Generating site

Gemfile.lock

@@ -1,51 +1,51 @@
 GEM
   remote: http://rubygems.org/
   specs:
-    activesupport (3.2.19)
+    activesupport (3.2.22)
       i18n (~> 0.6, >= 0.6.4)
       multi_json (~> 1.0)
     builder (3.2.2)
-    chunky_png (1.3.1)
+    chunky_png (1.3.4)
     coffee-script (2.2.0)
       coffee-script-source
       execjs
-    coffee-script-source (1.8.0)
-    compass (1.0.1)
+    coffee-script-source (1.9.1.1)
+    compass (1.0.3)
       chunky_png (~> 1.2)
-      compass-core (~> 1.0.1)
+      compass-core (~> 1.0.2)
       compass-import-once (~> 1.0.5)
       rb-fsevent (>= 0.9.3)
       rb-inotify (>= 0.9)
       sass (>= 3.3.13, < 3.5)
-    compass-core (1.0.1)
+    compass-core (1.0.3)
       multi_json (~> 1.0)
       sass (>= 3.3.0, < 3.5)
     compass-import-once (1.0.5)
       sass (>= 3.2, < 3.5)
-    cucumber (1.3.16)
+    cucumber (1.3.20)
       builder (>= 2.1.2)
       diff-lcs (>= 1.1.3)
       gherkin (~> 2.12)
       multi_json (>= 1.7.5, < 2.0)
-      multi_test (>= 0.1.1)
+      multi_test (>= 0.1.2)
     diff-lcs (1.2.5)
     em-websocket (0.5.1)
       eventmachine (>= 0.12.9)
       http_parser.rb (~> 0.6.0)
-    eventmachine (1.0.3)
-    execjs (1.4.0)
+    eventmachine (1.0.8)
+    execjs (1.4.1)
       multi_json (~> 1.0)
-    ffi (1.9.3)
+    ffi (1.9.10)
     gherkin (2.12.2)
       multi_json (~> 1.3)
-    haml (4.0.5)
+    haml (4.0.7)
       tilt
     hike (1.2.3)
     http_parser.rb (0.6.0)
     i18n (0.6.11)
-    json (1.8.1)
-    kramdown (1.4.1)
-    libv8 (3.16.14.3)
+    json (1.8.3)
+    kramdown (1.9.0)
+    libv8 (3.16.14.13)
     listen (1.3.1)
       rb-fsevent (>= 0.9.3)
       rb-inotify (>= 0.9)
@@ -79,33 +79,33 @@ GEM
       sprockets (~> 2.2)
       sprockets-helpers (~> 1.1.0)
       sprockets-sass (~> 1.1.0)
-    mini_portile (0.6.0)
-    multi_json (1.10.1)
-    multi_test (0.1.1)
-    nokogiri (1.6.3.1)
-      mini_portile (= 0.6.0)
-    rack (1.5.2)
-    rack-livereload (0.3.15)
+    mini_portile (0.6.2)
+    multi_json (1.11.2)
+    multi_test (0.1.2)
+    nokogiri (1.6.6.2)
+      mini_portile (~> 0.6.0)
+    rack (1.6.4)
+    rack-livereload (0.3.16)
       rack
-    rack-test (0.6.2)
+    rack-test (0.6.3)
       rack (>= 1.0)
-    rake (10.3.2)
-    rb-fsevent (0.9.4)
+    rake (10.4.2)
+    rb-fsevent (0.9.6)
     rb-inotify (0.9.5)
       ffi (>= 0.5.0)
-    rb-kqueue (0.2.3)
+    rb-kqueue (0.2.4)
       ffi (>= 0.5.0)
-    ref (1.0.5)
+    ref (2.0.0)
     rspec (2.99.0)
       rspec-core (~> 2.99.0)
       rspec-expectations (~> 2.99.0)
       rspec-mocks (~> 2.99.0)
     rspec-core (2.99.2)
     rspec-expectations (2.99.2)
       diff-lcs (>= 1.1.3, < 2.0)
-    rspec-mocks (2.99.2)
-    sass (3.4.3)
-    sprockets (2.12.2)
+    rspec-mocks (2.99.4)
+    sass (3.4.19)
+    sprockets (2.12.4)
       hike (~> 1.2)
       multi_json (~> 1.0)
       rack (~> 1.0)
@@ -115,22 +115,21 @@ GEM
     sprockets-sass (1.1.0)
       sprockets (~> 2.0)
       tilt (~> 1.1)
-    therubyracer (0.12.1)
+    therubyracer (0.12.2)
       libv8 (~> 3.16.14.0)
       ref
     thor (0.19.1)
-    thread (0.1.4)
+    thread (0.1.7)
     tilt (1.4.1)
     uglifier (2.4.0)
       execjs (>= 0.3.0)
       json (>= 1.8.0)
-    yard (0.8.7.4)
+    yard (0.8.7.6)
 
 PLATFORMS
   ruby
 
 DEPENDENCIES
-  bundler (~> 1.3)
   cucumber (~> 1.2)
   execjs
   middleman (~> 3.2.0)
@@ -142,3 +141,6 @@ DEPENDENCIES
   thread (~> 0.1.3)
   wdm (~> 0.1.0)
   yard (~> 0.7)
+
+BUNDLED WITH
+   1.10.6

scripts/create_biogems.info.sh

@@ -37,13 +37,14 @@ print_github_limits
 # curl http://github.com/api/v2/json/issues/list/pjotrp/bioruby-affy/open
 echo "RUNNING ./bin/fetch-gemlist.rb $* > data/gemlist_biogems.yaml"
 ./bin/fetch-gemlist.rb $* > data/gemlist_biogems.yaml
+[ $? -ne 0 ] && exit 1
 
 echo "RUNNING ./bin/fetch-geminfo.rb < data/gemlist_biogems.yaml >data/geminfo_biogems.yaml"
 ./bin/fetch-geminfo.rb < data/gemlist_biogems.yaml >data/geminfo_biogems.yaml
+[ $? -ne 0 ] && exit 1
 
-./bin/fetch-githubinfo.rg < data/geminfo_biogems.yaml > data/biogems.yaml
-
-bundle exec ./bin/fetch-geminfo.rb $* > ./data/biogems.yaml1
+echo "RUNNING ./bin/fetch-githubinfo.rb < data/geminfo_biogems.yaml > data/biogems.yaml"
+./bin/fetch-githubinfo.rb < data/geminfo_biogems.yaml > data/biogems.yaml
 [ $? -ne 0 ] && exit 1
 
 
@@ -54,13 +55,13 @@ bundle exec ./bin/fetch-geminfo.rb $* > ./data/biogems.yaml1
 # sed -e 's/!!null//g' < ./data/rubygems.yaml1 > ./data/rubygems.yaml
 
 # Create RSS feed for others to use
-echo "Fetching data/rss.xml"
-./bin/rss.rb $* > ./source/rss.xml
-[ $? -ne 0 ] && exit 1
+# echo "Fetching data/rss.xml"
+# ./bin/rss.rb $* > ./source/rss.xml
+# [ $? -ne 0 ] && exit 1
 
 # Generate site 
-bundle exec middleman build --verbose
-[ $? -ne 0 ] && exit 1
+# middleman build --verbose
+# [ $? -ne 0 ] && exit 1
 
 print_github_limits