Computational Techniques for Life Sciences

Installing an Application

Now we will try to install our own application from the web. We are going to try to install a spliced read mapper for RNA-seq called Tophat.

The first thing to do is decide a good place to install the application. The $WORK file system on TACC resources is suitable. Navigate to the $WORK file system, and make a new directory called apps, where we can put all of the applications we install:

$ cd $WORK
$ pwd
/work/03439/wallen/lonestar
$ mkdir apps
$ cd apps
$ pwd
/work/03439/wallen/lonestar/apps

According to the Tophat documentation, we need bowtie2 and boost are dependencies. Check your environment and load what we know we need for Tophat:

$ module load boost/1.59
$ module load bowtie/2.2.6
Lmod has detected the following error:  Cannot load module "bowtie/2.2.6" without these module(s)
loaded:
   perl

Whoops! We first need to load perl before we can load bowtie:

$ module load perl/5.22.1
$ module load bowtie/2.2.6
$ module list
Currently Loaded Modules:
  1) intel/16.0.1   2) cray_mpich/7.3.0   3) TACC/1.0   4) boost/1.59   5) perl/5.22.1   6) bowtie/2.2.6

We will use the wget command to download the Tophat source code straight from the web, and tar command to unpack the file. We also make a directory called tophat/2.1.1 which is where the installation will go:

$ wget https://ccb.jhu.edu/software/tophat/downloads/tophat-2.1.1.tar.gz
$ tar -xvzf tophat-2.1.1.tar.gz
$ mkdir -p tophat/2.1.1
$ cd tophat-2.1.1

According to the Tophat documentation, it follows a standard installation scheme of ./configure, make, make install. The first step checks your environment for all the right dependencies, the second step compiles the code, and the third step moves the appropriate binaries and libraries to your target install location. Try running the first step with a --help flag to see what information you can learn:

$ ./configure --help

A few things to note from the help text:

We cannot install into the default /usr/local folder, so we will have to specify our own prefix
We may try using the --enable-intel64 flag since we are compiling with intel processors
We may need to specify the location of boost with the --with-boost flag, even though it is already in our path
There is a helpful list of environment variables at the bottom

Try to configure using the --prefix and --enable-intel64 flags:

$ ./configure --prefix=/work/03439/wallen/lonestar/apps/tophat/2.1.1 \
              --enable-intel64
...
checking for boostlib >= 1.38.0... configure: error: We could not detect the
boost libraries (version 1.38 or higher). If you have a staged boost library
(still not installed) please specify $BOOST_ROOT in your environment and do not
give a PATH to --with-boost option.  If you are sure you have boost installed,
then check your version number looking in <boost/version.hpp>. See
http://randspringer.de/boost for more documentation.

It works for a little bit before giving the boost error above. Perhaps we do need to specify the boost path after all:

$ ./configure --prefix=/work/03439/wallen/lonestar/apps/tophat/2.1.1 \
              --with-boost=/opt/apps/intel16/boost/1.59 \
              --enable-intel64

This time it got all the way through the ./configure step, except there is something funny in the summary text:

...
-- tophat 2.1.1 Configuration Results --
  C++ compiler:        g++ -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized  -mtune=nocona -O3  -DNDEBUG -I./samtools-0.1.18 -pthread -I/opt/apps/intel16/boost/1.59/include -I./SeqAn-1.4.2
  Linker flags:        -L./samtools-0.1.18 -L/opt/apps/intel16/boost/1.59/lib
  BOOST libraries:     -lboost_thread -lboost_system
  GCC version:         gcc (GCC) 4.9.3
  Host System type:    x86_64-unknown-linux-gnu
  Install prefix:      /work/03439/wallen/lonestar/training/apps/tophat/2.1.1
  Install eprefix:     ${prefix}
...

It looks like it is still trying to use gcc compilers, even though we have intel compilers loaded. This is where the environment variables come in. As a reminder:

$ ./configure --help
Some influential environment variables:
  PYTHON      python program
  CXX         C++ compiler command
  CXXFLAGS    C++ compiler flags
  LDFLAGS     linker flags, e.g. -L<lib dir> if you have libraries in a
              nonstandard directory <lib dir>
  LIBS        libraries to pass to the linker, e.g. -l<library>
  CPPFLAGS    (Objective) C/C++ preprocessor flags, e.g. -I<include dir> if
              you have headers in a nonstandard directory <include dir>
  CC          C compiler command
  CFLAGS      C compiler flags
  CXXCPP      C++ preprocessor

The contents of the variables we are interested in are empty:

$ echo $CC
$ echo $CXX

We can force Tophat to use the intel compilers by pointing those variables to the appropriate C and C++ compilers:

$ which icc
/opt/apps/intel/16.0.1.150/compilers_and_libraries_2016.1.150/linux/bin/intel64/icc
$ export CC=`which icc`
echo $CC
/opt/apps/intel/16.0.1.150/compilers_and_libraries_2016.1.150/linux/bin/intel64/icc
$ export CXX=`which icpc`

And, if you recall from before, Lonestar5 has nodes with different architectures. Now is our chance to specify a few extra compilation flags so that the binaries can run anywhere:

$ export CFLAGS="-xAVX -axCORE-AVX2"
$ export CXXFLAGS="-xAVX -axCORE-AVX2"
$ export LDFLAGS="-xAVX -axCORE-AVX2"

Configure one more time and make sure the output makes sense:

$ ./configure --prefix=/work/03439/wallen/lonestar/apps/tophat/2.1.1 \
              --with-boost=/opt/apps/intel16/boost/1.59 \
              --enable-intel64
...
-- tophat 2.1.1 Configuration Results --
  C++ compiler:        /opt/apps/intel/16.0.1.150/compilers_and_libraries_2016.1.150/linux/bin/intel64/icpc -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized  -mtune=nocona -O3 -xAVX -axCORE-AVX2 -DNDEBUG -I./samtools-0.1.18 -pthread -I/opt/apps/intel16/boost/1.59/include -I./SeqAn-1.4.2
  Linker flags:        -L./samtools-0.1.18 -L/opt/apps/intel16/boost/1.59/lib -xAVX -axCORE-AVX
  BOOST libraries:     -lboost_thread -lboost_system
  GCC version:         icc (ICC) 16.0.1 20151021
  Host System type:    x86_64-unknown-linux-gnu
  Install prefix:      /work/03439/wallen/lonestar/apps/tophat/2.1.1
  Install eprefix:     ${prefix}
...

This looks better. Finish with:

$ make                # compiles code
$ make install        # moves binaries into $WORK/apps/tophat/2.1.1
$ ls -l ../tophat/2.1.1/
$ ls -l ../tophat/2.1.1/bin

The tophat/2.1.1/bin directory should be filled with executables.

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