diff options
Diffstat (limited to 'academic/pyCRAC/setup_slack.py')
| -rw-r--r-- | academic/pyCRAC/setup_slack.py | 104 |
1 files changed, 104 insertions, 0 deletions
diff --git a/academic/pyCRAC/setup_slack.py b/academic/pyCRAC/setup_slack.py new file mode 100644 index 0000000000..621b944573 --- /dev/null +++ b/academic/pyCRAC/setup_slack.py @@ -0,0 +1,104 @@ +#!/usr/bin/python +# not compatible with python 3 +__author__ = "Sander Granneman" +__copyright__ = "Copyright 2017" +__version__ = "1.2.3.0" +__credits__ = ["Sander Granneman","Hywell Dunn Davies"] +__maintainer__ = ["Rob van Nues, via SlackBuilds.org"] +__email__ = "sgrannem@staffmail.ed.ac.uk" +__status__ = "Production" + +import sys +import os +import platform +import setuptools +from setuptools import setup + +DEFAULT_PATH = "/usr/share/" + +if sys.version[0:3] < '2.7' : raise ImportError('Python version 2.7 or above is required for pyCRAC') +if sys.version[0:3] >= '3.0': raise ImportError('pyCRAC is not compatible with Python 3.0 or higher') + +sys.stdout.write("\nInstalling pyCRAC version %s...\n" % __version__) + +path_files = open("pyCRAC/defaults.py","w") +#path_files.write("DEFAULT_PATH=\"%s\"\n" % DEFAULT_PATH) +path_files.write("GTF=\"%spyCRAC-%s/db/Saccharomyces_cerevisiae.EF2.59.1.3.gtf\"\nTAB=\"%spyCRAC-%s/db/Saccharomyces_cerevisiae.EF2.59.1.0.fa.tab\"\nCHROM=\"%spyCRAC-%s/db/Saccharomyces_cerevisiae.EF2.59.1.0_chr_lengths.txt\"\n" % (DEFAULT_PATH,__version__,DEFAULT_PATH,__version__,DEFAULT_PATH,__version__)) +path_files.close() + +setup(name='pyCRAC', + version='%s' % __version__, + description='Python NextGen sequencing data processing software', + author='Sander Granneman', + author_email='sgrannem@staffmail.ed.ac.uk', + url='http://sandergranneman.bio.ed.ac.uk/Granneman_Lab/pyCRAC_software.html', + packages=['pyCRAC','pyCRAC.Parsers','pyCRAC.Classes','pyCRAC.Methods'], + install_requires=['numpy >= 1.5.1', 'cython >=0.19', 'pysam >= 0.6'], + scripts=[ + 'pyCRAC/pyReadAligner.py', + 'pyCRAC/pyMotif.py', + 'pyCRAC/pyPileup.py', + 'pyCRAC/pyBarcodeFilter.py', + 'pyCRAC/pyReadCounters.py', + 'pyCRAC/pyBinCollector.py', + 'pyCRAC/pyCalculateFDRs.py', + 'pyCRAC/pyClusterReads.py', + 'pyCRAC/pyCalculateMutationFrequencies.py', + 'pyCRAC/scripts/pyCalculateChromosomeLengths.py', + 'pyCRAC/scripts/pyFastqDuplicateRemover.py', + 'pyCRAC/scripts/pyAlignment2Tab.py', + 'pyCRAC/scripts/pyGetGTFSources.py', + 'pyCRAC/scripts/pySelectMotifsFromGTF.py', + 'pyCRAC/scripts/pyFasta2tab.py', + 'pyCRAC/scripts/pyFastqJoiner.py', + 'pyCRAC/scripts/pyFastqSplitter.py', + 'pyCRAC/scripts/pyExtractLinesFromGTF.py', + 'pyCRAC/scripts/pyGetGeneNamesFromGTF.py', + 'pyCRAC/scripts/pyCheckGTFfile.py', + 'pyCRAC/scripts/pybed2GTF.py', + 'pyCRAC/scripts/pyGTF2sgr.py', + 'pyCRAC/scripts/pyGTF2bed.py', + 'pyCRAC/scripts/pyGTF2bedGraph.py', + 'pyCRAC/scripts/pyFilterGTF.py', + 'pyCRAC/scripts/pyNormalizeIntervalLengths.py', + 'pyCRAC/kinetic_crac_pipeline/CRAC_pipeline_PE.py', + 'pyCRAC/kinetic_crac_pipeline/CRAC_pipeline_PeakFinder.py', + 'pyCRAC/kinetic_crac_pipeline/CRAC_pipeline_SE.py', + 'pyCRAC/kinetic_crac_pipeline/TrimNucs.py' + ], + classifiers=[ 'Development Status :: 5 - Production/Stable', + 'Environment :: Terminal', + 'Intended Audience :: Education', + 'Intended Audience :: Developers', + 'Intended Audience :: Science/Research', + 'License :: Freeware', + 'Operating System :: MacOS :: MacOS X', + 'Operating System :: POSIX', + 'Programming Language :: Python :: 2.7', + 'Topic :: Scientific/Engineering :: Bio-Informatics', + 'Topic :: Software Development :: Libraries :: Application Frameworks' + ], + data_files=[ ('%spyCRAC-%s/db/' % (DEFAULT_PATH,__version__), [ + 'pyCRAC/db/Saccharomyces_cerevisiae.EF2.59.1.0_chr_lengths.txt', + 'pyCRAC/db/Saccharomyces_cerevisiae.EF2.59.1.3.gtf', + 'pyCRAC/db/Saccharomyces_cerevisiae.EF2.59.1.0.fa', + 'pyCRAC/db/Saccharomyces_cerevisiae.EF2.59.1.0.fa.tab']), + ('%spyCRAC-%s/tests/' % (DEFAULT_PATH,__version__), [ + 'tests/test.novo', + 'tests/test.sh', + 'tests/test_coordinates.txt', + 'tests/test.gtf', + 'tests/test_f.fastq', + 'tests/test_f.fastq.gz', + 'tests/test_f_dm.fastq', + 'tests/test_r.fastq', + 'tests/test_r.fastq.gz', + 'tests/test_r_dm.fastq', + 'tests/indexes.txt', + 'tests/barcodes.txt', + 'tests/genes.list']) + ] + ) + + + |