Merge branch 'master' of http://git.genenetwork.org/guix-bioinformatics/guix-bioinformatics

6 files changed, 38 insertions, 20 deletions

diff --git a/gn/services/archive-pubmed.service b/gn/services/archive-pubmed.service
new file mode 100644
index 0000000..fd00b71
--- /dev/null
+++ b/gn/services/archive-pubmed.service
@@ -0,0 +1,13 @@
+[Unit]
+Description=Download PubMed Archives
+After=network-online.target
+Wants=network-online.target
+AssertPathExists=/export2/PubMed
+
+[Service]
+ExecStart=/usr/local/guix-profiles/ratspub/bin/archive-pubmed
+Environment="EDIRECT_PUBMED_MASTER=/export2/PubMed" "PERL_LWP_SSL_CA_FILE=/etc/ssl/certs/ca-certificates.crt" "PATH=/usr/local/guix-profiles/ratspub/bin:/usr/sbin:/usr/bin:/sbin:/bin:/sbin:/usr/sbin"
+User=hchen
+
+[Install]
+WantedBy=multi-user.target
diff --git a/gn/services/archive-pubmed.timer b/gn/services/archive-pubmed.timer
new file mode 100644
index 0000000..4bb27ba
--- /dev/null
+++ b/gn/services/archive-pubmed.timer
@@ -0,0 +1,9 @@
+[Unit]
+Description=Daily PubMed downloads
+
+[Timer]
+OnBootSec=5h
+OnUnitInactiveSec=15h
+
+[Install]
+WantedBy=default.target
diff --git a/gn/services/bnw-README b/gn/services/bnw-README
index ab7de53..d70b7fc 100644
--- a/gn/services/bnw-README
+++ b/gn/services/bnw-README
@@ -6,8 +6,8 @@ $ cd guix-bioinformatics && git pull
 # systemctl enable --now bnw.service
 
 for testing changes to the container, you'll want to do the following (or thereabouts):
-$ guix system container gn/services/GN1-container.scm --share=/home/bnw/server=/srv/http --network
-$ sudo -E $(guix system container gn/services/GN1-container.scm --share=/home/bnw/server=/srv/http --network)
+$ guix system container gn/servicebnwN1-container.scm --network
+$ sudo -E $(guix system container gn/services/bnw-container.scm --network)
 
 for running the service:
 see included bnw.service
diff --git a/gn/services/bnw-container.scm b/gn/services/bnw-container.scm
index 8463a75..39da38d 100644
--- a/gn/services/bnw-container.scm
+++ b/gn/services/bnw-container.scm
@@ -21,10 +21,6 @@
   (match-lambda
     (($ <bnw-configuration> package deploy-directory port)
      #~(begin
-         (use-modules (guix build utils))
-         (when (directory-exists? #$deploy-directory)
-           ;; Not 'delete-file-recursively' because the directory might be empty.
-           (system* "rm" "-r" #$(string-append deploy-directory "/*")))
          (mkdir-p #$deploy-directory)
          (copy-recursively #$package #$deploy-directory)
          (invoke #$(file-append coreutils "/bin/chmod") "a+w"
diff --git a/gn/services/bnw.service b/gn/services/bnw.service
index 5ba8f3f..6ac99a1 100644
--- a/gn/services/bnw.service
+++ b/gn/services/bnw.service
@@ -3,7 +3,7 @@ Description=BNW web server
 Wants=guix-daemon.service
 
 [Service]
-Environment="BNW_COMMAND=$(/bin/su -l bnw -c '/var/guix/profiles/per-user/bnw/current-guix/bin/guix system container /home/bnw/guix-bioinformatics/gn/services/bnw-container.scm --share=/home/bnw/server=/srv/http --share=/home/bnw/server/var-log=/var/log --network')"
+Environment="BNW_COMMAND=$(/bin/su -l bnw -c '/var/guix/profiles/per-user/bnw/current-guix/bin/guix system container /home/bnw/guix-bioinformatics/gn/services/bnw-container.scm --share=/home/bnw/server/var-log=/var/log --network')"
 ExecStart=/bin/bash -c '${BNW_COMMAND}'
 
 [Install]
diff --git a/gn/services/genenetwork.scm b/gn/services/genenetwork.scm
index 0978cd2..4693152 100644
--- a/gn/services/genenetwork.scm
+++ b/gn/services/genenetwork.scm
@@ -2,13 +2,13 @@
 
 (use-modules (gnu)
              (gn packages genenetwork)
-             (gn packages python)
+             (gn packages python24)
              (gn packages web))
 (use-service-modules web)
 (use-package-modules python)
 
 (define %mod-python-path
-  (file-append mod-python "/lib/python2.7/site-packages"))
+  (file-append mod-python "/lib/python2.4/site-packages"))
 
 (operating-system
   (host-name "genenetwork")
@@ -22,15 +22,15 @@
   ;; No firmware for VMs
   (firmware '())
 
-  (packages (cons* python-2
+  (packages (cons* python-2.4
                    mod-python
-                   python2-qtlreaper
-                   python2-htmlgen-gn
-                   python2-json-GN1
-                   python2-piddle
-                   python2-pyx-GN1
-                   python2-pyxlwriter
-                   python2-svg-GN1
+                   python24-qtlreaper
+                   ;python24-htmlgen-gn
+                   python24-json-GN1
+                   python24-piddle
+                   python24-pyx-GN1
+                   python24-pyxlwriter
+                   python24-svg-GN1
                    %base-packages))
 
   (services (list (service httpd-service-type
@@ -38,7 +38,7 @@
                              (config
                                (httpd-config-file
                                  (server-name "www.genenetwork.org")
-                                 (document-root (file-append genenetwork "/web"))
+                                 (document-root (file-append genenetwork1 "/web"))
                                  (listen '("8811"))
                                  (modules (cons*
                                             (httpd-module
@@ -46,8 +46,8 @@
                                               (file (file-append mod-python "/modules/mod_python.so")))
                                             %default-httpd-modules))
                                  (extra-config (list "\
-PythonPath \"sys.path+['" %mod-python-path "', '" (file-append genenetwork "/web/webqtl") "']\"
-<Directory " (file-append genenetwork "/web/webqtl") ">
+PythonPath \"sys.path+['" %mod-python-path "', '" (file-append genenetwork1 "/web/webqtl") "']\"
+<Directory " (file-append genenetwork1 "/web/webqtl") ">
   SetHandler python-program
   PythonHandler mod_python.publisher
   PythonAutoReload Off