Merge branch 'master' of https://github.com/genenetwork/genenetwork2

20 files changed, 600 insertions, 440 deletions

diff --git a/bin/genenetwork2 b/bin/genenetwork2
index 52d3155c..df688989 100755
--- a/bin/genenetwork2
+++ b/bin/genenetwork2
@@ -1,34 +1,39 @@
 #! /bin/bash
 #
 # This will run the GN2 server (with default settings if none
-# supplied). Pass in your own settings file, e.g.
+# supplied). Typically you need a GNU Guix profile which is set with
+# an environment variable (this profile is dictated by the
+# installation path of genenetwork). Say your profile is in
+# ~/opt/gn-latest-guix
 #
-#   ./bin/genenetwork2 ~/my_settings.py
+#   env GN2_PROFILE=~/opt/gn-latest-guix ./bin/genenetwork2
 #
-# But better is to retain the defaults and override them with
-# JSON file (see the deploy docs).
+# You can pass in your own settings file, e.g.
 #
-#   ./bin/genenetwork2 ~/my_overrides.json
+#   env GN2_PROFILE=~/opt/gn-latest-guix ./bin/genenetwork2 ~/my_settings.py
 #
 # To run a maintenance script with settings (instead of the webserver) add that with
 # a -c switch, e.g.
 #
-#   ./bin/genenetwork2 ~/my_overrides.json -c ./wqflask/maintenance/gen_select_dataset.py
-#
-# Environment settings can be used to preconfigure as well as a
-# settings.py file.
-#
-# GN2_BASE_PATH is base directory of wqflask source code
-#
+#   env GN2_PROFILE=~/opt/gn-latest-guix ./bin/genenetwork2 ~/my_overrides.json -c ./wqflask/maintenance/gen_select_dataset.py
 
 SCRIPT=$(readlink -f "$0")
 GN2_BASE_DIR=$(dirname $(dirname "$SCRIPT"))
+GN2_ID=$(cat /etc/hostname):$(basename $GN2_BASE_DIR)
 
 echo GN2_BASE_DIR=$GN2_BASE_DIR
 
-GIT_HASH=$(git rev-parse HEAD)
-GIT_BRANCH=$(git rev-parse --abbrev-ref HEAD)
-export GN_VERSION=$(cat $GN2_BASE_DIR/VERSION)-$GIT_BRANCH-${GIT_HASH:0:9}
+GUIX_SITE=$GN2_BASE_DIR/lib/python2.7/site-packages
+if [ -d $GUIX_SITE ]; then
+    echo INFO: GN2 is running from GNU Guix
+    GN2_BASE_DIR=$GUIX_SITE
+    export GN_VERSION=$GN2_ID:$(cat $GN2_BASE_DIR/etc/VERSION)
+else
+    echo INFO: GN2 is running from a source tree
+    GIT_HASH=$(git rev-parse HEAD)
+    GIT_BRANCH=$(git rev-parse --abbrev-ref HEAD)
+    export GN_VERSION=$GN2_ID:$(cat $GN2_BASE_DIR/etc/VERSION)-$GIT_BRANCH-${GIT_HASH:0:9}
+fi
 echo GN_VERSION=$GN_VERSION
 
 # Handle settings parameter (can be .py or .json)
@@ -41,13 +46,8 @@ else
     shift
 fi
 if [ ! -e $settings ]; then
-    GUIX_ETC=$GN2_BASE_DIR/lib/python2.7/site-packages/genenetwork2-2.0-py2.7.egg
-    if [ -d $GUIX_ETC ]; then
-        echo INFO: GN2 is actually running from GNU Guix
-    else
-        echo "ERROR: can not locate settings file - pass it in the command line"
-        exit 1
-    fi
+    echo "ERROR: can not locate settings file - pass it in the command line"
+    exit 1
 fi
 export WQFLASK_SETTINGS=$settings     # Python
 export WQFLASK_OVERRIDES=$overrides   # JSON
@@ -55,30 +55,40 @@ export WQFLASK_OVERRIDES=$overrides   # JSON
 echo WQFLASK_SETTINGS=$settings
 echo WQFLASK_OVERRIDES=$overrides
 
-# ---- Checks and balances
-if [ -z $GUIX_ETC ]; then
-    if [ -z $GN2_PROFILE ] ; then
-        echo "WARNING: GN2_PROFILE has not been set - I hope you know what you are doing!"
-    else
-        export PATH=$GN2_PROFILE/bin:$PATH
-        export PYTHONPATH=$GN2_PROFILE/lib/python2.7/site-packages
-        export R_LIBS_SITE=$GN2_PROFILE/site-library
-        export GUIX_GTK3_PATH="$GN2_PROFILE/lib/gtk-3.0"
-        export GI_TYPELIB_PATH="$GN2_PROFILE/lib/girepository-1.0"
-        export XDG_DATA_DIRS="$GN2_PROFILE/share"
-        export GIO_EXTRA_MODULES="$GN2_PROFILE/lib/gio/modules"
-        export LC_ALL=C
-    fi
-    if [ -z $PYTHONPATH ] ; then
-        echo "WARNING PYTHONPATH has not been set - use GN2_PROFILE!"
-    fi
-    if [ ! -d $R_LIBS_SITE ] ; then
-        echo "ERROR: R_LIBS_SITE has not been set correctly (we only allow one path) - use GN2_PROFILE!"
-        echo "Paste into your shell the output of (for example)"
-        echo "guix package -p \$GN2_PROFILE --search-paths"
-        exit 1
+if [ -z $GN2_PROFILE ] ; then
+    echo "WARNING: GN2_PROFILE has not been set - you need the environment, so I hope you know what you are doing!"
+    export GN2_PROFILE=$(dirname $(dirname $(which genenetwork2)))
+    if [ -d $GN2_PROFILE ]; then
+        echo "Best guess is $GN2_PROFILE"
     fi
 fi
+if [ -z $GN2_PROFILE ]; then
+    read -p "PRESS [ENTER] TO CONTINUE..."
+else
+    export PATH=$GN2_PROFILE/bin:$PATH
+    export PYTHONPATH=$GN2_PROFILE/lib/python2.7/site-packages
+    export R_LIBS_SITE=$GN2_PROFILE/site-library
+    export GUIX_JS_PATH=$GN2_PROFILE/share/genenetwork2/javascript
+    export GUIX_GTK3_PATH="$GN2_PROFILE/lib/gtk-3.0"
+    export GI_TYPELIB_PATH="$GN2_PROFILE/lib/girepository-1.0"
+    export XDG_DATA_DIRS="$GN2_PROFILE/share"
+    export GIO_EXTRA_MODULES="$GN2_PROFILE/lib/gio/modules"
+    export LC_ALL=C # FIXME
+    export GENENETWORK_FILES="$GN2_PROFILE/share/genenetwork2"
+    export PLINK_COMMAND="$GN2_PROFILE/bin/plink2"
+    export PYLMM_COMMAND="$GN2_PROFILE/bin/pylmm_redis"
+    export GEMMA_COMMAND="$GN2_PROFILE/bin/gemma"
+fi
+if [ -z $PYTHONPATH ] ; then
+    echo "ERROR PYTHONPATH has not been set - use GN2_PROFILE!"
+    exit 1
+fi
+if [ ! -d $R_LIBS_SITE ] ; then
+    echo "ERROR R_LIBS_SITE has not been set correctly (we only allow one path) - use GN2_PROFILE!"
+    echo "Paste into your shell the output of (for example)"
+    echo "guix package -p \$GN2_PROFILE --search-paths"
+    exit 1
+fi
 
 # We may change this one:
 export PYTHONPATH=$GN2_BASE_DIR/wqflask:$PYTHONPATH
@@ -88,6 +98,8 @@ if [ -z $TMPDIR ]; then
     TMPDIR="/tmp"
 fi
 
+# Show environment settings
+set|grep guix
 set|grep $GN2_PROFILE
 set|grep TMPDIR
 
@@ -97,7 +109,7 @@ if [ "$1" = '-c' ] ; then
     cmd=${2#wqflask/}
     echo PYTHONPATH=$PYTHONPATH
     echo RUNNING COMMAND $cmd
-    /usr/bin/env python $cmd
+    python $cmd
     exit 0
 fi
 
@@ -109,4 +121,4 @@ dbfilename gn2.rdb
 # Start the flask server running GN2
 cd $GN2_BASE_DIR/wqflask
 echo "Starting with $settings"
-/usr/bin/env python runserver.py
+python runserver.py
diff --git a/doc/GUIX-Reproducible-from-source.org b/doc/GUIX-Reproducible-from-source.org
index 4399ea26..83adce99 100644
--- a/doc/GUIX-Reproducible-from-source.org
+++ b/doc/GUIX-Reproducible-from-source.org
@@ -2,19 +2,188 @@
 
 * Table of Contents                                                     :TOC:
  - [[#introduction][Introduction]]
- - [[#binary-deployment][Binary deployment]]
+ - [[#binary-deployment-through-gnu-guix][Binary deployment through GNU Guix]]
+   - [[#quick-installation-recipe][Quick installation recipe]]
+   - [[#step-1-install-gnu-guix][Step 1: Install GNU Guix]]
+   - [[#step-2-checkout-the-gn2-git-repositories][Step 2: Checkout the GN2 git repositories]]
+   - [[#step-3-authorize-the-gn-guix-server][Step 3: Authorize the GN Guix server]]
+   - [[#step-4-install-and-run-gn2][Step 4: Install and run GN2]]
  - [[#from-source-deployment][From source deployment]]
  - [[#create-archive][Create archive]]
+ - [[#source-deployment][Source deployment]]
+   - [[#run-your-own-copy-of-gn2][Run your own copy of GN2]]
+   - [[#set-up-nginx-port-forwarding][Set up nginx port forwarding]]
+ - [[#source-deployment-and-other-information-on-reproducibility][Source deployment and other information on reproducibility]]
+   - [[#update-to-recent-guix][Update to recent guix]]
+   - [[#install-gn2][Install GN2]]
+   - [[#run-gn2][Run GN2]]
 
 * 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 Pjotr's [[https://github.com/pjotrp/guix-notes/blob/master/README.md][Guix-notes]]).
+(see Pjotr's [[https://github.com/pjotrp/guix-notes/blob/master/README.md][Guix-notes]] and the main [[README.org]] doc).
 
-* Binary deployment
+* Binary deployment through GNU Guix
+** Quick installation recipe
 
-NYA (will go to README)
+This is a recipe for quick and dirty installation of GN2. For
+convenience everything is installed as root, though in reality only
+GNU Guix has to be installed as root. I tested this recipe on a fresh
+install of Debian 8.3.0 (in KVM) though it should work on any modern
+Linux distribution (including CentOS).
+
+
+Note that GN2 consists of an approx. 5 GB installation including
+database. If you use a virtual machine we recommend to use at least
+double.
+
+** Step 1: Install GNU Guix
+
+Fetch the GNU Guix binary from [[https://www.gnu.org/software/guix/download/][here]] (middle panel) and follow
+[[https://www.gnu.org/software/guix/manual/html_node/Binary-Installation.html][instructions]]. Essentially, download and unpack the tar ball (which
+creates directories in /gnu and /var/guix), add build users and group
+(Guix builds software as unpriviliged users) and run the Guix daemon
+after fixing the paths (also known as the 'profile').
+
+Once you have succeeded, you have to [[https://github.com/pjotrp/guix-notes/blob/master/INSTALL.org#set-the-key][set the key]] (getting permission
+to download binaries from the GNU server) and you should be able to
+install the hello package using binary packages (no building)
+
+#+begin_src bash
+export PATH=~/.guix-profile/bin:$PATH
+guix pull
+guix package -i hello --dry-run
+#+end_src
+
+Which should show something like
+
+: The following files would be downloaded:
+:   /gnu/store/zby49aqfbd9w9br4l52mvb3y6f9vfv22-hello-2.10
+:   ...
+#+end_src
+
+means binary installs.  The actual installation command of 'hello' is
+
+#+begin_src bash
+guix package -i hello
+hello
+  Hello, world!
+#+end_src
+
+If you actually see things building it means that Guix is not yet
+properly installed and up-to-date, i.e., the key is missing or you
+need to do a 'guix pull'. Press Ctrl-C to interrupt.
+
+If you need more help we have another writeup in [[https://github.com/pjotrp/guix-notes/blob/master/INSTALL.org#binary-installation][guix-notes]]. To get
+rid of the locale warning see [[https://github.com/pjotrp/guix-notes/blob/master/INSTALL.org#set-locale][set-locale]].
+
+** Step 2: Checkout the GN2 git repositories
+
+To fixate the software dependency graph GN2 uses git repositories of
+Guix packages. First install git if it is missing
+
+#+begin_src bash
+guix package -i git
+export GIT_SSL_CAINFO=/etc/ssl/certs/ca-certificates.crt
+#+end_src
+
+check out the git repositories (gn-deploy branch)
+
+#+begin_src bash
+cd ~
+mkdir genenetwork
+cd genenetwork
+git clone --branch gn-deploy https://github.com/genenetwork/guix-bioinformatics
+git clone --branch gn-deploy --recursive https://github.com/genenetwork/guix guix-gn-deploy
+cd guix-gn-deploy
+#+end_src bash
+
+To test whether this is working try:
+
+#+begin_src bash
+#+end_src bash
+
+** Step 3: Authorize the GN Guix server
+
+GN2 has its own GNU Guix binary distribution server. To trust it you have
+to add the following key
+
+#+begin_src scheme
+(public-key
+ (ecc
+  (curve Ed25519)
+  (q #11217788B41ADC8D5B8E71BD87EF699C65312EC387752899FE9C888856F5C769#)
+ )
+)
+#+end_src
+
+by pasting it into the command
+
+#+begin_src bash
+guix archive --authorize
+#+end_src
+
+and hit Ctrl-D.
+
+Now you can use the substitute server to install GN2 binaries.
+
+** Step 4: Install and run GN2
+
+Since this is a quick and dirty install we are going to override the
+GNU Guix package path by pointing the package path to our repository:
+
+#+begin_src bash
+rm /root/.config/guix/latest
+ln -s ~/genenetwork/guix-gn-deploy/ /root/.config/guix/latest
+#+end_src
+
+Now check whether you can find the GN2 package with
+
+#+begin_src bash
+env GUIX_PACKAGE_PATH=~/genenetwork/guix-bioinformatics/ guix package -A genenetwork2
+  genenetwork2    2.0-a8fcff4     out     gn/packages/genenetwork.scm:144:2
+#+end_src
+
+(ignore the source file newer then ... messages, this is caused by the
+/root/.config/guix/latest override).
+
+And install with
+
+#+begin_src bash
+env GUIX_PACKAGE_PATH=~/genenetwork/guix-bioinformatics/ \
+  guix package -i genenetwork2 \
+  --substitute-urls="http://guix.genenetwork.org"
+#+end_src
+
+Note: the order of the substitute url's may make a difference in speed
+(put the one first that is fastest for your location and time of day).
+
+Note: if your system starts building or gives an error it may well be
+Step 3 did not succeed. The installation should actually be smooth at
+this point and only do binary installs (no compiling).
+
+After installation you should be able to run genenetwork2 after updating
+the Guix suggested environment vars. Check the output of
+
+#+begin_src bash
+guix package --search-paths
+export PYTHONPATH="/root/.guix-profile/lib/python2.7/site-packages"
+export R_LIBS_SITE="/root/.guix-profile/site-library/"
+#+end_src
+
+and copy-paste the listed exports into the terminal before running:
+
+#+begin_src bash
+genenetwork2
+#+end_src
+
+It will complain that the database is missing. See the next section on
+running MySQL server for downloading and installing a MySQL GN2
+database. After installing the database restart genenetwork2 and point
+your browser at [[http://localhost:5003/]].
+
+End of the GN2 installation recipe!
 
 * From source deployment
 
@@ -52,3 +221,182 @@ gn-stable-guix$ env GUIX_PACKAGE_PATH=../guix-bioinformatics ./pre-inst-env guix
 * Create archive
 
 : env GUIX_PACKAGE_PATH=../../genenetwork/guix-bioinformatics/ ./pre-inst-env guix archive --export -r genenetwork2 > guix_gn2-2.0-9e9475053.nar
+
+
+* Source deployment
+
+This section gives a more elaborate instruction for installing GN2
+from source.
+
+First execute above 4 steps:
+
+   - [[#step-1-install-gnu-guix][Step 1: Install GNU Guix]]
+   - [[#step-2-checkout-the-gn2-git-repositories][Step 2: Checkout the GN2 git repositories]]
+   - [[#step-3-authorize-the-gn-guix-server][Step 3: Authorize the GN Guix server]]
+   - [[#step-4-install-and-run-gn2-][Step 4: Install and run GN2 ]]
+
+
+** Run your own copy of GN2
+
+At some point you may want to fix the source code. Assuming you have
+Guix and Genenetwork2 installed (as described above) clone the GN2
+repository from https://github.com/genenetwork/genenetwork2.
+
+Copy-paste the paths into your terminal (mainly so PYTHON_PATH and
+R_LIBS_SITE are set) from the information given by guix:
+
+: guix package --search-paths
+
+Inside the repository:
+
+: cd genenetwork2
+: ./bin/genenetwork2
+
+Will fire up your local repo http://localhost:5003/ using the
+settings in ./etc/default_settings.py. These settings may
+not reflect your system. To override settings create your own from a copy of
+default_settings.py and pass it into GN2 with
+
+: ./bin/genenetwork2 $HOME/my_settings.py
+
+and everything *should* work (note the full path to the settings
+file). This way we develop against the exact same dependency graph of
+software.
+
+If something is not working, take a hint from the settings file
+that comes in the Guix installation. It sits in something like
+
+: cat ~/.guix-profile/lib/python2.7/site-packages/genenetwork2-2.0-py2.7.egg/etc/default_settings.py
+
+** Set up nginx port forwarding
+
+nginx can be used as a reverse proxy for GN2. For example, we want to
+expose GN2 on port 80 while it is running on port 5003. Essentially
+the configuration looks like
+
+#+begin_src js
+    server {
+        listen 80;
+        server_name test-gn2.genenetwork.org;
+        access_log  logs/test-gn2.access.log;
+
+        proxy_connect_timeout       3000;
+        proxy_send_timeout          3000;
+        proxy_read_timeout          3000;
+        send_timeout                3000;
+
+        location / {
+            proxy_set_header   Host      $http_host;
+            proxy_set_header   Connection keep-alive;
+            proxy_set_header   X-Real-IP $remote_addr;
+            proxy_set_header   X-Forwarded-For $proxy_add_x_forwarded_for;
+            proxy_set_header   X-Forwarded-Host $server_name;
+            proxy_pass         http://127.0.0.1:5003;
+        }
+}
+#+end_src js
+
+Install the nginx webserver (as root)
+
+: guix package -i nginx
+
+The nginx example configuration examples can be found in the Guix
+store through
+
+: ls -l /root/.guix-profile/sbin/nginx
+: lrwxrwxrwx 3 root guixbuild 66 Dec 31  1969 /root/.guix-profile/sbin/nginx -> /gnu/store/g0wrcl5z27rmk5b52rldzvk1bzzbnz2l-nginx-1.8.1/sbin/nginx
+
+Use that path
+
+: ls /gnu/store/g0wrcl5z27rmk5b52rldzvk1bzzbnz2l-nginx-1.8.1/share/nginx/conf/
+:   fastcgi.conf            koi-win             scgi_params
+:   fastcgi.conf.default    mime.types          scgi_params.default
+:   fastcgi_params          mime.types.default  uwsgi_params
+:   fastcgi_params.default  nginx.conf          uwsgi_params.default
+:   koi-utf                 nginx.conf.default  win-utf
+
+And copy any relevant files to /etc/nginx.  A configuration file for
+GeneNetwork (reverse proxy) port forwarding can be found in the source
+repository under ./etc/nginx-genenetwork.conf. Copy this file to /etc
+(still as root)
+: cp ./etc/nginx-genenetwork.conf /etc/nginx/
+
+Make dirs
+
+: mkdir -p /var/spool/nginx/logs
+
+Add users
+
+: adduser nobody ; addgroup nobody
+
+Run nginx
+
+: /root/.guix-profile/sbin/nginx -c /etc/nginx/nginx-genenetwork.conf -p /var/spool/nginx
+
+* Source deployment and other information on reproducibility
+
+See the document [[GUIX-Reproducible-from-source.org]].
+
+** Update to recent guix
+
+We now compile Guix from scratch.
+
+Create, install and run a recent version of the guix-daemon by
+compiling the guix repository you have installed with git in
+step 2. Follow [[https://github.com/pjotrp/guix-notes/blob/master/INSTALL.org#building-gnu-guix-from-source-using-guix][these]] steps carefully after
+
+: cd ~/genenetwork/guix-gn-deploy
+
+Make sure to restart the guix daemon and run guix client from this
+directory.
+
+** Install GN2
+
+Reinstall genenetwork2 using the new tree
+
+#+begin_src bash
+env GUIX_PACKAGE_PATH=~/genenetwork/guix-bioinformatics/ ./pre-inst-env guix package -i genenetwork2 --substitute-urls="http://guix.genenetwork.org https://mirror.guixsd.org"
+#+end_src bash
+
+Note the use of ./pre-inst-env here!
+
+Actually, it should be the same installation as in step 4, so nothing
+gets downloaded.
+
+** Run GN2
+
+Make a note of the paths with
+
+#+begin_src bash
+./pre-inst-env guix package --search-paths
+#+end_src bash
+
+or this should also work if guix is installed
+
+#+begin_src bash
+guix package --search-paths
+#+end_src bash
+
+After setting the paths for the server
+
+#+begin_src bash
+export PATH=~/.guix-profile/bin:$PATH
+export PYTHONPATH="$HOME/.guix-profile/lib/python2.7/site-packages"
+export R_LIBS_SITE="$HOME/.guix-profile/site-library/"
+export GUIX_GTK3_PATH="$HOME/.guix-profile/lib/gtk-3.0"
+export GI_TYPELIB_PATH="$HOME/.guix-profile/lib/girepository-1.0"
+export XDG_DATA_DIRS="$HOME/.guix-profile/share"
+export GIO_EXTRA_MODULES="$HOME/.guix-profile/lib/gio/modules"
+#+end_src bash
+
+run the main script (in ~/.guix-profile/bin)
+
+#+begin_src bash
+genenetwork2
+#+end_src bash
+
+will start the default server which listens on port 5003, i.e.,
+http://localhost:5003/.
+
+OK, we are where we were before with step 4. Only difference is that we
+used our own compiled guix server.
diff --git a/doc/README.org b/doc/README.org
index b38ea664..a39ef603 100644
--- a/doc/README.org
+++ b/doc/README.org
@@ -2,33 +2,27 @@
 
 * Table of Contents                                                     :TOC:
  - [[#introduction][Introduction]]
- - [[#quick-installation-recipe][Quick installation recipe]]
-   - [[#step-1-install-gnu-guix][Step 1: Install GNU Guix]]
-   - [[#step-2-checkout-the-gn2-git-repositories][Step 2: Checkout the GN2 git repositories]]
-   - [[#step-3-authorize-the-gn-guix-server][Step 3: Authorize the GN Guix server]]
-   - [[#step-4-install-and-run-gn2][Step 4: Install and run GN2]]
+ - [[#install][Install]]
+   - [[#tarball][Tarball]]
+   - [[#docker][Docker]]
+   - [[#with-source][With source]]
+ - [[#running-gn2][Running GN2]]
  - [[#run-mysql-server][Run MySQL server]]
+   - [[#install-mysql-with-gnu-guix][Install MySQL with GNU GUIx]]
+   - [[#load-the-small-database-in-mysql][Load the small database in MySQL]]
  - [[#gn2-dependency-graph][GN2 Dependency Graph]]
- - [[#source-deployment][Source deployment]]
-   - [[#run-your-own-copy-of-gn2][Run your own copy of GN2]]
-   - [[#set-up-nginx-port-forwarding][Set up nginx port forwarding]]
- - [[#source-deployment-and-other-information-on-reproducibility][Source deployment and other information on reproducibility]]
-   - [[#update-to-recent-guix][Update to recent guix]]
-   - [[#install-gn2][Install GN2]]
-   - [[#run-gn2][Run GN2]]
+ - [[#working-with-the-gn2-source-code][Working with the GN2 source code]]
  - [[#trouble-shooting][Trouble shooting]]
    - [[#importerror-no-module-named-jinja2][ImportError: No module named jinja2]]
    - [[#error-can-not-find-directory-homegn2_data][ERROR: can not find directory $HOME/gn2_data]]
    - [[#cant-run-a-module][Can't run a module]]
    - [[#rpy2-error-show-now-found][Rpy2 error 'show' now found]]
+   - [[#mysql-cant-connect-server-through-socket-error][Mysql can't connect server through socket ERROR]]
+ - [[#read-more][Read more]]
  - [[#irc-session][IRC session]]
 
 * Introduction
 
-If you want to understand the architecture of GN2 read
-[[Architecture.org]].  The rest of this document is mostly on deployment
-of GN2.
-
 Large system deployments can get very [[http://biogems.info/contrib/genenetwork/gn2.svg ][complex]]. In this document we
 explain the GeneNetwork version 2 (GN2) reproducible deployment system
 which is based on GNU Guix (see also [[https://github.com/pjotrp/guix-notes/blob/master/README.md][Guix-notes]]). The Guix
@@ -37,195 +31,113 @@ 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]].
+'gn-latest' branches of [[https://gitlab.com/genenetwork/guix-bioinformatics][Guix bioinformatics]] and [[https://gitlab.com/genenetwork/guix][GNU Guix]].
 
 For a full view of runtime dependencies as defined by GNU Guix, see
-the [[#gn2-dependency-graph][GN2 Dependency Graph]].
-
-* Quick installation recipe
-
-This is a recipe for quick and dirty installation of GN2. For
-convenience everything is installed as root, though in reality only
-GNU Guix has to be installed as root. I tested this recipe on a fresh
-install of Debian 8.3.0 (in KVM) though it should work on any modern
-Linux distribution (including CentOS). For more elaborate installation
-instructions see [[#source-deployment][Source deployment]].
-
-Note that GN2 consists of an approx. 5 GB installation including
-database. If you use a virtual machine we recommend to use at least
-double.
-
-** Step 1: Install GNU Guix
-
-Fetch the GNU Guix binary from [[https://www.gnu.org/software/guix/download/][here]] (middle panel) and follow
-[[https://www.gnu.org/software/guix/manual/html_node/Binary-Installation.html][instructions]]. Essentially, download and unpack the tar ball (which
-creates directories in /gnu and /var/guix), add build users and group
-(Guix builds software as unpriviliged users) and run the Guix daemon
-after fixing the paths (also known as the 'profile').
-
-Once you have succeeded, you have to [[https://github.com/pjotrp/guix-notes/blob/master/INSTALL.org#set-the-key][set the key]] (getting permission
-to download binaries from the GNU server) and you should be able to
-install the hello package using binary packages (no building)
-
-#+begin_src bash
-export PATH=~/.guix-profile/bin:$PATH
-guix pull
-guix package -i hello --dry-run
-#+end_src
-
-Which should show something like
-
-: The following files would be downloaded:
-:   /gnu/store/zby49aqfbd9w9br4l52mvb3y6f9vfv22-hello-2.10
-:   ...
-#+end_src
-
-means binary installs.  The actual installation command of 'hello' is
-
-#+begin_src bash
-guix package -i hello
-hello
-  Hello, world!
-#+end_src
-
-If you actually see things building it means that Guix is not yet
-properly installed and up-to-date, i.e., the key is missing or you
-need to do a 'guix pull'. Press Ctrl-C to interrupt.
-
-If you need more help we have another writeup in [[https://github.com/pjotrp/guix-notes/blob/master/INSTALL.org#binary-installation][guix-notes]]. To get
-rid of the locale warning see [[https://github.com/pjotrp/guix-notes/blob/master/INSTALL.org#set-locale][set-locale]].
-
-** Step 2: Checkout the GN2 git repositories
+an example of the [[#gn2-dependency-graph][GN2 Dependency Graph]].
 
-To fixate the software dependency graph GN2 uses git repositories of
-Guix packages. First install git if it is missing
+* Install
 
-#+begin_src bash
-guix package -i git
-export GIT_SSL_CAINFO=/etc/ssl/certs/ca-certificates.crt
-#+end_src
+The quickest way to install GN2 is by using a binary installation
+(tarball or Docker image).  These installations are bundled by GNU
+Guix and include all dependencies. You can install GeneNetwork on most
+Linux distributions, including Debian, Ubuntu, Fedora and CentOS,
+provided you have administrator privileges (root). The alternative is
+a Docker installation.
 
-check out the git repositories (gn-deploy branch)
+** Tarball
 
-#+begin_src bash
-cd ~
-mkdir genenetwork
-cd genenetwork
-git clone --branch gn-deploy https://github.com/genenetwork/guix-bioinformatics
-git clone --branch gn-deploy --recursive https://github.com/genenetwork/guix guix-gn-deploy
-cd guix-gn-deploy
-#+end_src bash
+Download the ~800Mb tarball from
+[[http://files.genenetwork.org/software/binary_tarball/]]. Validate the checksum and
+unpack to root, for example
 
-To test whether this is working try:
+: tar xvzf genenetwork2-2.10rc3-1538ffd-tarball-pack.tar.gz
+: mv /gnu /
+: mv /opt/genenetwork2 /opt/
 
-#+begin_src bash
-#+end_src bash
+Now you shoud be able to start the server with
 
+: /opt/genenetwork2/bin/genenetwork2
 
-** Step 3: Authorize the GN Guix server
+When the server stops with a MySQL error [[#run-mysql-server][Run MySQL server]]
+and set SQL_URI to point at it. For example:
 
-GN2 has its own GNU Guix binary distribution server. To trust it you have
-to add the following key
+: export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s
 
-#+begin_src scheme
-(public-key
- (ecc
-  (curve Ed25519)
-  (q #11217788B41ADC8D5B8E71BD87EF699C65312EC387752899FE9C888856F5C769#)
- )
-)
-#+end_src
+See also [[#mysql-cant-connect-server-through-socket-error][Mysql can't connect server through socket ERROR]].
 
-by pasting it into the command
+** Docker
 
-#+begin_src bash
-guix archive --authorize
-#+end_src
+Docker images are also available through
+[[http://files.genenetwork.org/software/]]. Validate the checksum and run
+with [[https://docs.docker.com/engine/reference/commandline/load/][Docker load]].
 
-and hit Ctrl-D.
+** With source
 
-Now you can use the substitute server to install GN2 binaries.
+For more elaborate installation instructions on deploying GeneNetwork from
+source see [[#source-deployment][Source deployment]].
 
-** Step 4: Install and run GN2
+* Running GN2
 
-Since this is a quick and dirty install we are going to override the
-GNU Guix package path by pointing the package path to our repository:
+Default settings for GN2 are listed in a file called
+[[../etc/default_settings.py][default_settings.py]]. You can copy this file and pass it as a new
+parameter to the genenetwork2 command, e.g.
 
-#+begin_src bash
-rm /root/.config/guix/latest
-ln -s ~/genenetwork/guix-gn-deploy/ /root/.config/guix/latest
-#+end_src
+: genenetwork2 mysettings.py
 
-Now check whether you can find the GN2 package with
+or you can set environment variables to override individual parameters, e.g.
 
-#+begin_src bash
-env GUIX_PACKAGE_PATH=~/genenetwork/guix-bioinformatics/ guix package -A genenetwork2
-  genenetwork2    2.0-a8fcff4     out     gn/packages/genenetwork.scm:144:2
-#+end_src
-
-(ignore the source file newer then ... messages, this is caused by the
-/root/.config/guix/latest override).
+: env SERVER_PORT=5004 SQL_URI=mysql://user:pwd@dbhostname/db_webqtl genenetwork2
 
-And install with
+the debug and logging switches can be particularly useful when
+developing GN2.
 
-#+begin_src bash
-env GUIX_PACKAGE_PATH=~/genenetwork/guix-bioinformatics/ \
-  guix package -i genenetwork2 \
-  --substitute-urls="http://guix.genenetwork.org"
-#+end_src
-
-Note: the order of the substitute url's may make a difference in speed
-(put the one first that is fastest for your location and time of day).
-
-Note: if your system starts building or gives an error it may well be
-Step 3 did not succeed. The installation should actually be smooth at
-this point and only do binary installs (no compiling).
-
-After installation you should be able to run genenetwork2 after updating
-the Guix suggested environment vars. Check the output of
-
-#+begin_src bash
-guix package --search-paths
-export PYTHONPATH="/root/.guix-profile/lib/python2.7/site-packages"
-export R_LIBS_SITE="/root/.guix-profile/site-library/"
-#+end_src
+* Run MySQL server
+** Install MySQL with GNU GUIx
 
-and copy-paste the listed exports into the terminal before running:
+These are the steps you can take to install a fresh installation of
+mysql (which comes as part of the GNU Guix genenetwork2 install).
 
-#+begin_src bash
-genenetwork2
-#+end_src
+As root configure and run
 
-It will complain that the database is missing. See the next section on
-running MySQL server for downloading and installing a MySQL GN2
-database. After installing the database restart genenetwork2 and point
-your browser at [[http://localhost:5003/]].
+:  adduser mysql && addgroup mysql
+:  mysqld --datadir=/var/mysql --initialize-insecure
+:  mkdir -p /var/run/mysqld
+:  chown mysql.mysql ~/mysql /var/run/mysqld
+:  su mysql -c mysqld --datadir=/var/mysql --explicit_defaults_for_timestamp -P 12048
 
-End of the GN2 installation recipe!
+/etc/my.cnf
+[mysqld]
+user=root
 
-* Run MySQL server
+** Load the small database in MySQL
 
 At this point we require the underlying distribution to install and
-run mysqld. Currently we have two databases for deployment,
+run mysqld (see next section for GNU Guix). Currently we have two databases for deployment,
 'db_webqtl_s' is the small testing database containing experiments
 from BXD mice and 'db_webqtl_plant' which contains all plant related
 material.
 
 Download one database from
 
-http://files.genenetwork.org/raw_database/
-https://s3.amazonaws.com/genenetwork2/db_webqtl_s.zip
+[[http://files.genenetwork.org/raw_database/]]
+
+[[https://s3.amazonaws.com/genenetwork2/db_webqtl_s.zip]]
 
 Check the md5sum.
 
 After installation inflate the database binary in the MySQL directory
-(this installation path is subject to change soon)
 
+: cd ~/mysql
 : chown -R mysql:mysql db_webqtl_s/
 : chmod 700 db_webqtl_s/
 : chmod 660 db_webqtl_s/*
 
-restart MySQL service (mysqld). Login as root and
+restart MySQL service (mysqld). Login as root
+
+: myslq -u root
+
+and
 
 : mysql> show databases;
 : +--------------------+
@@ -241,9 +153,12 @@ Set permissions and match password in your settings file below:
 
 : mysql> grant all privileges on db_webqtl_s.* to gn2@"localhost" identified by 'mysql_password';
 
+You may need to change "localhost" to whatever domain you are
+connecting from (mysql will give an error).
+
 Note that if the mysql connection is not working, try connecting to
 the IP address and check server firewall, hosts.allow and mysql IP
-configuration.
+configuration (see below).
 
 Note for the plant database you can rename it to db_webqtl_s, or
 change the settings in etc/default_settings.py to match your path.
@@ -255,183 +170,9 @@ Graph of all runtime dependencies as installed by GNU Guix.
 #+ATTR_HTML: :title GN2_graph
 http://biogems.info/contrib/genenetwork/gn2.svg
 
-* Source deployment
-
-This section gives a more elaborate instruction for installing GN2
-from source.
-
-First execute above 4 steps:
-
-   - [[#step-1-install-gnu-guix][Step 1: Install GNU Guix]]
-   - [[#step-2-checkout-the-gn2-git-repositories][Step 2: Checkout the GN2 git repositories]]
-   - [[#step-3-authorize-the-gn-guix-server][Step 3: Authorize the GN Guix server]]
-   - [[#step-4-install-and-run-gn2-][Step 4: Install and run GN2 ]]
-
-
-** Run your own copy of GN2
-
-At some point you may want to fix the source code. Assuming you have
-Guix and Genenetwork2 installed (as described above) clone the GN2
-repository from https://github.com/genenetwork/genenetwork2.
-
-Copy-paste the paths into your terminal (mainly so PYTHON_PATH and
-R_LIBS_SITE are set) from the information given by guix:
-
-: guix package --search-paths
-
-Inside the repository:
-
-: cd genenetwork2
-: ./bin/genenetwork2
-
-Will fire up your local repo http://localhost:5003/ using the
-settings in ./etc/default_settings.py. These settings may
-not reflect your system. To override settings create your own from a copy of
-default_settings.py and pass it into GN2 with
-
-: ./bin/genenetwork2 $HOME/my_settings.py
-
-and everything *should* work (note the full path to the settings
-file). This way we develop against the exact same dependency graph of
-software.
-
-If something is not working, take a hint from the settings file
-that comes in the Guix installation. It sits in something like
+* Working with the GN2 source code
 
-: cat ~/.guix-profile/lib/python2.7/site-packages/genenetwork2-2.0-py2.7.egg/etc/default_settings.py
-
-** Set up nginx port forwarding
-
-nginx can be used as a reverse proxy for GN2. For example, we want to
-expose GN2 on port 80 while it is running on port 5003. Essentially
-the configuration looks like
-
-#+begin_src js
-    server {
-        listen 80;
-        server_name test-gn2.genenetwork.org;
-        access_log  logs/test-gn2.access.log;
-
-        proxy_connect_timeout       3000;
-        proxy_send_timeout          3000;
-        proxy_read_timeout          3000;
-        send_timeout                3000;
-
-        location / {
-            proxy_set_header   Host      $http_host;
-            proxy_set_header   Connection keep-alive;
-            proxy_set_header   X-Real-IP $remote_addr;
-            proxy_set_header   X-Forwarded-For $proxy_add_x_forwarded_for;
-            proxy_set_header   X-Forwarded-Host $server_name;
-            proxy_pass         http://127.0.0.1:5003;
-        }
-}
-#+end_src js
-
-Install the nginx webserver (as root)
-
-: guix package -i nginx
-
-The nginx example configuration examples can be found in the Guix
-store through
-
-: ls -l /root/.guix-profile/sbin/nginx
-: lrwxrwxrwx 3 root guixbuild 66 Dec 31  1969 /root/.guix-profile/sbin/nginx -> /gnu/store/g0wrcl5z27rmk5b52rldzvk1bzzbnz2l-nginx-1.8.1/sbin/nginx
-
-Use that path
-
-: ls /gnu/store/g0wrcl5z27rmk5b52rldzvk1bzzbnz2l-nginx-1.8.1/share/nginx/conf/
-:   fastcgi.conf            koi-win             scgi_params
-:   fastcgi.conf.default    mime.types          scgi_params.default
-:   fastcgi_params          mime.types.default  uwsgi_params
-:   fastcgi_params.default  nginx.conf          uwsgi_params.default
-:   koi-utf                 nginx.conf.default  win-utf
-
-And copy any relevant files to /etc/nginx.  A configuration file for
-GeneNetwork (reverse proxy) port forwarding can be found in the source
-repository under ./etc/nginx-genenetwork.conf. Copy this file to /etc
-(still as root)
-: cp ./etc/nginx-genenetwork.conf /etc/nginx/
-
-Make dirs
-
-: mkdir -p /var/spool/nginx/logs
-
-Add users
-
-: adduser nobody ; addgroup nobody
-
-Run nginx
-
-: /root/.guix-profile/sbin/nginx -c /etc/nginx/nginx-genenetwork.conf -p /var/spool/nginx
-
-* Source deployment and other information on reproducibility
-
-See the document [[GUIX-Reproducible-from-source.org]].
-
-** Update to recent guix
-
-We now compile Guix from scratch.
-
-Create, install and run a recent version of the guix-daemon by
-compiling the guix repository you have installed with git in
-step 2. Follow [[https://github.com/pjotrp/guix-notes/blob/master/INSTALL.org#building-gnu-guix-from-source-using-guix][these]] steps carefully after
-
-: cd ~/genenetwork/guix-gn-deploy
-
-Make sure to restart the guix daemon and run guix client from this
-directory.
-
-** Install GN2
-
-Reinstall genenetwork2 using the new tree
-
-#+begin_src bash
-env GUIX_PACKAGE_PATH=~/genenetwork/guix-bioinformatics/ ./pre-inst-env guix package -i genenetwork2 --substitute-urls="http://guix.genenetwork.org https://mirror.guixsd.org"
-#+end_src bash
-
-Note the use of ./pre-inst-env here!
-
-Actually, it should be the same installation as in step 4, so nothing
-gets downloaded.
-
-** Run GN2
-
-Make a note of the paths with
-
-#+begin_src bash
-./pre-inst-env guix package --search-paths
-#+end_src bash
-
-or this should also work if guix is installed
-
-#+begin_src bash
-guix package --search-paths
-#+end_src bash
-
-After setting the paths for the server
-
-#+begin_src bash
-export PATH=~/.guix-profile/bin:$PATH
-export PYTHONPATH="$HOME/.guix-profile/lib/python2.7/site-packages"
-export R_LIBS_SITE="$HOME/.guix-profile/site-library/"
-export GUIX_GTK3_PATH="$HOME/.guix-profile/lib/gtk-3.0"
-export GI_TYPELIB_PATH="$HOME/.guix-profile/lib/girepository-1.0"
-export XDG_DATA_DIRS="$HOME/.guix-profile/share"
-export GIO_EXTRA_MODULES="$HOME/.guix-profile/lib/gio/modules"
-#+end_src bash
-
-run the main script (in ~/.guix-profile/bin)
-
-#+begin_src bash
-genenetwork2
-#+end_src bash
-
-will start the default server which listens on port 5003, i.e.,
-http://localhost:5003/.
-
-OK, we are where we were before with step 4. Only difference is that we
-used our own compiled guix server.
+See [[development.org]].
 
 * Trouble shooting
 
@@ -479,6 +220,31 @@ R_LIBS_SITE. Please check your GNU Guix GN2 installation paths,
 you man need to reinstall. Note that this may be the point you
 may want to start using profiles (see profile section).
 
+** Mysql can't connect server through socket ERROR
+
+The following error
+
+: sqlalchemy.exc.OperationalError: (_mysql_exceptions.OperationalError) (2002, 'Can\'t connect to local MySQL server through socket \'/run/mysqld/mysqld.sock\' (2 "No such file or directory")')
+
+means that MySQL is trying to connect locally to a non-existent MySQL
+server, something you may see in a container. Typically replicated with something like
+
+: mysql -h localhost
+
+try to connect over the network interface instead, e.g.
+
+: mysql -h 127.0.0.1
+
+if that works run genenetwork after setting SQL_URI to something like
+
+: export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s
+
+* Read more
+
+If you want to understand the architecture of GN2 read
+[[Architecture.org]].  The rest of this document is mostly on deployment
+of GN2.
+
 * IRC session
 
 Here an IRC session where we installed GN2 from scratch using GNU Guix
diff --git a/doc/development.org b/doc/development.org
new file mode 100644
index 00000000..bbb6084f
--- /dev/null
+++ b/doc/development.org
@@ -0,0 +1,23 @@
+* Development
+
+After cloning the git source tree you can run the contained GN2 using
+an existing GN2_PROFILE, i.e., use a profile that was create to run a
+binary installation of GN2. This profile may be found by typing
+
+: which genenetwork2
+:   /home/wrk/opt/gn-latest-guix/bin/genenetwork2
+
+An example of running the development version would be
+
+: env GN2_PROFILE=/home/wrk/opt/gn-latest-guix ./bin/genenetwork2
+
+Profiles are stored in /gnu/store, so you may pick one up there
+
+: readlink -f $(dirname $(dirname `which genenetwork2`))
+:   /gnu/store/dvckpaw770b00l6rv4ijql8wrk11iypv-profile
+
+and use that instead.
+
+Note that the genenetwork2 script sets up the environment for running
+the webserver. This includes path to R modules and python modules. These
+are output on startup. To make sure there is no environment pollution you can
diff --git a/etc/VERSION b/etc/VERSION
new file mode 100644
index 00000000..1785aa28
--- /dev/null
+++ b/etc/VERSION
@@ -0,0 +1 @@
+2.10rc3
diff --git a/etc/default_settings.py b/etc/default_settings.py
index 6acea637..4f3a6f5c 100644
--- a/etc/default_settings.py
+++ b/etc/default_settings.py
@@ -9,6 +9,8 @@
 #   env LOG_SQL=True USE_REDIS=False ./bin/genenetwork2
 #   env LOG_LEVEL=DEBUG ./bin/genenetwork2 ~/gn2_settings.py
 #
+# Typically you need to set GN2_PROFILE too.
+#
 # Note also that in the near future we will additionally fetch
 # settings from a JSON file
 #
@@ -18,10 +20,9 @@
 import os
 import sys
 
-GN_VERSION = open("../VERSION","r").read()
+GN_VERSION = open("../etc/VERSION","r").read()
 SQL_URI = "mysql://gn2:mysql_password@localhost/db_webqtl_s"
-SQLALCHEMY_DATABASE_URI = 'mysql://gn2:mysql_password@localhost/db_webqtl_s'
-SQLALCHEMY_POOL_RECYCLE = 3600
+SQL_ALCHEMY_POOL_RECYCLE = 3600
 GN_SERVER_URL = "http://localhost:8880/"
 
 # ---- Flask configuration (see website)
@@ -45,24 +46,24 @@ WEBSERVER_DEPLOY = None     # Deployment specifics (nyi)
 LOG_LEVEL       = 'WARNING' # Logger mode (DEBUG|INFO|WARNING|ERROR|CRITICAL)
 LOG_LEVEL_DEBUG = '0'       # logger.debugf log level (0-5, 5 = show all)
 LOG_SQL         = 'False'   # Log SQL/backend and GN_SERVER calls
-LOG_SQLALCHEMY  = 'False'
+LOG_SQL_ALCHEMY = 'False'
 LOG_BENCH       = True      # Log bench marks
 
 USE_REDIS       = True      # REDIS caching (note that redis will be phased out)
 USE_GN_SERVER   = 'False'   # Use GN_SERVER SQL calls
+HOME            = os.environ['HOME']
 
-# Paths to JS libraries
-
-TWITTER_POST_FETCHER_JS_PATH = os.environ['HOME']+"/genenetwork/Twitter-Post-Fetcher"
+# ---- Path overrides for Genenetwork - the defaults are normally
+#      picked up from Guix or in the HOME directory
 
-# ---- Path overrides for Genenetwork
 # TMPDIR is normally picked up from the environment
-HOME=os.environ['HOME']
-LOGFILE = HOME+"/genenetwork2.log"
-GENENETWORK_FILES = HOME+"/gn2_data"  # base dir for all static data files
-LOCAL_PRIVATE_FILES = HOME+"/gn2_private_data" # private static data files
+# GENENETWORK_FILES   = HOME+"/gn2_data"  # base dir for all static data files
+# PRIVATE_FILES = HOME+"/gn2_private_data" # private static data files (unused)
+
+# ---- Local path to JS libraries - for development modules (only)
+# GN2_JS_PATH = os.environ['HOME']+"/genenetwork/javascript" (unused)
 
-# ---- GN2 Executables
-PYLMM_COMMAND = str.strip(os.popen("which pylmm_redis").read())
-PLINK_COMMAND = str.strip(os.popen("which plink2").read())
-GEMMA_COMMAND = str.strip(os.popen("which gemma").read())
+# ---- GN2 Executables (overwrite for testing only)
+# PYLMM_COMMAND = str.strip(os.popen("which pylmm_redis").read())
+# PLINK_COMMAND = str.strip(os.popen("which plink2").read())
+# GEMMA_COMMAND = str.strip(os.popen("which gemma").read())
diff --git a/test/lib/main_web_functionality.rb b/test/lib/main_web_functionality.rb
index ec61de2d..9ae49995 100644
--- a/test/lib/main_web_functionality.rb
+++ b/test/lib/main_web_functionality.rb
@@ -13,16 +13,20 @@ describe MainWebFunctionality do
 
     it "Get to trait page" do
       page = @agent.get($host)
+      p page
       form = page.forms[1]
       form.buttons[0].value.must_equal "Search" # main menu is loaded
 
       # http://localhost:5003/search?species=mouse&group=BXD&type=Hippocampus+mRNA&dataset=HC_M2_0606_P&search_terms_or=&search_terms_and=MEAN%3D%2815+16%29+LRS%3D%2823+46%29&FormID=searchResult
+      form.fields[0].value.must_equal "searchResult"
       form.fields[2].value = "MEAN=(15 16) LRS=(23 46)"
       form.fields[3].value = "mouse"
       form.fields[4].value = "BXD"
       form.fields[5].value = "Hippocampus mRNA"
       form.fields[6].value = "HC_M2_0606_P"
       search_page = @agent.submit(form, form.buttons.first)
+      p "=================="
+      p search_page
       probe_link = search_page.links.find { |l| l.text =~ /1435395_s_at/ }
       probe_link.uri.to_s.must_equal "/show_trait?trait_id=1435395_s_at&dataset=HC_M2_0606_P"
       show_trait_page = probe_link.click
diff --git a/wqflask/base/webqtlConfig.py b/wqflask/base/webqtlConfig.py
index 1e47e183..e5f10edf 100644
--- a/wqflask/base/webqtlConfig.py
+++ b/wqflask/base/webqtlConfig.py
@@ -65,7 +65,7 @@ ENSEMBLETRANSCRIPT_URL="http://useast.ensembl.org/Mus_musculus/Lucene/Details?sp
 # want to reach this base dir
 assert_writable_dir(TEMPDIR)
 
-TMPDIR               = mk_dir(TEMPDIR+'gn2')
+TMPDIR               = mk_dir(TEMPDIR+'/gn2/')
 assert_writable_dir(TMPDIR)
 
 CACHEDIR             = mk_dir(TMPDIR+'/cache/')
diff --git a/wqflask/maintenance/gen_select_dataset.py b/wqflask/maintenance/gen_select_dataset.py
index e5726656..a5fd86e2 100644
--- a/wqflask/maintenance/gen_select_dataset.py
+++ b/wqflask/maintenance/gen_select_dataset.py
@@ -57,7 +57,7 @@ import urlparse
 
 from pprint import pformat as pf
 
-#Engine = sa.create_engine(zach_settings.SQLALCHEMY_DATABASE_URI)
+#Engine = sa.create_engine(zach_settings.SQL_URI)
 
 # build MySql database connection
 
diff --git a/wqflask/utility/tools.py b/wqflask/utility/tools.py
index c28c617a..d46a84ba 100644
--- a/wqflask/utility/tools.py
+++ b/wqflask/utility/tools.py
@@ -205,21 +205,24 @@ SQL_URI            = get_setting('SQL_URI')
 LOG_LEVEL          = get_setting('LOG_LEVEL')
 LOG_LEVEL_DEBUG    = get_setting_int('LOG_LEVEL_DEBUG')
 LOG_SQL            = get_setting_bool('LOG_SQL')
-LOG_SQLALCHEMY     = get_setting_bool('LOG_SQLALCHEMY')
+LOG_SQL_ALCHEMY    = get_setting_bool('LOG_SQL_ALCHEMY')
 LOG_BENCH          = get_setting_bool('LOG_BENCH')
 LOG_FORMAT         = "%(message)s"    # not yet in use
 USE_REDIS          = get_setting_bool('USE_REDIS')
 USE_GN_SERVER      = get_setting_bool('USE_GN_SERVER')
 
 GENENETWORK_FILES  = get_setting('GENENETWORK_FILES')
-TEMP_TRAITS        = get_setting('TEMP_TRAITS')
+GUIX_JS_PATH       = get_setting('GUIX_JS_PATH')
+assert_dir(GUIX_JS_PATH)
 
 PYLMM_COMMAND      = pylmm_command()
 GEMMA_COMMAND      = gemma_command()
-GEMMA_RESULTS_PATH = get_setting('GEMMA_RESULTS_PATH')
 PLINK_COMMAND      = plink_command()
 TEMPDIR            = tempdir() # defaults to UNIX TMPDIR
 
+TWITTER_POST_FETCHER_JS_PATH = GUIX_JS_PATH + "/Twitter-Post-Fetcher"
+assert_dir(TWITTER_POST_FETCHER_JS_PATH)
+
 from six import string_types
 
 if os.environ.get('WQFLASK_OVERRIDES'):
@@ -234,5 +237,3 @@ if os.environ.get('WQFLASK_OVERRIDES'):
             else:
                 OVERRIDES[k] = cmd
             logger.debug(OVERRIDES)
-
-assert_dir(get_setting("TWITTER_POST_FETCHER_JS_PATH"))
diff --git a/wqflask/wqflask/database.py b/wqflask/wqflask/database.py
index 4df872ad..96c2c301 100644
--- a/wqflask/wqflask/database.py
+++ b/wqflask/wqflask/database.py
@@ -22,8 +22,8 @@ def init_db():
     # they will be registered properly on the metadata.  Otherwise
     # you will have to import them first before calling init_db()
     #import yourapplication.models
+    logger.info("Initializing database connection")
     import wqflask.model
-    logger.debug("Creating all model metadata")
     Base.metadata.create_all(bind=engine)
     logger.info("Done creating all model metadata")
 
diff --git a/wqflask/wqflask/marker_regression/marker_regression.py b/wqflask/wqflask/marker_regression/marker_regression.py
index 87532445..8882c515 100644
--- a/wqflask/wqflask/marker_regression/marker_regression.py
+++ b/wqflask/wqflask/marker_regression/marker_regression.py
@@ -37,7 +37,7 @@ from utility import temp_data
 from utility.benchmark import Bench
 from wqflask.marker_regression import gemma_mapping, rqtl_mapping, qtlreaper_mapping, plink_mapping
 
-from utility.tools import locate, locate_ignore_error, PYLMM_COMMAND, GEMMA_COMMAND, GEMMA_RESULTS_PATH, PLINK_COMMAND, TEMPDIR
+from utility.tools import locate, locate_ignore_error, PYLMM_COMMAND, GEMMA_COMMAND, PLINK_COMMAND, TEMPDIR
 from utility.external import shell
 from base.webqtlConfig import TMPDIR, GENERATED_TEXT_DIR
 
diff --git a/wqflask/wqflask/marker_regression/marker_regression_gn1.py b/wqflask/wqflask/marker_regression/marker_regression_gn1.py
index 49959a74..82a44796 100644
--- a/wqflask/wqflask/marker_regression/marker_regression_gn1.py
+++ b/wqflask/wqflask/marker_regression/marker_regression_gn1.py
@@ -1018,7 +1018,7 @@ class MarkerRegression(object):
         else:
             if self.selectedChr > -1:
                 for i, qtlresult in enumerate(self.qtlresults):
-                    if qtlresult['Chr'] != self.selectedChr:
+                    if qtlresult['chr'] != self.selectedChr:
                         continue
 
                     if i==0 and qtlresult['Mb'] >= Mb:
@@ -1027,7 +1027,7 @@ class MarkerRegression(object):
 
                     #the trait's position is between two traits
                     if i > 0 and self.qtlresults[i-1]['Mb'] < Mb and qtlresult['Mb'] >= Mb:
-                        locPixel = xLeftOffset + plotXScale*(self.qtlresults[i-1]['cM']+(qtlresult['cM']-self.qtlresults[i-1]['cM'])*(Mb - self.qtlresults[i-1]['Mb'])/(qtlresult['Mb']-self.qtlresults[i-1]['Mb']))
+                        locPixel = xLeftOffset + plotXScale*(self.qtlresults[i-1]['Mb']+(qtlresult['Mb']-self.qtlresults[i-1]['Mb'])*(Mb - self.qtlresults[i-1]['Mb'])/(qtlresult['Mb']-self.qtlresults[i-1]['Mb']))
                         break
 
                     #the trait's position is on the right of the last genotype
@@ -1036,11 +1036,12 @@ class MarkerRegression(object):
             else:
                 locPixel = xLeftOffset
                 for i, _chr in enumerate(self.ChrList):
-                    if _chr != Chr:
-                        locPixel += (self.ChrLengthDistList[i] + self.GraphInterval)*plotXScale
-                    else:
-                        locPixel += (Mb*(_chr[-1].cM-_chr[0].cM)/self.ChrLengthCMList[i])*plotXScale
-                        break
+                    if i < (len(self.ChrList)-1):
+                        if _chr != Chr:
+                            locPixel += (self.ChrLengthDistList[i] + self.GraphInterval)*plotXScale
+                        else:
+                            locPixel += (Mb*(_chr[-1].cM-_chr[0].cM)/self.ChrLengthCMList[i])*plotXScale
+                            break
         if locPixel >= 0 and self.plotScale == 'physic':
             traitPixel = ((locPixel, yZero), (locPixel-6, yZero+12), (locPixel+6, yZero+12))
             canvas.drawPolygon(traitPixel, edgeColor=pid.black, fillColor=self.TRANSCRIPT_LOCATION_COLOR, closed=1)
diff --git a/wqflask/wqflask/templates/base.html b/wqflask/wqflask/templates/base.html
index ec55ebeb..9ca3d63a 100644
--- a/wqflask/wqflask/templates/base.html
+++ b/wqflask/wqflask/templates/base.html
@@ -144,7 +144,7 @@
         <p>
           Development and source code on <a href="https://github.com/genenetwork/">github</a> with <a href="https://github.com/genenetwork/genenetwork2/issues">issue tracker</a> and <a href="https://github.com/genenetwork/genenetwork2/blob/master/README.md">documentation</a>. Join the <a href="http://listserv.uthsc.edu/mailman/listinfo/genenetwork-dev">mailing list</a> and find us on <a href="https://webchat.freenode.net/">IRC</a> (#genenetwork channel).
         {% if version: %}
-        <p><small>GeneNetwork v{{ version }}</small></p>
+        <p><small>GeneNetwork {{ version }}</small></p>
         {% endif %}
 
       </div>
diff --git a/wqflask/wqflask/templates/error.html b/wqflask/wqflask/templates/error.html
index c707a4fc..2f1e06fa 100644
--- a/wqflask/wqflask/templates/error.html
+++ b/wqflask/wqflask/templates/error.html
@@ -35,7 +35,7 @@
   </p>
 
   <pre>
-    GeneNetwork v{{ version }} {{ stack[0] }}
+    GeneNetwork {{ version }} {{ stack[0] }}
     {{ message }} (error)
     {{ stack[-3] }}
     {{ stack[-2] }}
@@ -50,7 +50,7 @@
   <a href="#Stack" class="btn btn-default" data-toggle="collapse">Toggle full stack trace</a>
   <div id="Stack" class="collapse">
     <pre>
-      GeneNetwork v{{ version }} {% for line in stack %} {{ line }}
+      GeneNetwork {{ version }} {% for line in stack %} {{ line }}
       {% endfor %}
     </pre>
   </div>
diff --git a/wqflask/wqflask/templates/marker_regression_gn1.html b/wqflask/wqflask/templates/marker_regression_gn1.html
index 4cea51b2..65debd10 100644
--- a/wqflask/wqflask/templates/marker_regression_gn1.html
+++ b/wqflask/wqflask/templates/marker_regression_gn1.html
@@ -14,7 +14,7 @@
         <input type="hidden" name="temp_uuid" value="{{ temp_uuid }}">
         <input type="hidden" name="trait_id" value="{{ this_trait.name }}">
         <input type="hidden" name="dataset" value="{{ dataset.name }}">
-        {% if mapping_method == "reaper" %}
+        {% if mapping_method == "reaper" or mapping_method == "rqtl_geno" %}
         <input type="hidden" name="genofile" value="{{ dataset.group.genofile }}">
         {% endif %}
         <input type="hidden" name="method" value="{{ mapping_method }}">
diff --git a/wqflask/wqflask/templates/show_trait.html b/wqflask/wqflask/templates/show_trait.html
index 56b6cc62..5a880647 100644
--- a/wqflask/wqflask/templates/show_trait.html
+++ b/wqflask/wqflask/templates/show_trait.html
@@ -129,6 +129,7 @@
     <script type="text/javascript" src="/static/new/js_external/d3-tip.min.js"></script>
     <script type="text/javascript" src="/static/new/js_external/jstat.min.js"></script>
     <script type="text/javascript" src="/static/new/js_external/shapiro-wilk.js"></script>
+    <script type="text/javascript" src="/static/new/js_external/saveSvgAsPng.js"></script>
     <script type="text/javascript" src="/static/new/javascript/colorbrewer.js"></script>
 
     <script type="text/javascript" src="/static/new/javascript/stats.js"></script>
diff --git a/wqflask/wqflask/templates/show_trait_statistics.html b/wqflask/wqflask/templates/show_trait_statistics.html
index 0a0e9990..ac44b656 100644
--- a/wqflask/wqflask/templates/show_trait_statistics.html
+++ b/wqflask/wqflask/templates/show_trait_statistics.html
@@ -94,12 +94,15 @@
                 <div class="tab-pane" id="probability_plot">
                     <div style="padding: 20px" class="form-horizontal">
                         {% if sample_groups|length != 1 %}
+                        Select Group:
                         <select class="prob_plot_samples_group">
                             {% for group, pretty_group in sample_group_types.items() %}
                                 <option value="{{ group }}">{{ pretty_group }}</option>
                             {% endfor %}
                         </select>
-                        <br><br>
+                        <button type="button" class="btn btn-default" id="down_prob_plot">Export as PNG</button>
+                        <br>
+                        <br>
                         {% endif %}
 
                         <div id="prob_plot_container">
diff --git a/wqflask/wqflask/user_manager.py b/wqflask/wqflask/user_manager.py
index 1e831896..f7fcd2d0 100644
--- a/wqflask/wqflask/user_manager.py
+++ b/wqflask/wqflask/user_manager.py
@@ -46,7 +46,7 @@ from wqflask.database import db_session
 from wqflask import model
 
 from utility import Bunch, Struct, after
-from utility.tools import LOG_SQL, LOG_SQLALCHEMY
+from utility.tools import LOG_SQL, LOG_SQL_ALCHEMY
 
 import logging
 from utility.logger import getLogger
@@ -69,7 +69,7 @@ class AnonUser(object):
         if self.cookie:
             logger.debug("already is cookie")
             self.anon_id = verify_cookie(self.cookie)
-            
+
         else:
             logger.debug("creating new cookie")
             self.anon_id, self.cookie = create_signed_cookie()
@@ -78,17 +78,17 @@ class AnonUser(object):
         @after.after_this_request
         def set_cookie(response):
             response.set_cookie(self.cookie_name, self.cookie)
-            
+
     def add_collection(self, new_collection):
         collection_dict = dict(name = new_collection.name,
                                created_timestamp = datetime.datetime.utcnow().strftime('%b %d %Y %I:%M%p'),
                                changed_timestamp = datetime.datetime.utcnow().strftime('%b %d %Y %I:%M%p'),
                                num_members = new_collection.num_members,
                                members = new_collection.get_members())
-                               
+
         Redis.set(self.key, json.dumps(collection_dict))
         Redis.expire(self.key, 60 * 60 * 24 * 5)
-            
+
     def delete_collection(self, collection_name):
         existing_collections = self.get_collections()
         updated_collections = []
@@ -106,7 +106,7 @@ class AnonUser(object):
                 updated_collections.append(this_collection)
 
         Redis.set(self.key, json.dumps(updated_collections))
-            
+
     def get_collections(self):
         json_collections = Redis.get(self.key)
         if json_collections == None or json_collections == "None":
@@ -117,7 +117,7 @@ class AnonUser(object):
                 collection['created_timestamp'] = datetime.datetime.strptime(collection['created_timestamp'], '%b %d %Y %I:%M%p')
                 collection['changed_timestamp'] = datetime.datetime.strptime(collection['changed_timestamp'], '%b %d %Y %I:%M%p')
             return collections
-            
+
     def import_traits_to_user(self):
         collections_list = json.loads(Redis.get(self.key))
         for collection in collections_list:
@@ -131,7 +131,7 @@ class AnonUser(object):
                 uc.members = json.dumps(collection['members'])
                 db_session.add(uc)
                 db_session.commit()
-            
+
     def display_num_collections(self):
         """
         Returns the number of collections or a blank string if there are zero.
@@ -217,7 +217,7 @@ class UserSession(object):
         """Actual sqlalchemy record"""
         # Only look it up once if needed, then store it
         try:
-            if LOG_SQLALCHEMY:
+            if LOG_SQL_ALCHEMY:
                 logging.getLogger('sqlalchemy.pool').setLevel(logging.DEBUG)
 
             # Already did this before
@@ -237,7 +237,7 @@ class UserSession(object):
 def before_request():
     g.user_session = UserSession()
     g.cookie_session = AnonUser()
-    
+
 class UsersManager(object):
     def __init__(self):
         self.users = model.User.query.all()
@@ -541,9 +541,9 @@ class LoginUser(object):
                 import_col = "true"
             else:
                 import_col = "false"
-            
-            #g.cookie_session.import_traits_to_user()           
-                
+
+            #g.cookie_session.import_traits_to_user()
+
             return self.actual_login(user, import_collections=import_col)
 
         else:
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index 24a7cbca..44ca8de8 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -53,7 +53,7 @@ from wqflask.ctl import ctl_analysis
 #from wqflask.trait_submission import submit_trait
 
 from utility import temp_data
-from utility.tools import SQL_URI,TEMPDIR,USE_REDIS,USE_GN_SERVER,GN_SERVER_URL,GN_VERSION
+from utility.tools import SQL_URI,TEMPDIR,USE_REDIS,USE_GN_SERVER,GN_SERVER_URL,GN_VERSION,TWITTER_POST_FETCHER_JS_PATH
 from utility.helper_functions import get_species_groups
 
 from base import webqtlFormData
@@ -152,8 +152,7 @@ def tmp_page(img_path):
 
 @app.route("/twitter/<path:filename>")
 def bd_files(filename):
-    bd_path = app.config['TWITTER_POST_FETCHER_JS_PATH']
-    return send_from_directory(bd_path, filename)
+    return send_from_directory(TWITTER_POST_FETCHER_JS_PATH, filename)
 
 #@app.route("/data_sharing")
 #def data_sharing_page():