Recent changes to Installation

Installation modified by Keith Ching

Keith Ching — Tue, 01 Mar 2016 17:38:23 -0000

--- v33
+++ v34
@@ -152,7 +152,7 @@

 ~~~~~~

-#expand mysql tar (~38 GB space needed)
+#expand mysql tar (~45 GB space needed)
 obtain the database tarball from the files download section of sourceforge.

Installation modified by Keith Ching

Keith Ching — Wed, 13 Jan 2016 19:31:14 -0000

--- v32
+++ v33
@@ -56,7 +56,7 @@
 Timeout 600
 ~~~~~~

-On OSX, the Timeout parameter is in /etc/apache2/extra/httpd-default.conf
+On OSX, add the Timeout parameter to /etc/apache2/httpd.conf

 Start Apache

Installation modified by Keith Ching

Keith Ching — Wed, 13 Jan 2016 19:26:16 -0000

--- v31
+++ v32
@@ -67,6 +67,10 @@
 chkconfig --list httpd
 ~~~~~~

+on OSX
+~~~~~~
+sudo /usr/sbin/apachectl restart
+~~~~~~

 Set up web
 checkout the repository into a web folder

Installation modified by Keith Ching

Keith Ching — Wed, 13 Jan 2016 19:24:10 -0000

--- v30
+++ v31
@@ -56,6 +56,7 @@
 Timeout 600
 ~~~~~~

+On OSX, the Timeout parameter is in /etc/apache2/extra/httpd-default.conf

 Start Apache

Installation modified by Keith Ching

Keith Ching — Wed, 11 Nov 2015 21:50:21 -0000

--- v29
+++ v30
@@ -146,12 +146,9 @@
 My conclusion is that the AWS RDS service cannot be effectively utilized for CELLX. Instead, I have provided the pre-indexed MyISAM tables that one merely needs to copy into the correct location and the database is immediately ready for queries.

 ~~~~~~
-Deprecated:
-#Checkout database ~7 GB
-sudo svn checkout svn://svn.code.sf.net/p/cellx/code/data/mysql/MyISAM/ database
-#expand tar (~30 GB space needed)
-Update: obtain the database tarball from the files download section of sourceforge.
-It has been removed from svn version control.
+
+#expand mysql tar (~38 GB space needed)
+obtain the database tarball from the files download section of sourceforge.

 #shutdown mysqld
@@ -202,8 +199,6 @@
 source("http://bioconductor.org/biocLite.R")
 biocLite('gplots')
 biocLite('genefilter')
-# updates not tested
-#future requirements
 biocLite("mixtools")
 # start R serve
 cd src/rserve

Installation modified by Keith Ching

Keith Ching — Fri, 04 Sep 2015 19:10:11 -0000

--- v28
+++ v29
@@ -203,7 +203,7 @@
 biocLite('gplots')
 biocLite('genefilter')
 # updates not tested
-future requirement:
+#future requirements
 biocLite("mixtools")
 # start R serve
 cd src/rserve

Installation modified by Keith Ching

Keith Ching — Fri, 04 Sep 2015 19:09:26 -0000

--- v27
+++ v28
@@ -203,7 +203,8 @@
 biocLite('gplots')
 biocLite('genefilter')
 # updates not tested
-
+future requirement:
+biocLite("mixtools")
 # start R serve
 cd src/rserve
 sudo R CMD Rserve --RS-conf Rserv.conf

Installation modified by Keith Ching

Keith Ching — Thu, 23 Apr 2015 18:03:44 -0000

--- v26
+++ v27
@@ -150,7 +150,8 @@
 #Checkout database ~7 GB
 sudo svn checkout svn://svn.code.sf.net/p/cellx/code/data/mysql/MyISAM/ database
 #expand tar (~30 GB space needed)
-Update: obtain the database tarball from the files download section of sourceforge.  It has been removed from svn version control.
+Update: obtain the database tarball from the files download section of sourceforge.
+It has been removed from svn version control.

 #shutdown mysqld

Installation modified by Keith Ching

Keith Ching — Thu, 23 Apr 2015 18:03:05 -0000

--- v25
+++ v26
@@ -146,9 +146,12 @@
 My conclusion is that the AWS RDS service cannot be effectively utilized for CELLX. Instead, I have provided the pre-indexed MyISAM tables that one merely needs to copy into the correct location and the database is immediately ready for queries.

 ~~~~~~
+Deprecated:
 #Checkout database ~7 GB
 sudo svn checkout svn://svn.code.sf.net/p/cellx/code/data/mysql/MyISAM/ database
 #expand tar (~30 GB space needed)
+Update: obtain the database tarball from the files download section of sourceforge.  It has been removed from svn version control.
+

 #shutdown mysqld
 sudo service mysqld stop

Installation modified by Keith Ching

Keith Ching — Fri, 23 Jan 2015 17:53:55 -0000

--- v24
+++ v25
@@ -1,5 +1,7 @@
 Installation
 ===
+
+Currently, the installation procedure occurs through the SVN repository checkout. The files for CNV images are quite large, so it is not recommended to checkout the whole repository at once.  Separate downloadable tarballs will be created once all the files in the repository have stabilized.

 AWS instance installation.
 ~10 GB root