diff options
| -rw-r--r-- | var/spack/repos/builtin/packages/ncbi-rmblastn/package.py | 36 | ||||
| -rw-r--r-- | var/spack/repos/builtin/packages/repeatmasker/package.py | 80 | ||||
| -rw-r--r-- | var/spack/repos/builtin/packages/trf/package.py | 46 |
3 files changed, 162 insertions, 0 deletions
diff --git a/var/spack/repos/builtin/packages/ncbi-rmblastn/package.py b/var/spack/repos/builtin/packages/ncbi-rmblastn/package.py new file mode 100644 index 0000000000..57b918cde8 --- /dev/null +++ b/var/spack/repos/builtin/packages/ncbi-rmblastn/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/spack/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 NcbiRmblastn(AutotoolsPackage): + """RMBlast search engine for NCBI""" + + homepage = "https://www.ncbi.nlm.nih.gov/" + url = "ftp://ftp.ncbi.nlm.nih.gov/blast/executables/rmblast/LATEST/ncbi-rmblastn-2.2.28-src.tar.gz" + + version('2.2.28', 'fb5f4e2e02ffcb1b17af2e9f206c5c22') + + configure_directory = 'c++' diff --git a/var/spack/repos/builtin/packages/repeatmasker/package.py b/var/spack/repos/builtin/packages/repeatmasker/package.py new file mode 100644 index 0000000000..c9713c7892 --- /dev/null +++ b/var/spack/repos/builtin/packages/repeatmasker/package.py @@ -0,0 +1,80 @@ +############################################################################## +# 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/spack/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 inspect +import distutils.dir_util + + +class Repeatmasker(Package): + """RepeatMasker is a program that screens DNA sequences for interspersed + repeats and low complexity DNA sequences.""" + + homepage = "http://www.repeatmasker.org" + url = "http://www.repeatmasker.org/RepeatMasker-open-4-0-7.tar.gz" + + version('4.0.7', '4dcbd7c88c5343e02d819f4b3e6527c6') + + depends_on('perl', type=('build', 'run')) + depends_on('hmmer') + depends_on('ncbi-rmblastn') + depends_on('trf') + + def url_for_version(self, version): + url = 'http://www.repeatmasker.org/RepeatMasker-open-{0}.tar.gz' + return url.format(version.dashed) + + def install(self, spec, prefix): + # Config questions consist of: + # + # <PRESS ENTER TO CONTINUE> + # Enter perl path + # Enter where repeatmasker is being configured from + # Enter trf path + # Add a Search Engine: + # 1. CrossMatch + # 2. RMBlast - NCBI Blast with RepeatMasker extensions + # 3. WUBlast/ABBlast (required by DupMasker) + # 4. HMMER3.1 & DFAM + # 5. Done + # Enter RMBlast path + # Do you want RMBlast to be your default search engine for + # Repeatmasker? (Y/N) + # Add a Search Engine: Done + + config_answers = ['\n', '%s\n' % self.spec['perl'].prefix.bin.perl, + '%s\n' % self.stage.source_path, + '%s\n' % self.spec['trf'].prefix.bin.trf, '2\n', + '%s\n' % self.spec['ncbi-rmblastn'].prefix.bin, + 'Y\n', '5\n'] + + config_answers_filename = 'spack-config.in' + + with open(config_answers_filename, 'w') as f: + f.writelines(config_answers) + + with open(config_answers_filename, 'r') as f: + inspect.getmodule(self).perl('configure', input=f) + + distutils.dir_util.copy_tree(".", prefix) diff --git a/var/spack/repos/builtin/packages/trf/package.py b/var/spack/repos/builtin/packages/trf/package.py new file mode 100644 index 0000000000..f02e30302d --- /dev/null +++ b/var/spack/repos/builtin/packages/trf/package.py @@ -0,0 +1,46 @@ +############################################################################## +# 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/spack/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 os + + +class Trf(Package): + """Tandem Repeats Finder is a program to locate and display tandem repeats + in DNA sequences. + + Note: A manual download is required for TRF. + Spack will search your current directory for the download file. + Alternatively, add this file to a mirror so that Spack can find it. + For instructions on how to set up a mirror, see + http://spack.readthedocs.io/en/latest/mirrors.html""" + + homepage = "https://tandem.bu.edu/trf/trf.html" + + version('4.09', '0c594fe666e0332db1df9d160d7fabc8', expand=False, + url='file://{0}/trf409.linux64'.format(os.getcwd())) + + def install(self, spec, prefix): + mkdirp(prefix.bin) + install('trf409.linux64', prefix.bin.trf) |