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05-07-2013, 06:05 PM
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#21 |
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Junior Member
Location: Melbourne Join Date: May 2008
Posts: 7
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You need to make sure you run the setup.py script with python 2.7. First work out how to run python 2.7, eg rather than typing "python" you might need to type "python2.7". Then to install nesoni from source:
python2.7 setup.py install This should install a "nesoni" script on your path that uses the same version of python as the setup.py script used. I do still recommend using "virtualenv". I have a shell script to set up a virtualenv and install nesoni and a few other python tools that I use using pip. This serves as documentation of the entire processes of installing them, and of all their dependancies. |
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01-26-2016, 02:39 AM
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#22 | |
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Junior Member
Location: Bangladesh Join Date: Jan 2013
Posts: 1
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Quote:
Hi, I want eheck homopolymer error in my 454 reference assembly using illumina data by using nesoni. With your recommendation I have downloaded nesoni-0.36 and after running "nesoni shrimp" output a reference.fa file. But tuning "nesoni consensus" made the following error-- nesoni-0.36]$ ./nesoni_scripts/nesoni consensus Loading Error compiling Cython file: ------------------------------------------------------------ ... """ cdef public object seqs, seq_order, used_hit_file, unambiguous_seps, shrimp_threshold cdef public int infidelity cdef public bool is_paired_end, same_direction, is_monogamous, is_circular, only_pairs, whole_read_only ^ ------------------------------------------------------------ nesoni/consensus.pyx:475:16: 'bool' is not a type identifier Error compiling Cython file: ------------------------------------------------------------ ... """ cdef public object seqs, seq_order, used_hit_file, unambiguous_seps, shrimp_threshold cdef public int infidelity cdef public bool is_paired_end, same_direction, is_monogamous, is_circular, only_pairs, whole_read_only ^ ------------------------------------------------------------ nesoni/consensus.pyx:475:21: C attribute of type '<error>' cannot be accessed from Python Error compiling Cython file: ------------------------------------------------------------ ... """ cdef public object seqs, seq_order, used_hit_file, unambiguous_seps, shrimp_threshold cdef public int infidelity cdef public bool is_paired_end, same_direction, is_monogamous, is_circular, only_pairs, whole_read_only ^ ------------------------------------------------------------ nesoni/consensus.pyx:475:36: C attribute of type '<error>' cannot be accessed from Python Error compiling Cython file: ------------------------------------------------------------ ... """ cdef public object seqs, seq_order, used_hit_file, unambiguous_seps, shrimp_threshold cdef public int infidelity cdef public bool is_paired_end, same_direction, is_monogamous, is_circular, only_pairs, whole_read_only ^ ------------------------------------------------------------ nesoni/consensus.pyx:475:52: C attribute of type '<error>' cannot be accessed from Python Error compiling Cython file: ------------------------------------------------------------ ... """ cdef public object seqs, seq_order, used_hit_file, unambiguous_seps, shrimp_threshold cdef public int infidelity cdef public bool is_paired_end, same_direction, is_monogamous, is_circular, only_pairs, whole_read_only ^ ------------------------------------------------------------ nesoni/consensus.pyx:475:67: C attribute of type '<error>' cannot be accessed from Python Error compiling Cython file: ------------------------------------------------------------ ... """ cdef public object seqs, seq_order, used_hit_file, unambiguous_seps, shrimp_threshold cdef public int infidelity cdef public bool is_paired_end, same_direction, is_monogamous, is_circular, only_pairs, whole_read_only ^ ------------------------------------------------------------ nesoni/consensus.pyx:475:80: C attribute of type '<error>' cannot be accessed from Python Error compiling Cython file: ------------------------------------------------------------ ... """ cdef public object seqs, seq_order, used_hit_file, unambiguous_seps, shrimp_threshold cdef public int infidelity cdef public bool is_paired_end, same_direction, is_monogamous, is_circular, only_pairs, whole_read_only ^ ------------------------------------------------------------ nesoni/consensus.pyx:475:92: C attribute of type '<error>' cannot be accessed from Python Error compiling Cython file: ------------------------------------------------------------ ... cdef public int n_single, n_single_with_hits, n_single_unambiguous, n_pair, n_pair_with_hits, n_pair_valid, n_pair_valid_unambiguous ATTRIBUTES = [ 'seqs', 'seq_order' ] # Only those relevant to reconsensusing def __init__(self, bool is_paired_end, bool same_direction, int max_pair_sep, int trim, shrimp_threshold, int infidelity, bool is_monogamous, bool is_circular, bool only_pairs, bool whole_read_only, used_hit_file): ^ ------------------------------------------------------------ nesoni/consensus.pyx:482:23: 'bool' is not a type identifier Error compiling Cython file: ------------------------------------------------------------ ... cdef public int n_single, n_single_with_hits, n_single_unambiguous, n_pair, n_pair_with_hits, n_pair_valid, n_pair_valid_unambiguous ATTRIBUTES = [ 'seqs', 'seq_order' ] # Only those relevant to reconsensusing def __init__(self, bool is_paired_end, bool same_direction, int max_pair_sep, int trim, shrimp_threshold, int infidelity, bool is_monogamous, bool is_circular, bool only_pairs, bool whole_read_only, used_hit_file): ^ ------------------------------------------------------------ nesoni/consensus.pyx:482:43: 'bool' is not a type identifier Error compiling Cython file: ------------------------------------------------------------ ... cdef public int n_single, n_single_with_hits, n_single_unambiguous, n_pair, n_pair_with_hits, n_pair_valid, n_pair_valid_unambiguous ATTRIBUTES = [ 'seqs', 'seq_order' ] # Only those relevant to reconsensusing def __init__(self, bool is_paired_end, bool same_direction, int max_pair_sep, int trim, shrimp_threshold, int infidelity, bool is_monogamous, bool is_circular, bool only_pairs, bool whole_read_only, used_hit_file): ^ ------------------------------------------------------------ nesoni/consensus.pyx:482:126: 'bool' is not a type identifier Error compiling Cython file: ------------------------------------------------------------ ... cdef public int n_single, n_single_with_hits, n_single_unambiguous, n_pair, n_pair_with_hits, n_pair_valid, n_pair_valid_unambiguous ATTRIBUTES = [ 'seqs', 'seq_order' ] # Only those relevant to reconsensusing def __init__(self, bool is_paired_end, bool same_direction, int max_pair_sep, int trim, shrimp_threshold, int infidelity, bool is_monogamous, bool is_circular, bool only_pairs, bool whole_read_only, used_hit_file): ^ ------------------------------------------------------------ nesoni/consensus.pyx:482:146: 'bool' is not a type identifier Error compiling Cython file: ------------------------------------------------------------ ... cdef public int n_single, n_single_with_hits, n_single_unambiguous, n_pair, n_pair_with_hits, n_pair_valid, n_pair_valid_unambiguous ATTRIBUTES = [ 'seqs', 'seq_order' ] # Only those relevant to reconsensusing def __init__(self, bool is_paired_end, bool same_direction, int max_pair_sep, int trim, shrimp_threshold, int infidelity, bool is_monogamous, bool is_circular, bool only_pairs, bool whole_read_only, used_hit_file): ^ ------------------------------------------------------------ nesoni/consensus.pyx:482:164: 'bool' is not a type identifier Error compiling Cython file: ------------------------------------------------------------ ... cdef public int n_single, n_single_with_hits, n_single_unambiguous, n_pair, n_pair_with_hits, n_pair_valid, n_pair_valid_unambiguous ATTRIBUTES = [ 'seqs', 'seq_order' ] # Only those relevant to reconsensusing def __init__(self, bool is_paired_end, bool same_direction, int max_pair_sep, int trim, shrimp_threshold, int infidelity, bool is_monogamous, bool is_circular, bool only_pairs, bool whole_read_only, used_hit_file): ^ ------------------------------------------------------------ nesoni/consensus.pyx:482:181: 'bool' is not a type identifier /home/tamim/.pyxbld/temp.linux-x86_64-2.6/pyrex/nesoni/consensus.c:1:2: error: #error Do not use this file, it is the result of a failed Cython compilation. Traceback (most recent call last): File "./nesoni_scripts/nesoni", line 15, in <module> sys.exit(nesoni.main(sys.argv[1:])) File "/home/smp2_arr_j/tamim_analysis/tools/nesoni-0.36/nesoni/__init__.py", line 177, in main recombination File "/home/smp2_arr_j/tamim_analysis/tools/nesoni-0.36/nesoni/grace.py", line 160, in execute commands[args[start]](args[start+1:end]) File "/home/smp2_arr_j/tamim_analysis/tools/nesoni-0.36/nesoni/__init__.py", line 89, in consensus grace.load('consensus').main(args) File "/home/smp2_arr_j/tamim_analysis/tools/nesoni-0.36/nesoni/grace.py", line 44, in load m = __import__(module_name, globals()) File "/usr/lib64/python2.6/site-packages/Cython-0.23.4-py2.6-linux-x86_64.egg/pyximport/pyximport.py", line 435, in load_module language_level=self.language_level) File "/usr/lib64/python2.6/site-packages/Cython-0.23.4-py2.6-linux-x86_64.egg/pyximport/pyximport.py", line 227, in load_module exec("raise exc, None, tb", {'exc': exc, 'tb': tb}) File "/usr/lib64/python2.6/site-packages/Cython-0.23.4-py2.6-linux-x86_64.egg/pyximport/pyximport.py", line 209, in load_module inplace=build_inplace, language_level=language_level) File "/usr/lib64/python2.6/site-packages/Cython-0.23.4-py2.6-linux-x86_64.egg/pyximport/pyximport.py", line 186, in build_module reload_support=pyxargs.reload_support) File "/usr/lib64/python2.6/site-packages/Cython-0.23.4-py2.6-linux-x86_64.egg/pyximport/pyxbuild.py", line 100, in pyx_to_dll dist.run_commands() File "/usr/lib64/python2.6/distutils/dist.py", line 975, in run_commands self.run_command(cmd) File "/usr/lib64/python2.6/distutils/dist.py", line 995, in run_command cmd_obj.run() File "/usr/lib64/python2.6/site-packages/Cython-0.23.4-py2.6-linux-x86_64.egg/Cython/Distutils/build_ext.py", line 164, in run _build_ext.build_ext.run(self) File "/usr/lib64/python2.6/distutils/command/build_ext.py", line 340, in run self.build_extensions() File "/usr/lib64/python2.6/site-packages/Cython-0.23.4-py2.6-linux-x86_64.egg/Cython/Distutils/build_ext.py", line 172, in build_extensions self.build_extension(ext) File "/usr/lib64/python2.6/distutils/command/build_ext.py", line 499, in build_extension depends=ext.depends) File "/usr/lib64/python2.6/distutils/ccompiler.py", line 621, in compile self._compile(obj, src, ext, cc_args, extra_postargs, pp_opts) File "/usr/lib64/python2.6/distutils/unixccompiler.py", line 180, in _compile raise CompileError, msg ImportError: Building module nesoni.consensus failed: ["CompileError: command 'gcc' failed with exit status 1\n"] Can you please help me its urgent. |
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