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##
# This file is an EasyBuild recipy as per https://github.com/hpcugent/easybuild
#
# Copyright:: Copyright 2012-2013 University of Luxembourg/Luxembourg Centre for Systems Biomedicine
# Authors::   Fotis Georgatos <fotis.georgatos@uni.lu>
# License::   MIT/GPL
# $Id$
#
# This work implements a part of the HPCBIOS project and is a component of the policy:
# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html

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[pub@login10 1.10.0]$ cat easybuild/tools/module_naming_scheme/JustAppNameAndVersion.py
import os

from easybuild.tools.module_naming_scheme import ModuleNamingScheme


class JustAppNameAndVersion(ModuleNamingScheme):
    """Class implementing an example module naming scheme."""

    def det_full_module_name(self, ec):

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# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild
# Author: Pablo Escobar Lopez
# Swiss Institute of Bioinformatics
# Biozentrum - University of Basel

easyblock='MakeCp'

name = 'Bowtie2'
version = '2.0.5'

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"""
EasyBuild support for OpenStructure, implemented as an easyblock

@author: Pablo Escobar (University of Basel)
"""

from easybuild.easyblocks.generic.cmakemake import CMakeMake
from easybuild.tools.modules import get_software_root, get_software_version

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# Built with EasyBuild version 1.11.0 on 2014-03-26_18-21-21
easyblock='MakeCp'

name = 'PLINK'
version = '1.07'

homepage = 'http://pngu.mgh.harvard.edu/~purcell/plink/'
description = """ PLINK is a free, open-source whole genome association analysis toolset, 
 designed to perform a range of basic, large-scale analyses in a computationally efficient manner.
 The focus of PLINK is purely on analysis of genotype/phenotype data, so there is no support for 

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   def dependencies(self):
        """
        returns an array of parsed dependencies
        dependency = {'name': '', 'version': '', 'dummy': (False|True), 'versionsuffix': '', 'toolchain': ''}
        """
        full_dependencies = self['dependencies'] + self.builddependencies()

        # define dependencies we never want because we will use OS packages
        deps_to_remove = ["zlib", "ncurses", "libpng"]
        # remove unwanted deps

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def download_file(filename, url, path):
    """Download a file from the given URL, to the specified path."""

    _log.debug("Downloading %s from %s to %s" % (filename, url, path))

    # make sure directory exists
    basedir = os.path.dirname(path)
    mkdir(basedir, parents=True)

    downloaded = False

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easybuild@easybuild-debian:~$ type module
-su: type: module: not found
easybuild@easybuild-debian:~$ which lmod
/home/easybuild/lmod-install/lmod/5.5.1/libexec/lmod
easybuild@easybuild-debian:~$ python --version
Python 2.7.3
easybuild@easybuild-debian:~$ python bootstrap_eb.py $HOME/.local/easybuild
[[INFO]] Found module command 'lmod' (Lmod), so using it.
[[INFO]] 

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Test report for easybuilders/easybuild-easyconfigs#868

Test result

Build succeeded for 1 out of 1 (1 easyconfigs in this PR)

Overview of tested easyconfigs (in order)

• SUCCESS Jellyfish-2.1.3-goolf-1.4.10.eb

Time info

• start: Thu, 15 May 2014 12:55:04 +0000 (UTC)

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Test report for easybuilders/easybuild-easyconfigs#868

Test result

Build succeeded for 1 out of 1 (1 easyconfigs in this PR)

Overview of tested easyconfigs (in order)

• SUCCESS Jellyfish-2.1.3-goolf-1.4.10.eb

Time info

• start: Thu, 15 May 2014 13:06:13 +0000 (UTC)