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After you have carefully read the appropriate wiki pages: FAQ you can ask questions at the Biopieces Google Group.
Remember to state a reason for signing up to the group, since Google Groups are plagued by spam-bots.
Please report bugs and issues in the issue tracker here.
Several people have reported problems with Ruby's requirement on RubyInline.
Biopieces uses an external gem (or module) called RubyInline to allow embedded C code that speed certain things up dramatically, so RubyInline is great.
RubyInline should not be confused with the inline gem which is an entirely different gem that for
stupid reasons have been allowed on RubyForge even if RubyInline has been invoked by require inline
years before the confusing inline gem.
If running bp_test suggests that RubyInline is not installed, you should install it using the command:
sudo gem install RubyInline
Now, if you get the following error:
sudo gem install RubyInline
ERROR: Error installing RubyInline:
ZenTest requires RubyGems version ~> 1.8. Try 'gem update --system' to update
This indicates that your version of gem is too old. This has been observed on Debian, and Ubuntu.
One solution is to download, compile, and install your own version of Ruby along with the required gems gnuplot, narray, and RubyInline.
Remove everything Ruby from the system first and then download, compile and install Ruby from scratch. First prerequisites:
sudo apt-get install build-essential libyaml-dev
And then:
cd /usr/local/src
sudo wget http://ftp.ruby-lang.org/pub/ruby/1.9/ruby-1.9.3-p125.tar.gz
sudo tar -zxvf ruby-1.9.3-p125.tar.gz
cd ruby-1.9.3-p125
sudo ./configure
sudo ./make
sudo ./make install
sudo gem update --system
sudo gem install gnuplot
sudo gem install narray
sudo gem install RubyInline
This is what the ruby_installer.sh script in the download section does.
If you run the Biopieces installer or bp_test and encounter WARNINGS or ERRORS in the summary line like this:
Biopieces tested: 72 Tests run: 219 OK: 207 FAIL: 10 WARNING: 2 Time: 46 secs
This is most likely caused by missing auxiliary programs. Biopieces uses third-party programs required for specific Biopieces to work. When these programs are not found WARNINGS are issued and when testing the affected Biopieces ERRORS will be raised. However, the remaining Biopieces should work just fine. There is a list of required auxiliary programs here.
Now, to get rid of the warnings (and some of the errors) you need to find out what third-party
software is missing. Locate the Biopieces that when tested results in ERROR and run that Biopiece with the -? switch. The Description section should tell what
third-party programs are needed. So, to get e.g. create_blast_index
requires scan_for_matches which is found here.