From 7e973a20801953c7fb63b9e14636b830c0f2beb6 Mon Sep 17 00:00:00 2001
From: Paolo Cozzi <paolo.cozzi@ptp.it>
Date: Fri, 17 Nov 2017 12:54:38 +0100
Subject: [PATCH] Minor fixes

---
 compose/gbrowse/README.md             | 3 ++-
 compose/gbrowse/docker-compose.yml    | 4 ++++
 compose/gbrowse/gbrowse/gbrowse2.conf | 1 +
 3 files changed, 7 insertions(+), 1 deletion(-)

diff --git a/compose/gbrowse/README.md b/compose/gbrowse/README.md
index 99f081b..30346d4 100644
--- a/compose/gbrowse/README.md
+++ b/compose/gbrowse/README.md
@@ -142,7 +142,8 @@ Launch a gbrowse container:
 $ docker-compose run --no-deps --rm gbrowse /bin/bash
 $ cd /var/lib/gbrowse2/databases/gbrowse_syn/alignments
 $ gzip -d rice.aln.gz
-$ zcat rice.aln.gz perl | /usr/local/bin/gbrowse_syn_load_alignments_msa.pl -u root -p my-secret-pw --dsn='dbi:mysql:database=rice_synteny;host=db' -f clustalw -v -c -
+$ /usr/local/bin/gbrowse_syn_load_alignments_msa.pl -u root -p my-secret-pw --dsn='dbi:mysql:database=rice_synteny;host=db' -f clustalw -v -c rice.aln
+$ gzip --best rice.aln
 ```
 
 Then reach `gbrowse_syn` from this [link][local-gbrowse_syn]. More information on
diff --git a/compose/gbrowse/docker-compose.yml b/compose/gbrowse/docker-compose.yml
index ab03463..18aec51 100644
--- a/compose/gbrowse/docker-compose.yml
+++ b/compose/gbrowse/docker-compose.yml
@@ -31,6 +31,10 @@ services:
         source: gbrowse-cache
         target: /var/tmp/gbrowse2
 
+      - type: bind
+        source: ./gbrowse/gbrowse2.conf
+        target: /etc/apache2/conf-available/gbrowse2.conf
+
     links:
       - db
       - lb
diff --git a/compose/gbrowse/gbrowse/gbrowse2.conf b/compose/gbrowse/gbrowse/gbrowse2.conf
index f18267d..cbb1c28 100644
--- a/compose/gbrowse/gbrowse/gbrowse2.conf
+++ b/compose/gbrowse/gbrowse/gbrowse2.conf
@@ -32,6 +32,7 @@ ScriptAlias  "/gb2"      "/usr/lib/cgi-bin/gb2"
     SetHandler   fcgid-script
   </Location>
   FcgidInitialEnv GBROWSE_CONF /etc/gbrowse2
+  FcgidInitialEnv DOCUMENT_ROOT /var/www/html/
   # these directives prevent idle/busy timeouts and may need to be
   # adjusted up or down
   FcgidMinProcessesPerClass 6