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src/q/i/qiime-1.8.0/scripts/print_qiime_config.py   qiime(Download)
 
try:    
    from cogent.util.misc import app_path, get_random_directory_name, remove_files
    from cogent.app.util import ApplicationNotFoundError, ApplicationError
    from cogent import __version__ as pycogent_lib_version
 
        if fp:
            full_path = app_path(fp)
            if full_path:
                fp = full_path
    def test_uclust_supported_version(self):
        """uclust is in path and version is supported """
        acceptable_version = (1,2,22)
        self.assertTrue(app_path('uclust'),
         "uclust not found. This may or may not be a problem depending on "+\
    def test_FastTree_supported_version(self):
        """FastTree is in path and version is supported """
        acceptable_version = (2,1,3)
        self.assertTrue(app_path('FastTree'),
         "FastTree not found. This may or may not be a problem depending on "+\
         "$SEQ_LOOKUP_FILE variable is not set to an existing filepath.")
 
        self.assertTrue(app_path("SplitKeys.pl"),
         "Couldn't find SplitKeys.pl. "+\
         "Perhaps AmpliconNoise Scripts directory isn't in $PATH?"+\

src/c/o/cogent-1.5.3/cogent/app/rnaforester.py   cogent(Download)
#!/usr/bin/env python
 
from os import mkdir,getcwd,system,remove,close
from random import choice
from cogent.util.misc import app_path
    def _error_on_missing_application(self,params):
        """ Raise an ApplicationNotFoundError if the app is not accessible
        """
        if not app_path('RNAforester'):
            raise ApplicationNotFoundError,\
             "Cannot find RNAforester. Is it installed? Is it in your path?"
        if not app_path('RNAshapes'):

src/q/i/qiime-1.8.0/qiime/denoiser/make_cluster_jobs.py   qiime(Download)
from subprocess import Popen, PIPE, STDOUT
 
from cogent.util.misc import app_path, create_dir
from cogent.app.util import ApplicationNotFoundError
from qiime.util import get_tmp_filename
    verbose: a binary verbose flag
    """
    if(not app_path("qsub")):
        raise ApplicationNotFoundError,"qsub not found. Can't submit jobs."
 

src/p/y/pycogent-HEAD/cogent/app/rnaforester.py   pycogent(Download)
#!/usr/bin/env python
 
from os import mkdir,getcwd,system,remove,close
from random import choice
from cogent.util.misc import app_path
    def _error_on_missing_application(self,params):
        """ Raise an ApplicationNotFoundError if the app is not accessible
        """
        if not app_path('RNAforester'):
            raise ApplicationNotFoundError,\
             "Cannot find RNAforester. Is it installed? Is it in your path?"
        if not app_path('RNAshapes'):

src/c/o/cogent-1.5.3/cogent/app/util.py   cogent(Download)
from cogent.util.misc import if_
from cogent.util.transform import cartesian_product
from cogent.util.misc import app_path
 
__author__ = "Sandra Smit and Greg Caporaso"
        """
        command = self._command
        if not (exists(command) or app_path(command)):
            raise ApplicationNotFoundError,\
             "Cannot find %s. Is it installed? Is it in your path?"\

src/c/o/cogent-1.5.3/cogent/app/rtax.py   cogent(Download)
from cogent.app.util import CommandLineApplication, ResultPath,\
 get_tmp_filename, ApplicationError, ApplicationNotFoundError
from cogent.util.misc import remove_files, app_path
from cogent import DNA
import tempfile
 
    usearch_command = "usearch"
    if not (exists(usearch_command) or app_path(usearch_command)):
        raise ApplicationNotFoundError,\
         "Cannot find %s. Is it installed? Is it in your path?"\

src/p/y/pycogent-HEAD/cogent/app/util.py   pycogent(Download)
from cogent.util.misc import if_
from cogent.util.transform import cartesian_product
from cogent.util.misc import app_path
 
__author__ = "Sandra Smit and Greg Caporaso"
        """
        command = self._command
        if not (exists(command) or app_path(command)):
            raise ApplicationNotFoundError,\
             "Cannot find %s. Is it installed? Is it in your path?"\

src/p/y/pycogent-HEAD/cogent/app/rtax.py   pycogent(Download)
from cogent.app.util import CommandLineApplication, ResultPath,\
 get_tmp_filename, ApplicationError, ApplicationNotFoundError
from cogent.util.misc import remove_files, app_path
from cogent import DNA
import tempfile
 
    usearch_command = "usearch"
    if not (exists(usearch_command) or app_path(usearch_command)):
        raise ApplicationNotFoundError,\
         "Cannot find %s. Is it installed? Is it in your path?"\

src/c/o/cogent-1.5.3/cogent/app/rdp_classifier.py   cogent(Download)
    FilePath, ResultPath, guess_input_handler, system,\
    ApplicationNotFoundError, ApplicationError
from cogent.util.misc import app_path
 
class RdpClassifier(CommandLineApplication):
        In this case, checks for the java runtime and the RDP jar file.
        """
        if not (os.path.exists('java') or app_path('java')):
            raise ApplicationNotFoundError(
                "Cannot find java runtime. Is it installed? Is it in your "

src/c/o/cogent-1.5.3/cogent/app/blast.py   cogent(Download)
from cogent.parse.fasta import FastaFinder, LabeledRecordFinder, is_fasta_label
from cogent.parse.blast import LastProteinIds9, QMEBlast9, QMEPsiBlast9, BlastResult
from cogent.util.misc import app_path
from random import choice
from copy import copy
    def _error_on_missing_application(self,params):
        """ Raise an ApplicationNotFoundError if the app is not accessible
        """
        if not app_path('blastall'):
            raise ApplicationNotFoundError,\

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