bowtie-2.2.5-4.spec

#------------------------------------------------
# INITIAL DEFINITIONS
#------------------------------------------------
%define PNAME bowtie
Version:      2.2.5
Release:      4
License:      GPL
Group:        Applications/Life Sciences
Source:       http://downloads.sourceforge.net/project/bowtie-bio/bowtie2/2.2.5/bowtie2-2.2.5-source.zip
Packager:     TACC - jfonner@tacc.utexas.edu
Summary:      Memory-efficient short read (NGS) aligner


## System Definitions
%include ./include/system-defines.inc
%include ./include/%{PLATFORM}/rpm-dir.inc
## Compiler Family Definitions
# %include ./include/%{PLATFORM}/compiler-defines.inc
## MPI Family Definitions
# %include ./include/%{PLATFORM}/mpi-defines.inc
## directory and name definitions for relocatable RPMs
%include ./include/name-defines.inc

%define MODULE_VAR  %{MODULE_VAR_PREFIX}BOWTIE

## PACKAGE DESCRIPTION
%description
Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes. Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome, its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes.

## PREP
# Use -n <name> if source file different from <name>-<version>.tar.gz
%prep
rm -rf $RPM_BUILD_ROOT/%{INSTALL_DIR}
rm -rf $RPM_BUILD_ROOT/%{MODULE_DIR}

## SETUP
%setup -n %{PNAME}2-%{version}

## BUILD
%build

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

# Start with a clean environment
%include ./include/%{PLATFORM}/system-load.inc
mkdir -p $RPM_BUILD_ROOT/%{INSTALL_DIR}

#--------------------------------------
## Install Steps Start
module swap $TACC_FAMILY_COMPILER gcc

# Since LDFLAGS is not used in bowtie's compilation, we hijack EXTRA_FLAGS to carry the rpath payload
make EXTRA_FLAGS="-Wl,-rpath,$GCC_LIB"
## Install Steps End
#--------------------------------------

cp -R ./bowtie2* ./doc ./scripts $RPM_BUILD_ROOT/%{INSTALL_DIR}

#------------------------------------------------
# MODULEFILE CREATION
#------------------------------------------------
mkdir -p $RPM_BUILD_ROOT/%{MODULE_DIR}

#--------------------------------------
## Modulefile Start
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 %{name}
distribution. Documentation can be found online at http://bowtie-bio.sourceforge.net/bowtie2/

NOTE: Bowtie2 indexes are not backwards compatible with Bowtie1 indexes. 

This module provides the bowtie2, bowtie2-align, bowtie2-build, and bowtie2-inspect binaries + scripts

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/bowtie2/")
whatis("Description: Ultrafast, memory-efficient short read aligner")

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

prereq("perl")

EOF
## Modulefile End
#--------------------------------------

## Lua syntax check
if [ -f $SPEC_DIR/checkModuleSyntax ]; then
    $SPEC_DIR/checkModuleSyntax $RPM_BUILD_ROOT/%{MODULE_DIR}/%{version}.lua
fi

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

set     ModulesVersion      "%{version}"
EOF

#------------------------------------------------
# FILES SECTION
#------------------------------------------------
%files 
%defattr(-,root,install,)
%{INSTALL_DIR}
%{MODULE_DIR}

## POST 
%post 

## CLEAN UP
%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