1 | ## |
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2 | # Copyright 2009-2015 Ghent University |
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3 | # |
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4 | # This file is part of EasyBuild, |
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5 | # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en), |
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6 | # with support of Ghent University (http://ugent.be/hpc), |
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7 | # the Flemish Supercomputer Centre (VSC) (https://vscentrum.be/nl/en), |
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8 | # the Hercules foundation (http://www.herculesstichting.be/in_English) |
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9 | # and the Department of Economy, Science and Innovation (EWI) (http://www.ewi-vlaanderen.be/en). |
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10 | # |
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11 | # http://github.com/hpcugent/easybuild |
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12 | # |
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13 | # EasyBuild is free software: you can redistribute it and/or modify |
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14 | # it under the terms of the GNU General Public License as published by |
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15 | # the Free Software Foundation v2. |
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16 | # |
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17 | # EasyBuild is distributed in the hope that it will be useful, |
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18 | # but WITHOUT ANY WARRANTY; without even the implied warranty of |
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19 | # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the |
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20 | # GNU General Public License for more details. |
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21 | # |
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22 | # You should have received a copy of the GNU General Public License |
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23 | # along with EasyBuild. If not, see <http://www.gnu.org/licenses/>. |
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24 | ## |
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25 | """ |
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26 | Support for building and installing picard, implemented as an easyblock. |
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27 | |
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28 | @author: Stijn De Weirdt (Ghent University) |
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29 | @author: Dries Verdegem (Ghent University) |
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30 | @author: Kenneth Hoste (Ghent University) |
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31 | @author: Pieter De Baets (Ghent University) |
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32 | @author: Jens Timmerman (Ghent University) |
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33 | """ |
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34 | |
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35 | import os |
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36 | import re |
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37 | import shutil |
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38 | |
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39 | from distutils.version import LooseVersion |
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40 | from easybuild.framework.easyblock import EasyBlock |
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41 | |
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42 | |
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43 | class EB_picard(EasyBlock): |
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44 | """Support for building and installing picard.""" |
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45 | |
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46 | def configure_step(self): |
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47 | """No configure step for picard""" |
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48 | pass |
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49 | |
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50 | def build_step(self): |
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51 | """No build step for picard""" |
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52 | pass |
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53 | |
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54 | def install_step(self): |
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55 | """Install picard by copying required files""" |
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56 | # recent version may contain more than just the picard-tools subdirectory |
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57 | picard_tools_dir = 'picard-tools-%s' % self.version |
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58 | if not re.search("%s/?$" % picard_tools_dir, self.cfg['start_dir']): |
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59 | self.cfg['start_dir'] = os.path.join(self.cfg['start_dir'], picard_tools_dir) |
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60 | if not os.path.exists(self.cfg['start_dir']): |
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61 | self.log.error("Path %s to copy files from doesn't exist." % self.cfg['start_dir']) |
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62 | |
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63 | for jar in os.listdir(self.cfg['start_dir']): |
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64 | src = os.path.join(self.cfg['start_dir'], jar) |
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65 | dst = os.path.join(self.installdir, jar) |
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66 | try: |
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67 | shutil.copy2(src, dst) |
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68 | self.log.info("Successfully copied %s to %s" % (src, dst)) |
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69 | except OSError, err: |
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70 | self.log.error("Failed to copy %s to %s (%s)" % (src, dst, err)) |
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71 | |
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72 | def sanity_check_step(self): |
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73 | """Custom sanity check for picard""" |
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74 | if LooseVersion(self.version) < LooseVersion('1.120'): |
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75 | jar_files = ['picard'] |
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76 | if LooseVersion(self.version) < LooseVersion('1.115'): |
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77 | jar_files.append('sam') |
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78 | custom_paths = { |
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79 | 'files': ["%s-%s.jar" % (x, self.version) for x in jar_files], |
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80 | 'dirs': [], |
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81 | } |
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82 | else: |
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83 | jar_files = ['picard', 'picard-lib', "htsjdk-%s" % (self.version)] |
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84 | custom_paths = { |
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85 | 'files': ["%s.jar" % (x) for x in jar_files], |
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86 | 'dirs': [], |
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87 | } |
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88 | super(EB_picard, self).sanity_check_step(custom_paths=custom_paths) |
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89 | |
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90 | def make_module_extra(self): |
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91 | """Add module entries specific to picard""" |
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92 | txt = super(EB_picard, self).make_module_extra() |
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93 | txt += self.module_generator.prepend_paths('PATH', '') |
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94 | return txt |
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