bfast-0.7.0a-1.spec

Summary:    Blat-like Fast Accurate Search Tool 
Name:       bfast
Version:    0.7.0a
Release:    1
License:    GNU GENERAL PUBLIC LICENSE
Group: Applications/Life Sciences
Source:     bfast-%{version}.tar.gz
Packager:   TACC - jiao@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
%include ../system-defines.inc
# Compiler Family Definitions
# %include compiler-defines.inc
# MPI Family Definitions
# %include mpi-defines.inc
# Other defs

# 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
Blat-like Fast Accurate Search Tool. BFAST facilitates the fast and accurate mapping of short reads to reference sequences. 
#------------------------------------------------
# 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 bfast-%{version}

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

%install
%include ../system-load.inc

module purge
module load TACC

sh autogen.sh
./configure --prefix=%{INSTALL_DIR}

make

mkdir -p $RPM_BUILD_ROOT%{INSTALL_DIR}
make DESTDIR=$RPM_BUILD_ROOT install

# 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 (
[[
Documentation is available online - http://sourceforge.net/apps/mediawiki/bfast/index.php?title=Main_Page 

The bfast executables including "bfast" can be found in %{MODULE_VAR}_BIN. Useful commands include:


Version %{version}
]])

whatis("Name: bfast")
whatis("Version: %{version}")
whatis("Category: computational biology, genomics")
whatis("Keywords: Biology, Genomics, Blat, Search, Sequencing")
whatis("Description: BFAST: Blat-like Fast Accurate Search Tool")
whatis("URL: http://sourceforge.net/apps/mediawiki/bfast/index.php?title=Main_Page")

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