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10 files changed, 387 insertions, 0 deletions
diff --git a/var/spack/repos/builtin/packages/mirdeep/package.py b/var/spack/repos/builtin/packages/mirdeep/package.py new file mode 100644 index 0000000000..0b7129b4c8 --- /dev/null +++ b/var/spack/repos/builtin/packages/mirdeep/package.py @@ -0,0 +1,67 @@ +############################################################################## +# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the NOTICE and LICENSE files for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * +import glob + + +class Mirdeep(Package): + """miRDeep2 is a completely overhauled tool which discovers microRNA genes + by analyzing sequenced RNAs.""" + + homepage = "https://www.mdc-berlin.de/8551903/en/" + url = "https://www.mdc-berlin.de/45995549/en/research/research_teams/systems_biology_of_gene_regulatory_elements/projects/miRDeep/mirdeep2_0_0_8.zip" + + version('2.0.0.8', 'a707f7d7ad4a2975fb8b2e78c5bcf483') + + depends_on('perl', type=('build', 'run')) + depends_on('perl-pdf-api2', type=('build', 'run')) + depends_on('bowtie') + depends_on('viennarna') + depends_on('squid') + depends_on('randfold') + + def url_for_version(self, version): + url = 'https://www.mdc-berlin.de/45995549/en/research/research_teams/systems_biology_of_gene_regulatory_elements/projects/miRDeep/mirdeep{0}.zip' + return url.format(version.underscored) + + def patch(self): + with working_dir('src'): + files = glob.iglob("*.pl") + for file in files: + change = FileFilter(file) + change.filter('usr/bin/perl', 'usr/bin/env perl') + change.filter('perl -W', 'perl') + change.filter("../Rfam_for_miRDeep.fa", + "Rfam_for_miRDeep.fa") + change.filter("../install_successful", + "install_successful") + + def install(self, spec, prefix): + install_tree('src', prefix.bin) + install('Rfam_for_miRDeep.fa', prefix.bin) + # miRDeep looks for the install_sucessful file to check if you used + # their automated install script which we'll just be kind of hacking + # around + touch(prefix.bin.install_successful) diff --git a/var/spack/repos/builtin/packages/perl-devel-cycle/package.py b/var/spack/repos/builtin/packages/perl-devel-cycle/package.py new file mode 100644 index 0000000000..39295ca0f0 --- /dev/null +++ b/var/spack/repos/builtin/packages/perl-devel-cycle/package.py @@ -0,0 +1,34 @@ +############################################################################## +# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the NOTICE and LICENSE files for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class PerlDevelCycle(PerlPackage): + """Find memory cycles in objects""" + + homepage = "http://search.cpan.org/~lds/Devel-Cycle-1.12/lib/Devel/Cycle.pm" + url = "http://search.cpan.org/CPAN/authors/id/L/LD/LDS/Devel-Cycle-1.12.tar.gz" + + version('1.12', '3d9a963da87b17398fab9acbef63f277') diff --git a/var/spack/repos/builtin/packages/perl-font-ttf/package.py b/var/spack/repos/builtin/packages/perl-font-ttf/package.py new file mode 100644 index 0000000000..aec59efc95 --- /dev/null +++ b/var/spack/repos/builtin/packages/perl-font-ttf/package.py @@ -0,0 +1,34 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the NOTICE and LICENSE files for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class PerlFontTtf(PerlPackage): + """Perl module for TrueType Font hacking""" + + homepage = "http://search.cpan.org/~bhallissy/Font-TTF-1.06/lib/Font/TTF.pm" + url = "http://search.cpan.org/CPAN/authors/id/B/BH/BHALLISSY/Font-TTF-1.06.tar.gz" + + version('1.06', '241b59310ad4450e6e050d5e790f1b21') diff --git a/var/spack/repos/builtin/packages/perl-padwalker/package.py b/var/spack/repos/builtin/packages/perl-padwalker/package.py new file mode 100644 index 0000000000..70d512acad --- /dev/null +++ b/var/spack/repos/builtin/packages/perl-padwalker/package.py @@ -0,0 +1,34 @@ +############################################################################## +# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the NOTICE and LICENSE files for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class PerlPadwalker(PerlPackage): + """play with other peoples' lexical variables""" + + homepage = "http://search.cpan.org/~robin/PadWalker-2.2/PadWalker.pm" + url = "http://search.cpan.org/CPAN/authors/id/R/RO/ROBIN/PadWalker-2.2.tar.gz" + + version('2.2', '6bcc741f77b1831a893b2a22c785e31a') diff --git a/var/spack/repos/builtin/packages/perl-pdf-api2/package.py b/var/spack/repos/builtin/packages/perl-pdf-api2/package.py new file mode 100644 index 0000000000..3a91056a1b --- /dev/null +++ b/var/spack/repos/builtin/packages/perl-pdf-api2/package.py @@ -0,0 +1,38 @@ +############################################################################## +# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the NOTICE and LICENSE files for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class PerlPdfApi2(PerlPackage): + """Facilitates the creation and modification of PDF files""" + + homepage = "http://search.cpan.org/~ssimms/PDF-API2-2.033/lib/PDF/API2.pm" + url = "http://search.cpan.org/CPAN/authors/id/S/SS/SSIMMS/PDF-API2-2.033.tar.gz" + + version('2.033', '4223a38add42741f996bd67d5f2f8e5b') + + depends_on('perl-test-exception', type=('build', 'run')) + depends_on('perl-test-memory-cycle', type=('build', 'run')) + depends_on('perl-font-ttf', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/perl-sub-uplevel/package.py b/var/spack/repos/builtin/packages/perl-sub-uplevel/package.py new file mode 100644 index 0000000000..de0581943b --- /dev/null +++ b/var/spack/repos/builtin/packages/perl-sub-uplevel/package.py @@ -0,0 +1,34 @@ +############################################################################## +# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the NOTICE and LICENSE files for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class PerlSubUplevel(PerlPackage): + """apparently run a function in a higher stack frame""" + + homepage = "http://search.cpan.org/~dagolden/Sub-Uplevel-0.2800/lib/Sub/Uplevel.pm" + url = "http://search.cpan.org/CPAN/authors/id/D/DA/DAGOLDEN/Sub-Uplevel-0.2800.tar.gz" + + version('0.2800', '6c6a174861fd160e8d5871a86df00baf') diff --git a/var/spack/repos/builtin/packages/perl-test-exception/package.py b/var/spack/repos/builtin/packages/perl-test-exception/package.py new file mode 100644 index 0000000000..d18f7379cd --- /dev/null +++ b/var/spack/repos/builtin/packages/perl-test-exception/package.py @@ -0,0 +1,36 @@ +############################################################################## +# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the NOTICE and LICENSE files for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class PerlTestException(PerlPackage): + """Test exception-based code""" + + homepage = "http://search.cpan.org/~exodist/Test-Exception-0.43/lib/Test/Exception.pm" + url = "http://search.cpan.org/CPAN/authors/id/E/EX/EXODIST/Test-Exception-0.43.tar.gz" + + version('0.43', '572d355026fb0b87fc2b8c64b83cada0') + + depends_on('perl-sub-uplevel', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/perl-test-memory-cycle/package.py b/var/spack/repos/builtin/packages/perl-test-memory-cycle/package.py new file mode 100644 index 0000000000..660a3c023d --- /dev/null +++ b/var/spack/repos/builtin/packages/perl-test-memory-cycle/package.py @@ -0,0 +1,37 @@ +############################################################################## +# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the NOTICE and LICENSE files for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class PerlTestMemoryCycle(PerlPackage): + """Check for memory leaks and circular memory references""" + + homepage = "http://search.cpan.org/~petdance/Test-Memory-Cycle-1.06/Cycle.pm" + url = "http://search.cpan.org/CPAN/authors/id/P/PE/PETDANCE/Test-Memory-Cycle-1.06.tar.gz" + + version('1.06', '397e709ba33d3883b5fb2bc49e3a70b0') + + depends_on('perl-padwalker', type=('build', 'run')) + depends_on('perl-devel-cycle', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/randfold/package.py b/var/spack/repos/builtin/packages/randfold/package.py new file mode 100644 index 0000000000..42eced74a2 --- /dev/null +++ b/var/spack/repos/builtin/packages/randfold/package.py @@ -0,0 +1,40 @@ +############################################################################## +# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the NOTICE and LICENSE files for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class Randfold(MakefilePackage): + """Minimum free energy of folding randomization test software""" + + homepage = "http://bioinformatics.psb.ugent.be/supplementary_data/erbon/nov2003/" + url = "http://bioinformatics.psb.ugent.be/supplementary_data/erbon/nov2003/downloads/randfold-2.0.1.tar.gz" + + version('2.0.1', 'c9ebf7dc9d62fa4554a738a15fe1ded8') + + depends_on('squid') + + def install(self, spec, prefix): + mkdirp(prefix.bin) + install('randfold', prefix.bin) diff --git a/var/spack/repos/builtin/packages/squid/package.py b/var/spack/repos/builtin/packages/squid/package.py new file mode 100644 index 0000000000..1edb314c5a --- /dev/null +++ b/var/spack/repos/builtin/packages/squid/package.py @@ -0,0 +1,33 @@ +############################################################################## +# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the NOTICE and LICENSE files for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class Squid(AutotoolsPackage): + """C function library for sequence analysis.""" + + homepage = "http://eddylab.org/software.html" + + version('1.9g', 'b9bf480c65d01417b7894c82d094ce07', url='http://eddylab.org/software/squid/squid.tar.gz') |