Exemplos de Pipeline.getParameters em Python

Exemplo n.º 1

Arquivo: conf.py Projeto: MikeDMorgan/scRNAseq

logopath = os.path.join(themedir, "cgat_logo.png")

################################################################
# Import pipeline configuration from pipeline.ini in the current
# directory and the common one.

# PATH were code for pipelines is stored
pipelinesdir = os.path.dirname(CGATPipelines.__file__)

# The default configuration file - 'inifile' is read by
# sphinx-report.
inifile = os.path.join(os.path.dirname(CGATPipelines.__file__),
                       'configuration',
                       'pipeline.ini')

PARAMS = P.getParameters([inifile, "pipeline.ini"])

# Definition now part of CGATReport
# def setup(app):
#     app.add_config_value('PARAMS', {}, True)

################################################################
################################################################
################################################################
# The pipeline assumes that sphinxreport is called within the
# working directory. If the report is in a separate build directory,
# change the paths below.
#
# directory with export directory from pipeline
# This should be a directory in the build directory - you can
# link from here to a directory outside the build tree, though.

Exemplo n.º 2

Arquivo: pipeline_scRNASeq.py Projeto: shulp2211/UMIpipe

import os
import CGAT.Experiment as E
import CGATPipelines.Pipeline as P
import CGAT.Sra as SRA
import CGAT.IOTools as IOTools

import CGATPipelines.PipelinePreprocess as PipelinePreprocess
import CGATPipelines.PipelineMapping as PipelineMapping
import PipelineScRNASeq

###################################################
# Pipeline configuration
###################################################
P.getParameters([
    "%s/pipeline.ini" % os.path.splitext(__file__)[0], "../pipeline.ini",
    "pipeline.ini"
],
                defaults={'paired_end': False},
                only_import=__name__ != "__main__")

PARAMS = P.PARAMS

###############################################################################
# Section - START - GSE53638 - Soumillon et al 2014
###############################################################################


@follows(mkdir("GSE53638"))
@originate([
    "GSE53638/SRR1058003.sra", "GSE53638/SRR1058023.sra",
    "GSE53638/SRR1058032.sra", "GSE53638/SRR1058038.sra"
])

Exemplo n.º 3

Arquivo: iCLIPTracker.py Projeto: CGATOxford/UMI-tools_pipelines

from CGATReport.Tracker import *

import CGATPipelines.Pipeline as P

#############################################################################
# Get parameterization

P.getParameters( 
    ["%s/pipeline.ini" % __file__[:-len(".py")],
     "../pipeline.ini",
     "pipeline.ini" ] )

LOCALPARAMS = P.PARAMS

P.getParameters( ["%s/pipeline.ini" % __file__[:-len(".py")],
                  "../pipeline.ini",
                  "%s/pipeline.ini" % LOCALPARAMS["iclip_dir"],
                  "pipeline.ini" ])

PARAMS = P.PARAMS
class ProjectTracker(TrackerSQL):


    PARAMS = P.PARAMS

    def __init__(self, *args, **kwargs ):
        database_path = os.path.join(PARAMS["iclip_dir"], PARAMS["iclip_database"])
        database = database_path
        
        TrackerSQL.__init__(self, *args, backend = "sqlite:///" + database , **kwargs )
        

Exemplo n.º 4

Arquivo: pipeline_poolreads.py Projeto: microbialman/PoolReads

#load modules
from ruffus import *
import os
import sys
import math

###################################################
###################################################
###################################################
# Pipeline configuration
###################################################
# load options from the config file
import CGATPipelines.Pipeline as P
P.getParameters(
       ["%s.ini" % __file__[:-len(".py")],
       "../pipeline.ini",
       "pipeline.ini" ] )
PARAMS = P.PARAMS

#add Pipeline functions
import PipelineMetaAssemblyKit
import PipelinePoolReads

#get all files within the directory to process
SEQUENCEFILES = ("*.fasta", "*.fasta.gz", "*.fasta.1.gz", "*.fasta.1",
                 "*.fna", "*.fna.gz", "*.fna.1.gz", "*.fna.1",
                 "*.fa", "*.fa.gz", "*.fa.1.gz", "*.fa.1", 
                 "*.fastq", "*.fastq.gz", "*.fastq.1.gz","*.fastq.1")

#using log files to track progression as ruffus cant parse inputs within merge

Exemplo n.º 5

Arquivo: pipeline_project035.py Projeto: MikeDMorgan/proj035

from ruffus import *

import sys
import os
import sqlite3
import CGAT.Experiment as E
import CGATPipelines.Pipeline as P
import CGATPipelines.PipelineTracks as PipelineTracks
import PipelineProject035 as P35
import glob
import itertools


# load options from the config file
PARAMS = P.getParameters(
    ["%s/pipeline.ini" % os.path.splitext(__file__)[0],
     "../pipeline.ini",
     "pipeline.ini"])

# add configuration values from associated pipelines
#
# 1. pipeline_annotations: any parameters will be added with the
#    prefix "annotations_". The interface will be updated with
#    "annotations_dir" to point to the absolute path names.
PARAMS.update(P.peekParameters(
    PARAMS["annotations_dir"],
    "pipeline_annotations.py",
    on_error_raise=__name__ == "__main__",
    prefix="annotations_",
    update_interface=True))

Exemplo n.º 6

Arquivo: pipeline_rnaseqlncrna.py Projeto: gjaime/CGATPipelines

from rpy2.robjects import r as R

import CGAT.Experiment as E
import CGATPipelines.Pipeline as P
import CGAT.GTF as GTF
import CGAT.IOTools as IOTools
import CGATPipelines.PipelineLncRNA as PipelineLncRNA

###################################################
# Pipeline configuration
###################################################
P.getParameters(
    ["%s/pipeline.ini" % os.path.splitext(__file__)[0],
     "../pipeline.ini",
     "pipeline.ini"],
    defaults={"annotations_dir": "",
              "genesets_abinitio_coding": "pruned.gtf.gz",
              "genesets_abinitio_lncrna": "pruned.gtf.gz",
              "genesets_reference": "reference.gtf.gz",
              "genesets_refcoding": "refcoding.gtf.gz",
              "genesets_previous": ""})

PARAMS = P.PARAMS

PARAMS.update(P.peekParameters(
    PARAMS["annotations_dir"],
    "pipeline_annotations.py",
    prefix="annotations_",
    update_interface=True))

PREVIOUS = P.asList(PARAMS["genesets_previous"])

Exemplo n.º 7

Arquivo: pipeline_ancestral_repeats.py Projeto: Acribbs/CGATPipelines

import MySQLdb
import CGAT.Experiment as E
import logging as L

from ruffus import *

###################################################
###################################################
###################################################
# Pipeline configuration
###################################################
import CGATPipelines.Pipeline as P
P.getParameters(
    ["%s/pipeline.ini" % os.path.splitext(__file__)[0],
     "../pipeline.ini",
     "pipeline.ini"],
    defaults={
        'query': "",
        'target': ""})
PARAMS = P.PARAMS

if os.path.exists("pipeline_conf.py"):
    L.info("reading additional configuration from pipeline_conf.py")
    exec(compile(open("pipeline_conf.py").read(), "pipeline_conf.py", 'exec'))


def getGenomes():
    '''return genome names of query and target.'''

    genome_query = os.path.join(PARAMS["genome_dir"], PARAMS["query"])
    genome_target = os.path.join(PARAMS["genome_dir"], PARAMS["target"])

Exemplo n.º 8

Arquivo: pipeline_exome_cancer.py Projeto: gjaime/CGATPipelines

def connect():
    '''connect to database.
    Use this method to connect to additional databases.
    Returns a database connection.
    '''
    dbh = sqlite3.connect(PARAMS["database_name"])

    return dbh


#########################################################################
P.getParameters(
    ["%s/pipeline.ini" % os.path.splitext(__file__)[0],
     "../pipeline.ini",
     "pipeline.ini"],
    defaults={
        'paired_end': False},
    only_import=__name__ != "__main__")

PARAMS = P.PARAMS

PipelineMapping.PARAMS = PARAMS
PipelineMappingQC.PARAMS = PARAMS
PipelineExome.PARAMS = PARAMS
#########################################################################


#########################################################################
# Load manual annotations
#########################################################################

Exemplo n.º 9

"""
from ruffus import *

import sys
import glob
import os
import CGAT.Experiment as E
import CGATPipelines.PipelineChipseq as PIntervals
import CGATPipelines.PipelineTracks as PipelineTracks
import CGATPipelines.PipelineMapping as PipelineMapping
import CGATPipelines.Pipeline as P

USECLUSTER = True

P.getParameters(["%s.ini" % os.path.splitext(__file__)[0],  "pipeline.ini"])
PARAMS = P.PARAMS

###################################################################
###################################################################
###################################################################
# Helper functions mapping tracks to conditions, etc
###################################################################
# load all tracks - exclude input/control tracks
Sample = PipelineTracks.Sample3

#TRACKS = PipelineTracks.Tracks( PipelineTracks.Sample3 ).loadFromDirectory( [x for x in glob.glob( "*.fastq.gz" ) if PARAMS["tracks_control"] not in x], "(\S+).fastq.gz" )
TRACKS = PipelineTracks.Tracks(Sample).loadFromDirectory(
    [x.replace("../", "")
     for x in glob.glob("*.export.txt.gz") if PARAMS["tracks_control"] not in x],
    "(\S+).export.txt.gz" ) +\

Exemplo n.º 10

Arquivo: pipeline_expression.py Projeto: gjaime/CGATPipelines

if os.path.exists("conf.py"):
    execfile("conf.py")

TARGET_ANNOTATION = 'ensembl_regions.gff'
TARGET_GENESET = 'ensembl.gtf'
TARGET_PROMOTORS = 'promotors.gtf'
TARGET_TSS = 'tss.gtf'
TARGET_REPEATS = 'repeats.gff'
TARGET_TRANSCRIPTS = 'transcripts.gtf.gz'
TARGET_PROBESET = 'probeset.gtf'
TARGET_TRANSCRIPTS_TSS = 'transcripts_tss.gtf'
TARGET_TRANSCRIPTS_PROMOTORS = 'transcripts_promotors.gtf'
TARGET_ANNOTATOR_GENETERRITORIES = 'annotator_geneterritories.gff'
TARGET_MAPPABILITY = 'mappability.bed'

PARAMS = P.getParameters()


@files(((None, "probeset2gene.table"), ))
def buildProbeset2Gene(infile, outfile):
    '''build map relating a probeset to an ENSEMBL gene_id'''
    Expression.buildProbeset2Gene(infile, outfile)


@follows(buildProbeset2Gene)
def prepare():
    pass


@files([((x, "%s.map" % x), "%s_levels.import" % x[:-len("_series_matrix.txt.gz")])
        for x in glob.glob("*_series_matrix.txt.gz")])

Exemplo n.º 11

Arquivo: pipeline_motifs.py Projeto: wbyu/CGATPipelines

import CGAT.Experiment as E
import CGAT.IOTools as IOTools

import CGATPipelines.PipelineMotifs as PipelineMotifs
import CGATPipelines.PipelineTracks as PipelineTracks

###################################################
###################################################
###################################################
# Pipeline configuration
###################################################
import CGATPipelines.Pipeline as P
P.getParameters([
    "%s/pipeline.ini" % os.path.splitext(__file__)[0], "../pipeline.ini",
    "pipeline.ini"
],
                defaults={'annotations_dir': ""})

PARAMS = P.PARAMS

PARAMS_ANNOTATIONS = P.peekParameters(PARAMS["annotations_dir"],
                                      "pipeline_genesets.py")

###################################################################
###################################################################
###################################################################
# Helper functions mapping tracks to conditions, etc
###################################################################
# load all tracks - exclude input/control tracks
Sample = PipelineTracks.Sample

Exemplo n.º 12

Arquivo: pipeline_proj020.py Projeto: CGATOxford/CGATPipelines

import sqlite3
import io
import fileinput
import CGAT.Fastq as fq
import logging as L
import CGAT.Experiment as E
import CGATPipelines.PipelineMapping as PipelineMapping
from ruffus import *


###################################################################
###################################################################
###################################################################
# Pipeline configuration
import CGATPipelines.Pipeline as P
P.getParameters(["pipeline.ini"])
PARAMS = P.PARAMS
USECLUSTER = True

###################################################################
###################################################################
###################################################################
# Count raw reads


@transform("*.fastq.1.gz", regex(r"(\S+).fastq.1.gz"), r"\1.nreads")
def countReads(infile, outfile):
    '''count number of reads in input files.'''
    to_cluster = True
    m = PipelineMapping.Counter()
    statement = m.build((infile,), outfile)

Exemplo n.º 13

import sqlite3

import CGAT.Experiment as E
import CGAT.IOTools as IOTools
import CGATPipelines.PipelineMapping as PipelineMapping
import PipelineiCLIP
###################################################
###################################################
###################################################
# Pipeline configuration
###################################################

# load options from the config file
import CGATPipelines.Pipeline as P
P.getParameters([
    os.path.join(os.path.dirname(__file__), "configuration", "pipeline.ini"),
    "pipeline.ini"
])

PARAMS = P.PARAMS
PARAMS_ANNOTATIONS = P.peekParameters(PARAMS["annotations_dir"],
                                      "pipeline_annotations.py")

PipelineiCLIP.PARAMS = PARAMS
PipelineiCLIP.PARAMS_ANNOTATIONS = PARAMS_ANNOTATIONS
PARAMS["project_src"] = os.path.join(os.path.dirname(__file__), "..")

###################################################################
# Helper functions mapping tracks to conditions, etc
###################################################################
import CGATPipelines.PipelineTracks as PipelineTracks

Exemplo n.º 14

Arquivo: pipeline_fastqToBigWig.py Projeto: gjaime/CGATPipelines

"""
from ruffus import *

import sys
import glob
import os
import CGAT.Experiment as E
import PipelineChipseq as PIntervals
import CGATPipelines.PipelineTracks as PipelineTracks
import CGATPipelines.PipelineMapping as PipelineMapping
import CGATPipelines.Pipeline as P

USECLUSTER = True

P.getParameters(["%s.ini" % os.path.splitext(__file__)[0],  "pipeline.ini"])
PARAMS = P.PARAMS

###################################################################
###################################################################
###################################################################
# Helper functions mapping tracks to conditions, etc
###################################################################
# load all tracks - exclude input/control tracks
Sample = PipelineTracks.Sample3

#TRACKS = PipelineTracks.Tracks( PipelineTracks.Sample3 ).loadFromDirectory( [x for x in glob.glob( "*.fastq.gz" ) if PARAMS["tracks_control"] not in x], "(\S+).fastq.gz" )
TRACKS = PipelineTracks.Tracks(Sample).loadFromDirectory(
    [x.replace("../", "")
     for x in glob.glob("*.export.txt.gz") if PARAMS["tracks_control"] not in x],
    "(\S+).export.txt.gz" ) +\

Exemplo n.º 15

Arquivo: pipeline_expression.py Projeto: wbyu/CGATPipelines

if os.path.exists("conf.py"):
    exec(compile(open("conf.py").read(), "conf.py", 'exec'))

TARGET_ANNOTATION = 'ensembl_regions.gff'
TARGET_GENESET = 'ensembl.gtf'
TARGET_PROMOTORS = 'promotors.gtf'
TARGET_TSS = 'tss.gtf'
TARGET_REPEATS = 'repeats.gff'
TARGET_TRANSCRIPTS = 'transcripts.gtf.gz'
TARGET_PROBESET = 'probeset.gtf'
TARGET_TRANSCRIPTS_TSS = 'transcripts_tss.gtf'
TARGET_TRANSCRIPTS_PROMOTORS = 'transcripts_promotors.gtf'
TARGET_ANNOTATOR_GENETERRITORIES = 'annotator_geneterritories.gff'
TARGET_MAPPABILITY = 'mappability.bed'

PARAMS = P.getParameters()


@files(((None, "probeset2gene.table"), ))
def buildProbeset2Gene(infile, outfile):
    '''build map relating a probeset to an ENSEMBL gene_id'''
    Expression.buildProbeset2Gene(infile, outfile)


@follows(buildProbeset2Gene)
def prepare():
    pass


@files([((x, "%s.map" % x),
         "%s_levels.import" % x[:-len("_series_matrix.txt.gz")])

Exemplo n.º 16

Arquivo: pipeline_polyphen.py Projeto: wbyu/CGATPipelines

import sys
import glob
import os
import itertools
import sqlite3
import CGAT.Experiment as E
import CGATPipelines.Pipeline as P
import PipelineGeneset as PGeneset

###################################################################
###################################################################
###################################################################
# read global options from configuration file
P.getParameters(
    ["%s/pipeline.ini" % os.path.splitext(__file__)[0],
     "../pipeline.ini",
     "pipeline.ini"],
    defaults={'polyphen_modes': ""})

P.PARAMS.update(
    {"transcripts": "transcripts.gtf.gz",
     "genes": 'genes.gtf.gz',
     "annotation": 'geneset_regions.gff.gz',
     "peptides": 'peptides.fasta',
     "cdna": 'cdna.fasta',
     "cds": 'cds.fasta'})

PARAMS = P.PARAMS

PGeneset.PARAMS = PARAMS

Exemplo n.º 17

import CGAT.Experiment as E
import CGATPipelines.Pipeline as P
import CGAT.IOTools as IOTools
import CGAT.Bed as Bed
import CGATPipelines.PipelinePeakcalling as PipelinePeakcalling
import PipelineDeNovoMotifs as PipelineMotifs
import CGATPipelines.PipelineTracks as PipelineTracks

###################################################
###################################################
###################################################
# Pipeline configuration
###################################################
P.getParameters([
    "%s/pipeline.ini" % os.path.splitext(__file__)[0], "../pipeline.ini",
    "pipeline.ini"
],
                defaults={'paired_end': False})

PARAMS = P.PARAMS

PARAMS.update(
    P.peekParameters(PARAMS["annotations_dir"],
                     "pipeline_annotations.py",
                     prefix="annotations_",
                     update_interface=True))

PipelinePeakcalling.PARAMS = PARAMS
PipelineMotifs.PARAMS = PARAMS

###################################################################

Exemplo n.º 18

from CGATReport.Tracker import *

import CGATPipelines.Pipeline as P

#############################################################################
# Get parameterization

P.getParameters([
    "%s/pipeline.ini" % __file__[:-len(".py")], "../pipeline.ini",
    "pipeline.ini"
])

LOCALPARAMS = P.PARAMS

P.getParameters([
    "%s/pipeline.ini" % __file__[:-len(".py")], "../pipeline.ini",
    "%s/pipeline.ini" % LOCALPARAMS["iclip_dir"], "pipeline.ini"
])

PARAMS = P.PARAMS


class ProjectTracker(TrackerSQL):

    PARAMS = P.PARAMS

    def __init__(self, *args, **kwargs):
        database_path = os.path.join(PARAMS["iclip_dir"],
                                     PARAMS["iclip_database"])
        database = database_path

Exemplo n.º 19

import CGAT.IOTools as IOTools
import CGAT.Database as Database
import CGAT.FastaIterator as FastaIterator
import numpy as np
from PipelinePrimerDesign import PrimerSet

###################################################
###################################################
###################################################
## Pipeline configuration
###################################################

# load options from the config file
import CGATPipelines.Pipeline as P

P.getParameters(["pipeline.ini"])

PARAMS = P.PARAMS

###################################################
###################################################
###################################################


def readIdentifiers(identifiers):
    '''
    return list of identifiers from file
    '''
    ids = [x.strip("\n") for x in IOTools.openFile(identifiers).readlines()]
    return ids

Exemplo n.º 20

Arquivo: PipelineIntervalAnnotation.py Projeto: BioXiao/CGATPipelines

import CGAT.IndexedFasta as IndexedFasta
import CGAT.IndexedGenome as IndexedGenome
import CGAT.FastaIterator as FastaIterator
import CGAT.Genomics as Genomics
import CGAT.GTF as GTF
import CGAT.Bed as Bed
import pysam
import numpy
import CGAT.Experiment as E
import CGATPipelines.Pipeline as P

############################################################
############################################################
############################################################
# Pipeline configuration
P.getParameters(["%s.ini" % __file__[:-len(".py")], "pipeline.ini"])
PARAMS = P.PARAMS

############################################################
############################################################
############################################################


def exportIntervalsAsBed(database, query, outfile):
    '''export intervals from SQlite database as bed files. '''

    dbhandle = sqlite3.connect(database)
    cc = dbhandle.cursor()
    cc.execute(query)

    outs = IOTools.openFile(outfile, "w")

Exemplo n.º 21

Arquivo: pipeline_ancestral_repeats.py Projeto: gjaime/CGATPipelines

import MySQLdb
import CGAT.Experiment as E
import logging as L

from ruffus import *

###################################################
###################################################
###################################################
# Pipeline configuration
###################################################
import CGATPipelines.Pipeline as P
P.getParameters(
    ["%s/pipeline.ini" % os.path.splitext(__file__)[0],
     "../pipeline.ini",
     "pipeline.ini"],
    defaults={
        'query': "",
        'target': ""})
PARAMS = P.PARAMS

if os.path.exists("pipeline_conf.py"):
    L.info("reading additional configuration from pipeline_conf.py")
    execfile("pipeline_conf.py")


def getGenomes():
    '''return genome names of query and target.'''

    genome_query = os.path.join(PARAMS["genome_dir"], PARAMS["query"])
    genome_target = os.path.join(PARAMS["genome_dir"], PARAMS["target"])

Exemplo n.º 22

Arquivo: pipeline_rnaseqlncrna.py Projeto: Acribbs/CGATPipelines

from rpy2.robjects import r as R

import CGAT.Experiment as E
import CGATPipelines.Pipeline as P
import CGAT.GTF as GTF
import CGAT.IOTools as IOTools
import CGATPipelines.PipelineLncRNA as PipelineLncRNA

###################################################
# Pipeline configuration
###################################################
P.getParameters(
    ["%s/pipeline.ini" % os.path.splitext(__file__)[0],
     "../pipeline.ini",
     "pipeline.ini"],
    defaults={"annotations_dir": "",
              "genesets_abinitio_coding": "pruned.gtf.gz",
              "genesets_abinitio_lncrna": "pruned.gtf.gz",
              "genesets_reference": "reference.gtf.gz",
              "genesets_refcoding": "refcoding.gtf.gz",
              "genesets_previous": ""})

PARAMS = P.PARAMS

PARAMS.update(P.peekParameters(
    PARAMS["annotations_annotations_dir"],
    "pipeline_annotations.py",
    prefix="annotations_",
    update_interface=True))

PREVIOUS = P.asList(PARAMS["genesets_previous"])

Exemplo n.º 23

"""

from ruffus import *

import sys
import os
import glob
import sqlite3
import CGAT.Experiment as E
import CGATPipelines.Pipeline as P
import CGATPipelines.PipelineTracks as PipelineTracks
import pysam

# load options from the config file
PARAMS = P.getParameters(
    ["%s/pipeline.ini" % os.path.splitext(__file__)[0],
     "../pipeline.ini",
     "pipeline.ini"])

# add configuration values from associated pipelines
#
# 1. pipeline_annotations: any parameters will be added with the
#    prefix "annotations_". The interface will be updated with
#    "annotations_dir" to point to the absolute path names.
PARAMS.update(P.peekParameters(
    PARAMS["annotations_dir"],
    "pipeline_annotations.py",
    on_error_raise=__name__ == "__main__",
    prefix="annotations_",
    update_interface=True))

# define some tracks if needed

Exemplo n.º 24

Arquivo: pipeline_cufflinks_optimization.py Projeto: CGATOxford/CGATPipelines

import CGAT.GTF as GTF
import CGAT.IOTools as IOTools

###################################################
###################################################
###################################################
# Pipeline configuration
###################################################

# load options from the config file
import CGATPipelines.Pipeline as P
from functools import reduce
P.getParameters(
    ["%s/pipeline.ini" % os.path.splitext(__file__)[0],
     "../pipeline.ini",
     "pipeline.ini"],
    defaults={
        'annotations_dir': "",
        'paired_end': False})

PARAMS = P.PARAMS

PARAMS_ANNOTATIONS = P.peekParameters(
    PARAMS["annotations_dir"],
    "pipeline_annotations.py")

# get options that are to be tested
cufflinks_options = {}
if "cufflinks_test_options" in PARAMS:
    options = P.asList(PARAMS["cufflinks_test_options"])
    for option in options:

Exemplo n.º 25

                        'pipeline_docs', 'themes')
logopath = os.path.join(themedir, "cgat_logo.png")

################################################################
# Import pipeline configuration from pipeline.ini in the current
# directory and the common one.

# PATH were code for pipelines is stored
pipelinesdir = os.path.dirname(CGATPipelines.__file__)

# The default configuration file - 'inifile' is read by
# sphinx-report.
inifile = os.path.join(os.path.dirname(CGATPipelines.__file__),
                       'configuration', 'pipeline.ini')

PARAMS = P.getParameters([inifile, "pipeline.ini"])


def setup(app):
    app.add_config_value('PARAMS', {}, True)


################################################################
################################################################
################################################################
# The pipeline assumes that sphinxreport is called within the
# working directory. If the report is in a separate build directory,
# change the paths below.
#
# directory with export directory from pipeline
# This should be a directory in the build directory - you can

Exemplo n.º 26

Arquivo: pipeline_chains.py Projeto: wbyu/CGATPipelines

import CGAT.Experiment as E
import CGATPipelines.Pipeline as P
import CGAT.IOTools as IOTools
import CGAT.IndexedFasta as IndexedFasta

###################################################
###################################################
###################################################
# Pipeline configuration
###################################################

# load options from the config file

P.getParameters([
    "%s/pipeline.ini" % os.path.splitext(__file__)[0], "../pipeline.ini",
    "pipeline.ini"
],
                defaults={"maps": ""})
PARAMS = P.PARAMS

###################################################################
###################################################################
###################################################################
##
###################################################################
if os.path.exists("pipeline_conf.py"):
    L.info("reading additional configuration from pipeline_conf.py")
    exec(compile(open("pipeline_conf.py").read(), "pipeline_conf.py", 'exec'))

PARAMS = P.getParameters()

Exemplo n.º 27

Arquivo: pipeline_chains.py Projeto: CGATOxford/CGATPipelines

import CGAT.Experiment as E
import CGATPipelines.Pipeline as P
import CGAT.IOTools as IOTools
import CGAT.IndexedFasta as IndexedFasta

###################################################
###################################################
###################################################
# Pipeline configuration
###################################################

# load options from the config file

P.getParameters(
    ["%s/pipeline.ini" % os.path.splitext(__file__)[0],
     "../pipeline.ini",
     "pipeline.ini"],
    defaults={"maps": ""})
PARAMS = P.PARAMS

###################################################################
###################################################################
###################################################################
##
###################################################################
if os.path.exists("pipeline_conf.py"):
    L.info("reading additional configuration from pipeline_conf.py")
    exec(compile(open("pipeline_conf.py").read(), "pipeline_conf.py", 'exec'))

PARAMS = P.getParameters()

Exemplo n.º 28

            INI_file = os.path.abspath(path)
            print(
                'You have no project configuration (".ini") file or more than one',
                'in the directory:', '\n', path)
            sys.exit(''' No ini file found. Exiting.
                         You will have to manually edit the Sphinx conf.py file.
                 ''')
    return (INI_file)


modulename = 'P'
if modulename in sys.modules:
    ini_file = 'pipelin{}.ini'.format(r'(.*)')
    P.getParameters([
        "{}/{}".format(os.path.splitext(__file__)[0], ini_file),
        "../{}".format(ini_file),
        "{}".format(ini_file),
    ], )

    PARAMS = P.PARAMS

else:
    # Get location to this file:
    here = os.path.abspath(os.path.dirname(__file__))
    print('This directory is:', '\n', here, '\n')

    #ini_file = getINIdir(os.path.join(here, '..'))
    ini_file = getINIdir(os.path.abspath(here))

    # Print keys (sections):
    print('Values found in INI file:', '\n')