bowtie-0.12.7-1.spec

# $Id$

## Edited SeqAn-1.1/seqan/platform.h and repackaged as bowtie-0.12.7.tgz

Summary: Memory-efficient short read (NGS) aligner
Name: bowtie
Version: 0.12.7
Release: 1
License: GPL
Group: Applications/Life Sciences
Source0:  bowtie-0.12.7.tgz
Packager: TACC - vaughn@tacc.utexas.edu
BuildRoot: /var/tmp/%{name}_%{version}-buildroot

#------------------------------------------------
# BASIC DEFINITIONS
#------------------------------------------------
%define debug-package %{nil}
# This will define the correct _topdir
%include rpm-dir.inc
# Compiler Family Definitions
# %include compiler-defines.inc
# MPI Family Definitions
# %include mpi-defines.inc
# Other defs
%define system linux
%define APPS    /opt/apps
%define MODULES modulefiles
%define PNAME bowtie

# Allow for creation of multiple packages with this spec file
# Any tags right after this line apply only to the subpackage
# Summary and Group are required.
# %package -n %{name}-%{comp_fam_ver}
# Summary: HMMER biosequence analysis using profile hidden Markov models
# Group: Applications/Life Sciences

#------------------------------------------------
# PACKAGE DESCRIPTION
#------------------------------------------------
%description
Bowtie is an ultrafast, memory-efficient short read aligner. It aligns short DNA sequences (reads) to the human genome at a rate of over 25 million 35-bp reads per hour. Bowtie indexes the genome with a Burrows-Wheeler index to keep its memory footprint small: typically about 2.2 GB for the human genome (2.9 GB for paired-end).

#------------------------------------------------
# INSTALLATION DIRECTORY
#------------------------------------------------
# Buildroot: defaults to null if not included here
%define INSTALL_DIR %{APPS}/%{name}/%{version}
%define MODULE_DIR  %{APPS}/%{MODULES}/%{name}
%define MODULE_VAR TACC_BOWTIE

#------------------------------------------------
# PREPARATION SECTION
#------------------------------------------------
# Use -n <name> if source file different from <name>-<version>.tar.gz
%prep

# Remove older attempts
rm   -rf $RPM_BUILD_ROOT/%{INSTALL_DIR}
mkdir -p $RPM_BUILD_ROOT/%{INSTALL_DIR}

# Unpack source
# This will unpack the source to /tmp/BUILD/*
%setup -n %{name}-%{version}

#------------------------------------------------
# BUILD SECTION
#------------------------------------------------
%build

# Start with a clean environment
if [ -f "$BASH_ENV" ]; then
   . $BASH_ENV
   export MODULEPATH=/opt/apps/teragrid/modulefiles:/opt/apps/modulefiles:/opt/modulefiles
fi

# Load correct compiler
# %include compiler-load.inc
# Load correct mpi stack
#%include mpi-load.inc
#%include mpi-env-vars.inc
# Load additional modules here (as needed)

module purge
module load TACC

#-----------------------------
# Build parallel version
#-----------------------------

make CC=icc CXX=icpc

#------------------------------------------------
# INSTALL SECTION
#------------------------------------------------
%install
cp -R ./bowtie ./bowtie-build ./bowtie-inspect ./doc ./genomes ./indexes ./reads ./scripts ./SeqAn-1.1 $RPM_BUILD_ROOT/%{INSTALL_DIR}
 
 
# ADD ALL MODULE STUFF HERE
# TACC module

rm   -rf $RPM_BUILD_ROOT/%{MODULE_DIR}
mkdir -p $RPM_BUILD_ROOT/%{MODULE_DIR}
cat > $RPM_BUILD_ROOT/%{MODULE_DIR}/%{version}.lua << 'EOF'
help (
[[
The %{PNAME} module file defines the following environment variables:
%{MODULE_VAR}_DIR and %{MODULE_VAR}_SCRIPTS for the location of the %{PNAME}
distribution. Documentation can be found online at http://bowtie-bio.sourceforge.net/

Version %{version}

Version %{version}
]])

whatis("Name: Bowtie")
whatis("Version: %{version}")
whatis("Category: computational biology, genomics")
whatis("Keywords: Biology, Genomics, Alignment, Sequencing")
whatis("URL: http://bowtie-bio.sourceforge.net/index.shtml")
whatis("Description: Ultrafast, memory-efficient short read aligner")

setenv("%{MODULE_VAR}_DIR","%{INSTALL_DIR}/")
setenv("%{MODULE_VAR}_SCRIPTS","%{INSTALL_DIR}/scripts")
prepend_path("PATH"       ,"%{INSTALL_DIR}/")

EOF

#--------------
#  Version file.
#--------------

cat > $RPM_BUILD_ROOT%{MODULE_DIR}/.version.%{version} << 'EOF'
#%Module3.1.1#################################################
##
## version file for %{PNAME}-%{version}
##

set     ModulesVersion      "%{version}"
EOF



#------------------------------------------------
# FILES SECTION
#------------------------------------------------
%files

# Define files permisions, user and group
%defattr(755,root,root,-)
%{INSTALL_DIR}
%{MODULE_DIR}

#------------------------------------------------
# CLEAN UP SECTION
#------------------------------------------------
%post
%clean
# Make sure we are not within one of the directories we try to delete
cd /tmp

# Remove the installation files now that the RPM has been generated
rm -rf $RPM_BUILD_ROOT