `.config`
+
+The shell scripts sit in the home directory.
diff --git a/cron/gitea-dump.guile b/cron/gitea-dump.guile
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+++ b/cron/gitea-dump.guile
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+(job '(next-day)
+  "/usr/bin/sudo /home/shepherd/run_gitea-dump.sh")
diff --git a/run_bnw.sh b/run_bnw.sh
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+#!/bin/sh
+$(/var/guix/profiles/per-user/shepherd/current-guix/bin/guix system container /home/shepherd/guix-bioinformatics/gn/services/bnw-container.scm --share=/home/shepherd/logs/bnw-server=/var/log --network)
diff --git a/run_gitea-dump.sh b/run_gitea-dump.sh
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+++ b/run_gitea-dump.sh
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+#!/bin/sh
+bin/su -l gitea -c 'GITEA_WORK_DIR=/var/lib/git/gitea HOME=/var/lib/git/gitea $(/var/guix/profiles/per-user/shepherd/current-guix/bin/guix build gitea)/bin/gitea dump --verbose'
diff --git a/run_gitea.sh b/run_gitea.sh
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+++ b/run_gitea.sh
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+#!/bin/sh
+/bin/su -l gitea -c 'GITEA_WORK_DIR=/var/lib/git/gitea HOME=/var/lib/git/gitea $(/var/guix/profiles/per-user/shepherd/current-guix/bin/guix build gitea)/bin/gitea --port 3300'
diff --git a/run_ipfs.sh b/run_ipfs.sh
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+++ b/run_ipfs.sh
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+#!/bin/sh
+/bin/su -l ipfs -c 'IPFS_PATH=/export/ipfs $(/var/guix/profiles/per-user/shepherd/current-guix/bin/guix build go-ipfs)/bin/ipfs daemon'
diff --git a/run_power.sh b/run_power.sh
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+++ b/run_power.sh
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+#!/bin/sh
+/var/guix/profiles/per-user/shepherd/current-guix/bin/guix environment --ad-hoc bxd-power-calculator-app -- sh -c 'R_LIBS_USER=$GUIX_ENVIRONMENT/site-library/ bxd-power-calculator-app'
diff --git a/run_rn6app.sh b/run_rn6app.sh
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+++ b/run_rn6app.sh
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+#!/bin/sh
+/var/guix/profiles/per-user/shepherd/current-guix/bin/guix environment --ad-hoc rn6-assembly-error-app -- sh -c 'R_LIBS_USER=$GUIX_ENVIRONMENT/site-library/ rn6-assembly-error-app'
diff --git a/shepherd/init.scm b/shepherd/init.scm
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+++ b/shepherd/init.scm
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+(use-modules (shepherd service))
+
+(define date+%s
+  (strftime "%s" (gmtime (current-time))))
+
+(define bnw
+  (make <service>
+	#:provides '(bnw)
+	#:docstring "Run the Beyesian Network Webserver"
+	#:start (make-forkexec-constructor
+		  '("/usr/bin/sudo" "/home/shepherd/run_bnw.sh")
+		  #:log-file (string-append "/home/shepherd/logs/bnw-"
+					    date+%s ".log"))
+	#:stop (make-kill-destructor)
+	#:respawn? #t))
+(register-services bnw)
+
+(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 (string-append "/home/shepherd/logs/gitea-"
+					    date+%s ".log"))
+	#:stop (make-kill-destructor)
+	#:respawn? #t))
+(register-services gitea)
+
+(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 (string-append "/home/shepherd/logs/ipfs-"
+					    date+%s ".log"))
+	#:stop (make-kill-destructor)
+	#:respawn? #t))
+(register-services ipfs)
+
+(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 (string-append "/home/shepherd/logs/mcron-"
+					    date+%s ".log"))
+	#:stop (make-kill-destructor)
+	#:respawn? #t))
+(register-services mcron)
+
+(define power
+  (make <service>
+	#:provides '(power)
+	#:docstring "Run the BXD Power Calculator app"
+	#:start (make-forkexec-constructor
+		  ;'(system* "/var/guix/profiles/per-user/shepherd/current-guix/bin/guix" "environment" "--ad-hoc" "rn6-assembly-error-app" "--" "/bin/sh -c 'R_LIBS_USER=$GUIX_ENVIRONMENT/site-library/ rn6-assembly-error-app'")
+		  '("/home/shepherd/run_power.sh")
+		  #:log-file (string-append "/home/shepherd/logs/power-"
+					    date+%s ".log"))
+	#:stop (make-kill-destructor)
+	#:respawn? #t))
+(register-services power)
+
+(define rn6app
+  (make <service>
+	#:provides '(rn6app)
+	#:docstring "Run RN6 Assembly Error app"
+	#:start (make-forkexec-constructor
+		  ;'(system* "/var/guix/profiles/per-user/shepherd/current-guix/bin/guix" "environment" "--ad-hoc" "rn6-assembly-error-app" "--" "/bin/sh -c 'R_LIBS_USER=$GUIX_ENVIRONMENT/site-library/ rn6-assembly-error-app'")
+		  '("/home/shepherd/run_rn6app.sh")
+		  #:log-file (string-append "/home/shepherd/logs/rn6app-"
+					    date+%s ".log"))
+	#:stop (make-kill-destructor)
+	#:respawn? #t))
+(register-services rn6app)
+
+(define test-upgrade
+  (make <service>
+	#:provides '(test-upgrade)
+	#:docstring "Build all the services to make sure they work on an upgrade"
+	#:start (make-forkexec-constructor
+		  (when (zero? (system* "guix" "build" "-L" "/home/shepherd/guix-bioinformatics"
+					"--no-grafts" "bnw" "gitea" "go-ipfs" "edirect-gn"
+					"bxd-power-calculator-app" "rn6-assembly-error-app"))
+		    (zero? (system* "guix" "system" "-L" "/home/shepherd/guix-bioinformatics"
+				    "container" "/home/shepherd/guix-bioinformatics/gn/services/bnw-container.scm"
+				    "--share=/home/shepherd/logs/bnw-server=/var/log" "--network")))
+		  #:log-file (string-append "/home/shepherd/logs/test-upgrade-"
+					    date+%s ".log"))
+	#:one-shot? #t))
+(register-services test-upgrade)
+
+;; Send shepherd into the background
+(action 'shepherd 'daemonize)
+
+;; Services to start when shepherd starts:
+;; Add the name of each service that should be started to the list
+;; below passed to 'for-each'.
+(for-each start '(bnw gitea ipfs mcron power rn6app))
diff --git a/update_archive-pubmed.sh b/update_archive-pubmed.sh
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+++ b/update_archive-pubmed.sh
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+#!/bin/sh
+/bin/su -l hchen -c 'export EDIRECT_PUBMED_MASTER=/export2/PubMed; export PERL_LWP_SSL_CA_FILE=/etc/ssl/certs/ca-certificates.crt; export NLTK_DATA=/export2/PubMed/nltk_data; export PATH=$(/var/guix/profiles/per-user/shepherd/current-guix/bin/guix build edirect-gn)/bin:$PATH; $(/var/guix/profiles/per-user/shepherd/current-guix/bin/guix build edirect-gn)/bin/archive-pubmed'