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 --- run_genome_browser.sh | 2 +- run_pluto.sh | 8 ++++++++ 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 +++++++++++++ shepherd/init.d/covid19-pubseq.scm | 12 ------------ shepherd/init.d/genenetwork1.scm | 12 ------------ shepherd/init.d/gitea.scm | 12 ------------ shepherd/init.d/hrdp-project.scm | 14 -------------- shepherd/init.d/ipfs.scm | 12 ------------ shepherd/init.d/mcron.scm | 12 ------------ shepherd/init.d/pluto.scm | 16 ++++++++-------- shepherd/init.d/ratspub.scm | 19 ------------------- shepherd/init.d/test-upgrade.scm | 27 --------------------------- shepherd/init.d/virtuoso.scm | 13 ------------- update_archive-pubmed.sh | 2 +- 22 files changed, 151 insertions(+), 143 deletions(-) create mode 100755 run_pluto.sh 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 delete mode 100644 shepherd/init.d/covid19-pubseq.scm delete mode 100644 shepherd/init.d/genenetwork1.scm delete mode 100644 shepherd/init.d/gitea.scm delete mode 100644 shepherd/init.d/hrdp-project.scm delete mode 100644 shepherd/init.d/ipfs.scm delete mode 100644 shepherd/init.d/mcron.scm delete mode 100644 shepherd/init.d/ratspub.scm delete mode 100644 shepherd/init.d/test-upgrade.scm delete mode 100644 shepherd/init.d/virtuoso.scm 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/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 + #: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 + #: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 + #: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 + #: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 + #: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 + #: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 + #: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 + #: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 + #: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) 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 - #: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 - #: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 - #: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 - #: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 - #: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 - #: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 - #: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 - #: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 - #: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 - #: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) 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' -- cgit v1.2.3