Bioinformatics applications at University of Canterbury HPC

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A number of Bioinformatics applications have been already installed on the University of Canterbury HPC (p575). This page lists the tricks that very necessary to compile the applications.

Note: this page has been replicated from the UCSC Admin wiki, where it has its master copy as AppsBioinformatics. Please contact the author (Vladimir Mencl) before modifying this page.

Contents

[edit] List of Bioinformatics applications

Unless noted otherwise, the packages are installed on both AIX and Linux. They are installed in /usr/local/pkg/<appname>/<version> and binaries are symlinked to /usr/local/bin.

  • BayesPhylogenies 1.0
  • BEAST 1.4.4
  • LAMARC 2.1 (Linux only)
  • MrBayes 3.1.2 (with local modifications)
  • ClustalW 1.83
  • ClustalW-MPI 0.13
  • ModelTest 3.7
  • PAUP 4.0beta
  • Structure 2.2.2

[edit] Installing BayesPhylogenies

Download link: http://www.evolution.rdg.ac.uk/BayesPhy.html Note that source code is not publicly available, the page contains only precompiled binaries - including support for Linux x86. If you need the source code, contact either Vladimir Mencl, or the authors directly.

  • AIX: fix source code :-)
    • in pmatrix.c, comment out
            extern int isnan (double);
    • in BayesPhylogenies.c, line 589
            fix C++ style comment (//) to /* */
    • (reported only by mpcc)
  • AIX UP compile: 
 xlc  -o BayesPhylogenies -lm -w -O3 *.c ./MathLib/*.c
  • AIX MPI compile: 
 mpcc -o BayesPhylogenies -lm -w -O3 -DMPI_ENABLED *.c ./MathLib/*.c
  • Linux-UP: 
 xlc -o BayesPhylogenies -lm -w -O3 *.c ./MathLib/*.c
    • or could also 
 gcc -o BayesPhylogenies -lm -w -O3 *.c ./MathLib/*.c
  • Linux-MPI 
    mpcc -compiler xlc -o BayesPhylogenies-xlc -lm -w -O3 -DMPI_ENABLED *.c ./MathLib/*.c

[edit] Installing ClustalW

Download link: ftp://ftp.ebi.ac.uk/pub/software/unix/clustalw/

  • optionally edit makefile and set CC=xlc
  • linux and AIX: make

[edit] Installing ClustalW-MPI

Download link: http://packages.debian.org/unstable/source/clustalw-mpi

  • edit Makefile and set
    • Linux: 
       CC      = mpcc -compiler xlc
    • AIX: 
       CC      = mpcc


[edit] Installing ModelTest

Download link: http://darwin.uvigo.es/software/modeltest.html

Linux and AIX: edit Makefile

  1. set CMP and LD to xlc
  2. remove "-fast" from LD options

[edit] Installing PAUP

Download: this is commercial software and you need to purchase a license. See http://paup.csit.fsu.edu/ for more information.

Nothing to do: already binary

[edit] Installing Structure

Downloads link: http://pritch.bsd.uchicago.edu/software/ Only binaries available at the site - email authors for source code.

Structure: no changes, "make"

Compiled with gcc. Could compile with xlc (edit Makefile, remove "-shared" option), but xlc gives warnings about -O3 optimization - so rather stay with author's decision on how to optimize.

[edit] Installing LAMARC

Download link: http://evolution.genetics.washington.edu/lamarc/lamarc.html

  • AIX: not supported OS
  • Linux: depends on wxWidgets (at least 2.8.3).
    • install gtk2-devel from RPM (thanks Colin!)
    • compile and install wxWidgets 
  cd wxWidgets-2.8.4/
  ./configure --prefix=/usr/local/pkg/wxWidgets/2.8.4/
  make
  make install
  • compile and install LAMARC 
  cd ../lamarc
  ./configure --prefix=/usr/local/pkg/lamarc/2.1 --with-wx-config=/usr/local/pkg/wxWidgets/2.8.4/bin/wx-config

[edit] Installing BEAST

Download link: http://beast.bio.ed.ac.uk/Main_Page

BEAST comes as a precompiled Java package, but uses a native library for optimized computation. If the library is not available, BEAST uses an alternative non-optimized Java implementation - so we want the library to be available. The source code of the library is in the native directory, and the compiled library should replace the precompiled Linux x86 file in the lib directory.

  • Check if the native libraries work: run 
./bin/beast ./examples/testMCMC.xml

and check if the output includes 

TreeLikelihood using native nucleotide likelihood core


In BEAST-1/native:

  • AIX: 
 cd BEAST.v1.4.4/native
 JAVA_HOME=/usr/java14 gmake -f Makefile.linux
  • New try (64-bit): 
OBJECT_MODE=64 JAVA_HOME=/usr/local/pkg/java/version/sdk gmake -f Makefile.linux
  • fails with 
gcc -O2 -funroll-loops -fPIC -I/usr/local/pkg/java/version/sdk/include/ -I/usr/local/pkg/java/version/sdk/include/linux -c NucleotideLikelihoodCore.c
Assembler:
/tmp//ccBWYEhZ.s: line 10: 1252-191 Only .llong should be used for relocatable expressions.
/tmp//ccBWYEhZ.s: line 317: 1252-191 Only .llong should be used for relocatable expressions.
/tmp//ccBWYEhZ.s: line 648: 1252-191 Only .llong should be used for relocatable expressions.
/tmp//ccBWYEhZ.s: line 964: 1252-191 Only .llong should be used for relocatable expressions.
gmake: *** [NucleotideLikelihoodCore.o] Error 1
  • try 3: 
OBJECT_MODE=64 xlc  -I/usr/local/pkg/java/version/sdk/include/ -I/usr/local/pkg/java/version/sdk/include/linux -c NucleotideLikelihoodCore.c
OBJECT_MODE=64 xlc -o libNucleotideLikelihoodCore.so -qmkshrobj NucleotideLikelihoodCore.o
    • WORKED - same worked for Linux 64-bit 
* Linux:

 cd BEAST.v1.4.4/native
 JAVA_HOME=/opt/IBMJava2-ppc-142 make -f Makefile.linux
  • Linux: fix java startup/PATH - edit bin/beast 
JAVA_HOME=/opt/IBMJava2-ppc-142
JRE_HOME=$JAVA_HOME/jre
PATH=$JAVA_HOME/bin:$JRE_HOME/bin:$PATH
export JAVA_HOME
export PATH

And in both cases, copy ./native/libNucleotideLikelihoodCore.so into ./lib/libNucleotideLikelihoodCore.so

  • Linux on x86 (CentOS)
    • no changes necessary, runs straight out of the box.

[edit] Installing MrBayes

Download link: http://mrbayes.csit.fsu.edu/download.php

Installing MrBayes is theoretically just the matter of typing make - but there is a number of tweaks involved, so here they are documented: 

    patch -R -p 1 < ~/mrbayes-patches/downloaded/mb_64bit-safe.patch
    OBJECT_MODE=64 make _64BIT=yes

[edit] Infernal

Infernal "is for searching DNA sequence databases for RNA structure and sequence similarities.".

I have installed Infernal just on the Linux part of the IBM p575.

I have tried installing it on AIX: 

wget ftp://selab.janelia.org/pub/software/infernal/infernal.tar.gz
gtar xzf infernal.tar.gz
cd infernal-1.0
CC=xlc MPICC=mpcc ./configure --enable-mpi

But it failed with: 

mpcc -g  -DHAVE_CONFIG_H  -L.. -o esl-afetch esl-afetch.o  -leasel   -lm
ld: 0711-317 ERROR: Undefined symbol: .va_copy
ld: 0711-345 Use the -bloadmap or -bnoquiet option to obtain more information.

It looks like va_copy is not supported by the XLC runtime libraries, not evne on Linux.

I have however succeeded compiling it with gcc on Linux, as a 64-bit parallel + serial application.

  • Parallel version: 
export OBJECT_MODE=64 MP_COMPILER=gcc CC="gcc -m64" MPICC=mpcc
./configure --enable-mpi
gmake
  • Serial version: 
export OBJECT_MODE=64 MP_COMPILER=gcc CC="gcc -m64" MPICC=mpcc
./configure
gmake

Works all fine.

[edit] MsBayes

Install MsBayes from http://msbayes.sourceforge.net/

  • So far installed on ngcompute.canterbury.ac.nz
  • Download tarball, extract
  • Edit Makefile and change PREFIX=/opt/shared/msbayes/20081106
  • Install dependency libraries:
    yum install gsl gsl-devel
  • Compile:
    gmake
  • To run AcceptRej, one also needs R, available in the EPEL repository 
rpm -Uvh http://download.fedora.redhat.com/pub/epel/4/i386/epel-release-4-9.noarch.rpm
yum install R
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