bedtools-2.16.1-1.spec

# http://bedtools.googlecode.com/files/BEDTools.v2.16.1.tar.gz

Summary:    bedtools: a flexible suite of utilities for comparing genomic features
Name:       bedtools
Version:    2.16.1
Release:    1
License:    GPLv2
Group: Applications/Life Sciences
Source:     BEDTools.v%{version}.tar.gz
Packager:   TACC - vaughn@tacc.utexas.edu
# This is the actual installation directory - Careful
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 bedtools

# 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
BEDTools is a software suite for the comparison, manipulation and annotation of genomic features in Browser Extensible Data (BED) and General Feature Format (GFF) format. BEDTools also supports the comparison of sequence alignments in BAM format to both BED and GFF features.

#------------------------------------------------
# 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_BEDTOOLS

#------------------------------------------------
# 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/BEDTools-Version-%{version}
%setup -n BEDTools-Version-%{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 unload $TACC_FAMILY_COMPILER

module purge
module load TACC
module unload $TACC_FAMILY_COMPILER 
module load intel

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

make CC=icc CXX=icpc

#------------------------------------------------
# INSTALL SECTION
#------------------------------------------------
%install

 cp -R ./bin ./genomes ./data $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 (
[[
This module loads %{name} built with icc and makes available all the BEDtools executables. Documentation is available online at the publisher's website: http://code.google.com/p/bedtools/

The BEDTools executable can be found in %{MODULE_VAR}_BIN

Version %{version}
]])

whatis("Name: bedtools")
whatis("Version: %{version}")
whatis("Category: computational biology, genomics")
whatis("Keywords: Biology, Genomics, Utility, Interval, Sequencing")
whatis("Description: bedtools: a flexible suite of utilities for comparing genomic features")
whatis("URL: http://code.google.com/p/bedtools/")

setenv("%{MODULE_VAR}_DIR","%{INSTALL_DIR}/")
setenv("%{MODULE_VAR}_BIN","%{INSTALL_DIR}/bin/")

prepend_path("PATH","%{INSTALL_DIR}/bin/")

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