Installing miRNAkey on Mac OS X 10.6 Snow Leopard

Submitted by John on Tue, 2011-02-01 16:33

The following is a transcript of an installation of miRNAkey on Mac OS X 10.6. Actually it has more do with installation of the prerequisites. There is a handy script included with the miRNAkey distribution but I elected to do it by hand since some version numbers had changed and the Fastx-Toolkit binaries were for 10.5, not 10.6.

Step 1: Install bwa

The Burrows-Wheeler Aligner can be downloaded from Sourceforge.

tar xvfj bwa-0.5.9.tar.bz2
cd bwa-0.5.9
make
sudo cp bwa /usr/local/bin/bwa

Step 2: Install Required Perl Modules

I should note that my Perl is a MacPorts install.

sudo cpan
cpan[1]> install Math::CDF

Spreadsheet::WriteExcel and Getopt::Long were already fine on our machine:

cpan[2]> install Spreadsheet::WriteExcel
Spreadsheet::WriteExcel is up to date (2.37).

cpan[3]> install Getopt::Long
Getopt::Long is up to date (2.38).

Prior to installing GD::Graph::bars I needed to install libgd:

curl -O http://www.libgd.org/releases/gd-2.0.35.tar.bz2
tar xfjv gd-2.0.35.tar.bz2
cd gd-2.0.35
./configure
make
sudo make install

The GD perl module would not install because some tests would not pass:

Running make test
PERL_DL_NONLAZY=1 /opt/local/bin/perl "-MExtUtils::Command::MM" "-e" "test_harness(0, 'blib/lib', 'blib/arch')" t/*.t
t/GD.t ........ 1/12 Testing using png support.
t/GD.t ........ Failed 1/12 subtests
(less 1 skipped subtest: 10 okay)
t/Polyline.t .. ok  

Test Summary Report
-------------------
t/GD.t      (Wstat: 0 Tests: 12 Failed: 1)
  Failed test:  10
Files=2, Tests=13,  0 wallclock secs ( 0.02 usr  0.01 sys +  0.07 cusr  0.02 csys =  0.12 CPU)
Result: FAIL
Failed 1/2 test programs. 1/13 subtests failed.
make: *** [test_dynamic] Error 255
  LDS/GD-2.45.tar.gz
  /usr/bin/make test -- NOT OK
//hint// to see the cpan-testers results for installing this module, try:
  reports LDS/GD-2.45.tar.gz
Running make install
  make test had returned bad status, won't install without force

So I decided to install it with force:

sudo perl -MCPAN -e "CPAN::Shell->force(qw(install GD));"

Then I could install GD::Graph::bars:

sudo cpan
cpan[1]> install GD::Graph::bars

Step 3: Install FASTX-Toolkit

First, libgtextutils:

curl -O http://hannonlab.cshl.edu/fastx_toolkit/libgtextutils-0.6.tar.bz2
tar xvjf libgtextutils-0.6.tar.bz2
cd libgtextutils-0.6
./configure
make
sudo make install

Then the FASTX-Toolkit itself. Note the need to define PKG_CONFIG_PATH:

curl -O http://hannonlab.cshl.edu/fastx_toolkit/fastx_toolkit-0.0.13.tar.bz2
tar xjvf fastx_toolkit-0.0.13.tar.bz2
cd fastx_toolkit-0.0.13
export PKG_CONFIG_PATH=/usr/local/lib/pkgconfig:$PKG_CONFIG_PATH
./configure
make
sudo make install

Step 4: Install miRNAkey

For this, I simply put miRNAkey into the /Applications directory.

curl -O http://ibis.tau.ac.il/miRNAkey/downloads/miRNAkey.tar.gz
tar xvzf miRNAkey.tar.gz
mv miRNAkey /Applications/miRNAkey

Topic: 
Bioinformatics