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authorroot2021-02-05 14:06:23 +0000
committerroot2021-02-05 14:06:23 +0000
commit8b29e4bdfa9c2b90abe87b5876cb58e22406990d (patch)
treeb2bfb400a44b48b6c3d4f5279fe67ffa6975c6ab
parent5329ba6cb2c303765dbb6eeef5f60667fb6e362c (diff)
downloadguix-bioinformatics-8b29e4bdfa9c2b90abe87b5876cb58e22406990d.tar.gz
gn1: make run in a container
-rw-r--r--gn/packages/edash.scm1
-rw-r--r--gn/packages/genenetwork.scm2
-rw-r--r--gn/packages/jupyterhub.scm1
-rw-r--r--gn/packages/python.scm1
-rw-r--r--gn/services/gn1-httpd-config.scm6
5 files changed, 7 insertions, 4 deletions
diff --git a/gn/packages/edash.scm b/gn/packages/edash.scm
index 7f52393..ac88e22 100644
--- a/gn/packages/edash.scm
+++ b/gn/packages/edash.scm
@@ -7,6 +7,7 @@
#:use-module (gnu packages web)
#:use-module (gnu packages base)
#:use-module (gnu packages python)
+ #:use-module (gnu packages python-build)
#:use-module (gnu packages python-check)
#:use-module (gnu packages python-web)
#:use-module (gnu packages python-xyz)
diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm
index a3ed18f..0db7032 100644
--- a/gn/packages/genenetwork.scm
+++ b/gn/packages/genenetwork.scm
@@ -764,7 +764,7 @@ written in C")
;; Where GN1 is located: (GNROOT)
(("/gnshare/gn") out)
;; Where the database is located: (sql_host)
- (("tux01") "localhost"))
+ (("tux01.uthsc.edu") "127.0.0.1"))
(substitute* '("web/webqtl/maintainance/QTL_Reaper_cal_lrs.py")
(("128\\.169\\.5\\.59") "localhost"))
;; This directory (TMPDIR) is expected to be writable by apache.
diff --git a/gn/packages/jupyterhub.scm b/gn/packages/jupyterhub.scm
index cec115b..838412b 100644
--- a/gn/packages/jupyterhub.scm
+++ b/gn/packages/jupyterhub.scm
@@ -12,6 +12,7 @@
#:use-module (gnu packages monitoring)
#:use-module (gnu packages openstack)
#:use-module (gnu packages protobuf)
+ #:use-module (gnu packages python-build)
#:use-module (gnu packages python-crypto)
#:use-module (gnu packages python-web)
#:use-module (gnu packages python-xyz)
diff --git a/gn/packages/python.scm b/gn/packages/python.scm
index 9208a7a..226f179 100644
--- a/gn/packages/python.scm
+++ b/gn/packages/python.scm
@@ -11,6 +11,7 @@
#:use-module (gnu packages linux)
#:use-module (gnu packages pcre)
#:use-module (gnu packages python)
+ #:use-module (gnu packages python-build)
#:use-module (gnu packages python-compression)
#:use-module (gnu packages python-crypto)
#:use-module (gnu packages python-science)
diff --git a/gn/services/gn1-httpd-config.scm b/gn/services/gn1-httpd-config.scm
index a8c7f3f..0511810 100644
--- a/gn/services/gn1-httpd-config.scm
+++ b/gn/services/gn1-httpd-config.scm
@@ -64,11 +64,11 @@
(define GN1-httpd-config
(httpd-config-file
- (server-name "gn1-test.genenetwork.org")
+ (server-name "gn1-new.genenetwork.org")
;; Defaults to httpd, should be same as 'package' above to launch service.
(server-root httpd22-with-mod-python)
- (user "nobody")
- (group "root")
+ (user "gn1")
+ (group "users")
(pid-file "/tmp/guix-gn1/httpd-genenetwork1.pid")
(error-log "/tmp/guix-gn1/httpd-genenetwork1-error-log")
(listen '("8042"))