From af7d0bca229f3ebaa80a16d1ce3a2bf1a8abd5df Mon Sep 17 00:00:00 2001 From: Pjotr Prins Date: Wed, 20 Apr 2016 08:37:55 +0000 Subject: [PATCH 023/100] WIP fixing all paths --- README.md | 2 ++ 1 file changed, 2 insertions(+) (limited to 'README.md') diff --git a/README.md b/README.md index 3d95d05f..db495910 100644 --- a/README.md +++ b/README.md @@ -17,6 +17,8 @@ Elissa Chesler, Jintao Wang, Kenneth Manly, Robert W. Williams, and colleagues. Code and primary web service managed by Dr. Robert W. Williams and the University of Tennessee Health Science Center, Memphis TN, USA. +Join #genenetwork on irc.freenode.net. + Email labwilliams@gmail.com or rwilliams@uthsc.edu Older version available on SourceForge http://sourceforge.net/projects/genenetwork/ -- cgit v1.2.3 From 95d9380be80738d85ae85c3232ea1741fa07232a Mon Sep 17 00:00:00 2001 From: Pjotr Prins Date: Fri, 4 Mar 2016 10:17:03 +0000 Subject: Simplify the README so people can actually READ it. --- README.md | 27 ++++----------------------- 1 file changed, 4 insertions(+), 23 deletions(-) (limited to 'README.md') diff --git a/README.md b/README.md index db495910..98cb3e80 100644 --- a/README.md +++ b/README.md @@ -1,30 +1,11 @@ -genenetwork on github (May 7, 2012 by Lei Yan and Rob Williams) - -www.genenetwork.org +Source code for the GeneNetwork2 server http://www.genenetwork.org/ Released under Affero General Public License 3 (AGPLv3). See also LICENSE.txt -For background see: http://en.wikipedia.org/wiki/Genenetwork - -WWW service initiated January, 1994 as The Portable Dictionary of the Mouse Genome and -June 15, 2001 as WebQTL. - -This code and the main web service is currently operated by Lei Yan, Zachary Sloan, -Arthur Centeno. Design and code by Xiaodong Zhou, Christian Fernandez, Sam Ockman, Ning Liu, Rudi Alberts, -Elissa Chesler, Jintao Wang, Kenneth Manly, Robert W. Williams, and colleagues. - -Code and primary web service managed by Dr. Robert W. Williams and the University of Tennessee Health Science Center, -Memphis TN, USA. +See also: http://en.wikipedia.org/wiki/Genenetwork Join #genenetwork on irc.freenode.net. -Email labwilliams@gmail.com or rwilliams@uthsc.edu - -Older version available on SourceForge http://sourceforge.net/projects/genenetwork/ - -Funded by the National Institutes of Health and -University of Tennessee Center for Integrative and Translational Genomics - - -=========== +Code and primary web service managed by Dr. Robert W. Williams and the +University of Tennessee Health Science Center, Memphis TN, USA. -- cgit v1.2.3 From a1e77b1dbd308a376e0e8c7c02d71f0b4b669241 Mon Sep 17 00:00:00 2001 From: Pjotr Prins Date: Fri, 4 Mar 2016 10:21:13 +0000 Subject: README --- README.md | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) (limited to 'README.md') diff --git a/README.md b/README.md index 98cb3e80..d07abc42 100644 --- a/README.md +++ b/README.md @@ -1,11 +1,12 @@ Source code for the GeneNetwork2 server http://www.genenetwork.org/ -Released under Affero General Public License 3 (AGPLv3). See also -LICENSE.txt +This GeneNetwork2 source code is released under the Affero General +Public License 3 (AGPLv3). See also LICENSE.txt -See also: http://en.wikipedia.org/wiki/Genenetwork +For more information visit http://www.genenetwork.org/ and +http://en.wikipedia.org/wiki/Genenetwork -Join #genenetwork on irc.freenode.net. +IRC on #genenetwork on irc.freenode.net. Code and primary web service managed by Dr. Robert W. Williams and the University of Tennessee Health Science Center, Memphis TN, USA. -- cgit v1.2.3 From f7a6c602c36bd3905aaa4d743a1ae1933d6bfcf9 Mon Sep 17 00:00:00 2001 From: Pjotr Prins Date: Fri, 4 Mar 2016 10:23:01 +0000 Subject: README --- README.md | 10 ++++++++++ 1 file changed, 10 insertions(+) (limited to 'README.md') diff --git a/README.md b/README.md index d07abc42..6a69d6cd 100644 --- a/README.md +++ b/README.md @@ -1,8 +1,18 @@ +# GENENETWORK + Source code for the GeneNetwork2 server http://www.genenetwork.org/ +## Install + +See the [installation docs](doc/README.org) + +## License + This GeneNetwork2 source code is released under the Affero General Public License 3 (AGPLv3). See also LICENSE.txt +## More information + For more information visit http://www.genenetwork.org/ and http://en.wikipedia.org/wiki/Genenetwork -- cgit v1.2.3 From 791a80c3409327e5578dc36cc575169b8ee5b13b Mon Sep 17 00:00:00 2001 From: Pjotr Prins Date: Fri, 4 Mar 2016 10:41:14 +0000 Subject: README --- README.md | 5 ++++- doc/README.org | 5 +++-- 2 files changed, 7 insertions(+), 3 deletions(-) (limited to 'README.md') diff --git a/README.md b/README.md index 6a69d6cd..d2d15781 100644 --- a/README.md +++ b/README.md @@ -4,7 +4,10 @@ Source code for the GeneNetwork2 server http://www.genenetwork.org/ ## Install -See the [installation docs](doc/README.org) +The recommended installation is with GNU Guix which allows you to +deploy GN2 and dependencies as a self contained unit on any machine. +The database can be run separately as well as the source tree (for +developers). See the [installation docs](doc/README.org). ## License diff --git a/doc/README.org b/doc/README.org index d9730948..fd19141c 100644 --- a/doc/README.org +++ b/doc/README.org @@ -1,4 +1,4 @@ -#+TITLE: Installing GeneNetwork services with GNU Guix +#+TITLE: Installing GeneNetwork services * Table of Contents :TOC: - [[#introduction][Introduction]] @@ -12,7 +12,8 @@ Large system deployments tend to get very complex. In this document we explain the GeneNetwork deployment system which is based on GNU Guix -(see Pjotr's [[https://github.com/pjotrp/guix-notes/blob/master/README.md][Guix-notes]]). +(see also Pjotr's [[https://github.com/pjotrp/guix-notes/blob/master/README.md][Guix-notes]]). The Guix system can be used to install +GN with all its files and dependencies. * Binary deployment (WIP) -- cgit v1.2.3 From 1017f7b45c8102793c6d75959ae1eeb680ed3544 Mon Sep 17 00:00:00 2001 From: Pjotr Prins Date: Tue, 29 Mar 2016 15:19:16 -0500 Subject: Main README --- README.md | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) (limited to 'README.md') diff --git a/README.md b/README.md index d2d15781..ce435f61 100644 --- a/README.md +++ b/README.md @@ -1,6 +1,7 @@ # GENENETWORK -Source code for the GeneNetwork2 server http://www.genenetwork.org/ +This repository contains the source code for the GeneNetwork server +http://www.genenetwork.org/ (version 2 aka GN2). ## Install @@ -11,13 +12,14 @@ developers). See the [installation docs](doc/README.org). ## License -This GeneNetwork2 source code is released under the Affero General +The GeneNetwork2 source code is released under the Affero General Public License 3 (AGPLv3). See also LICENSE.txt ## More information -For more information visit http://www.genenetwork.org/ and -http://en.wikipedia.org/wiki/Genenetwork +For more information visit http://www.genenetwork.org/ + +## Contact IRC on #genenetwork on irc.freenode.net. -- cgit v1.2.3 From aa47bf9d94c3f5232cabfd1bef2eb3b54241d076 Mon Sep 17 00:00:00 2001 From: Pjotr Prins Date: Mon, 4 Apr 2016 11:38:15 +0000 Subject: README: point to gn-latest SHA values --- README.md | 2 +- doc/README.org | 17 +++++++++-------- 2 files changed, 10 insertions(+), 9 deletions(-) (limited to 'README.md') diff --git a/README.md b/README.md index ce435f61..4fe739bf 100644 --- a/README.md +++ b/README.md @@ -13,7 +13,7 @@ developers). See the [installation docs](doc/README.org). ## License The GeneNetwork2 source code is released under the Affero General -Public License 3 (AGPLv3). See also LICENSE.txt +Public License 3 (AGPLv3). See [LICENSE.txt](LICENSE.txt). ## More information diff --git a/doc/README.org b/doc/README.org index 1894d8d3..5fffa108 100644 --- a/doc/README.org +++ b/doc/README.org @@ -14,14 +14,15 @@ * Introduction -Large system deployments tend to get very complex. In this document we -explain the GeneNetwork deployment system which is based on GNU Guix -(see also Pjotr's [[https://github.com/pjotrp/guix-notes/blob/master/README.md][Guix-notes]]). The Guix system can be used to install -GN with all its files and dependencies. - -The official installation path is via a GNU Guix installation from a -checked out version of the Guix package tree (this is required for -reproducibility). +Large system deployments can get very complex. In this document we +explain the GeneNetwork version 2 (GN2) reproducible deployment system +which is based on GNU Guix (see also Pjotr's [[https://github.com/pjotrp/guix-notes/blob/master/README.md][Guix-notes]]). The Guix +system can be used to install GN with all its files and dependencies. + +The official installation path is from a checked out version of the +main Guix package tree and that of the Genenetwork package +tree. Current supported versions can be found as the SHA values of +'gn-latest' branches of [[https://github.com/genenetwork/guix-bioinformatics/tree/gn-latest][Guix bioinformatics]] and [[https://github.com/genenetwork/guix/tree/gn-latest][GNU Guix main]]. * Source deployment ** Install guix -- cgit v1.2.3