general service updates

13 files changed, 18 insertions, 10 deletions

diff --git a/run_genome_browser.sh b/run_genome_browser.sh
index 50ddf0f..edf2fb5 100755
--- a/run_genome_browser.sh
+++ b/run_genome_browser.sh
@@ -1,3 +1,3 @@
 #!/bin/sh
 /home/shepherd/guix-profiles/genome-browser/bin/guix build --no-grafts ucsc-genome-browser
-$(/home/shepherd/guix-profiles/genome-browser/bin/guix system container /home/shepherd/guix-bioinformatics/gn/services/genome-browser.scm --network --share=/export/efraimf/UCSC_Genome/gbdb=/gbdb --share=/export/efraimf/UCSC_Genome/var-lib-mysql=/var/lib/mysql --share=/export/efraimf/UCSC_Genome/var-cache-genome=/var/cache/genome --share=/export/efraimf/UCSC_Genome/var-cache-genome=/var/www/html/trash)
+$(/home/shepherd/guix-profiles/genome-browser/bin/guix system container /home/shepherd/guix-bioinformatics/gn/services/genome-browser.scm --network --share=/export4/efraimf/UCSC_Genome/gbdb=/gbdb --share=/export4/efraimf/UCSC_Genome/var-lib-mysql=/var/lib/mysql --share=/export4/efraimf/UCSC_Genome/var-cache-genome=/var/cache/genome --share=/export4/efraimf/UCSC_Genome/var-cache-genome=/var/www/html/trash)
diff --git a/run_pluto.sh b/run_pluto.sh
new file mode 100755
index 0000000..0acf720
--- /dev/null
+++ b/run_pluto.sh
@@ -0,0 +1,8 @@
+#!/bin/sh
+
+# 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
+
+# Path found in the manifest file in the guix-profile
+#$(/home/shepherd/guix-profiles/pluto/bin/guix system container /gnu/store/7zhrc956fl9v4x0fvaav5w8fj1ch3rpa-gn-bioinformatics/share/guile/site/3.0/gn/services/pluto.scm --network)
+#$(/home/shepherd/guix-profiles/pluto/bin/guix system container -L /home/shepherd/guix-past/modules/ -L /home/shepherd/guix-bioinformatics/ /home/shepherd/guix-bioinformatics/gn/services/pluto.scm --network)
diff --git a/shepherd/init.d/covid19-pubseq.scm b/shepherd/disabled/covid19-pubseq.scm
index 0d1709d..0d1709d 100644
--- a/shepherd/init.d/covid19-pubseq.scm
+++ b/shepherd/disabled/covid19-pubseq.scm
diff --git a/shepherd/init.d/genenetwork1.scm b/shepherd/disabled/genenetwork1.scm
index 31f1bb0..31f1bb0 100644
--- a/shepherd/init.d/genenetwork1.scm
+++ b/shepherd/disabled/genenetwork1.scm
diff --git a/shepherd/init.d/gitea.scm b/shepherd/disabled/gitea.scm
index b5d77f0..b5d77f0 100644
--- a/shepherd/init.d/gitea.scm
+++ b/shepherd/disabled/gitea.scm
diff --git a/shepherd/init.d/hrdp-project.scm b/shepherd/disabled/hrdp-project.scm
index 54ad53a..54ad53a 100644
--- a/shepherd/init.d/hrdp-project.scm
+++ b/shepherd/disabled/hrdp-project.scm
diff --git a/shepherd/init.d/ipfs.scm b/shepherd/disabled/ipfs.scm
index 1b8d21a..1b8d21a 100644
--- a/shepherd/init.d/ipfs.scm
+++ b/shepherd/disabled/ipfs.scm
diff --git a/shepherd/init.d/mcron.scm b/shepherd/disabled/mcron.scm
index 415e1f0..415e1f0 100644
--- a/shepherd/init.d/mcron.scm
+++ b/shepherd/disabled/mcron.scm
diff --git a/shepherd/init.d/ratspub.scm b/shepherd/disabled/ratspub.scm
index c1d552a..c1d552a 100644
--- a/shepherd/init.d/ratspub.scm
+++ b/shepherd/disabled/ratspub.scm
diff --git a/shepherd/init.d/test-upgrade.scm b/shepherd/disabled/test-upgrade.scm
index 6750ede..6750ede 100644
--- a/shepherd/init.d/test-upgrade.scm
+++ b/shepherd/disabled/test-upgrade.scm
diff --git a/shepherd/init.d/virtuoso.scm b/shepherd/disabled/virtuoso.scm
index 241fe23..241fe23 100644
--- a/shepherd/init.d/virtuoso.scm
+++ b/shepherd/disabled/virtuoso.scm
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/update_archive-pubmed.sh b/update_archive-pubmed.sh
index 2e9d129..b8bc87d 100755
--- a/update_archive-pubmed.sh
+++ b/update_archive-pubmed.sh
@@ -1,2 +1,2 @@
 #!/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; unset PATH; $(/var/guix/profiles/per-user/genecup/current-guix/bin/guix build edirect)/bin/archive-pubmed'
+/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; unset PATH; $(/home/shepherd/guix-profiles/genecup/bin/guix build edirect)/bin/archive-pubmed'