general service updates

10 files changed, 8 insertions, 141 deletions

diff --git a/shepherd/init.d/covid19-pubseq.scm b/shepherd/init.d/covid19-pubseq.scm
deleted file mode 100644
index 0d1709d..0000000
--- a/shepherd/init.d/covid19-pubseq.scm
+++ /dev/null
@@ -1,12 +0,0 @@
-(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/init.d/genenetwork1.scm b/shepherd/init.d/genenetwork1.scm
deleted file mode 100644
index 31f1bb0..0000000
--- a/shepherd/init.d/genenetwork1.scm
+++ /dev/null
@@ -1,12 +0,0 @@
-(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/init.d/gitea.scm b/shepherd/init.d/gitea.scm
deleted file mode 100644
index b5d77f0..0000000
--- a/shepherd/init.d/gitea.scm
+++ /dev/null
@@ -1,12 +0,0 @@
-(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/init.d/hrdp-project.scm b/shepherd/init.d/hrdp-project.scm
deleted file mode 100644
index 54ad53a..0000000
--- a/shepherd/init.d/hrdp-project.scm
+++ /dev/null
@@ -1,14 +0,0 @@
-(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/init.d/ipfs.scm b/shepherd/init.d/ipfs.scm
deleted file mode 100644
index 1b8d21a..0000000
--- a/shepherd/init.d/ipfs.scm
+++ /dev/null
@@ -1,12 +0,0 @@
-(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/init.d/mcron.scm b/shepherd/init.d/mcron.scm
deleted file mode 100644
index 415e1f0..0000000
--- a/shepherd/init.d/mcron.scm
+++ /dev/null
@@ -1,12 +0,0 @@
-(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/init.d/pluto.scm b/shepherd/init.d/pluto.scm
index 81c7fe6..23a696e 100644
--- a/shepherd/init.d/pluto.scm
+++ b/shepherd/init.d/pluto.scm
@@ -1,13 +1,13 @@
 (define pluto
   (make <service>
-        #:provides '(pluto)
-        #:docstring "Run a pluto web server"
-        #:start (make-forkexec-constructor
-                  ;; Update the path to runpluto as the guix-profile changes.
-                  '("/home/shepherd/guix-profiles/pluto/bin/guix" "shell" "--container" "--network" "--no-cwd" "julia-visuals" "--" "/gnu/store/wbci39sd5pqrjrb5ak0lkmv9jhnl35kv-julia-visuals-0.0.0-1.e7d670e/runpluto.sh")
-                  #:log-file "/home/shepherd/logs/pluto.log")
-        #:stop (make-kill-destructor)
-        #:respawn? #t))
+	#:provides '(pluto)
+	#:docstring "Run a pluto web server"
+	#:start (make-forkexec-constructor
+		  ;; Update the path to runpluto as the guix-profile changes.
+		  '("/home/shepherd/guix-profiles/pluto/bin/guix" "shell" "--container" "--network" "--no-cwd" "julia-visuals" "--" "/gnu/store/wbci39sd5pqrjrb5ak0lkmv9jhnl35kv-julia-visuals-0.0.0-1.e7d670e/runpluto.sh")
+		  #:log-file "/home/shepherd/logs/pluto.log")
+	#:stop (make-kill-destructor)
+	#:respawn? #t))
 (register-services pluto)
 
 (start pluto)
diff --git a/shepherd/init.d/ratspub.scm b/shepherd/init.d/ratspub.scm
deleted file mode 100644
index c1d552a..0000000
--- a/shepherd/init.d/ratspub.scm
+++ /dev/null
@@ -1,19 +0,0 @@
-(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/init.d/test-upgrade.scm b/shepherd/init.d/test-upgrade.scm
deleted file mode 100644
index 6750ede..0000000
--- a/shepherd/init.d/test-upgrade.scm
+++ /dev/null
@@ -1,27 +0,0 @@
-(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/init.d/virtuoso.scm b/shepherd/init.d/virtuoso.scm
deleted file mode 100644
index 241fe23..0000000
--- a/shepherd/init.d/virtuoso.scm
+++ /dev/null
@@ -1,13 +0,0 @@
-(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)