giugi
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Dear all,
I am trying to install QIIME on my PC but I have some problems.
I had to install python2.7 on usr/local/bin because on usr/bin there is the previous version 2.6. I set the PYTHONPATH in the .bashrc:
export PYTHONPATH=/usr/local/bin/:$PYTHONPATH
export PYTHONPATH=/usr/local/lib/:$PYTHONPATH
when I run print_qiime_config.py I get this result:
System information
==================
Platform: linux2
Python version: 2.7.3 (default, Dec 18 2012, 12:56:50) [GCC 4.4.6 20120305 (Red Hat 4.4.6-4)]
Python executable: /usr/local/bin/python2.7
Dependency versions
===================
PyCogent version: 1.5.3
NumPy version: 1.6.2
matplotlib version: 1.1.0
biom-format version: 1.0.0c
QIIME library version: 1.5.0
QIIME script version: 1.5.0
PyNAST version (if installed): 1.2
RDP Classifier version (if installed): Not installed.
QIIME config values
===================
blastmat_dir: None
sc_queue: all.q
topiaryexplorer_project_dir: None
pynast_template_alignment_fp: None
cluster_jobs_fp: None
pynast_template_alignment_blastdb: None
assign_taxonomy_reference_seqs_fp: None
torque_queue: friendlyq
qiime_test_data_dir: None
template_alignment_lanemask_fp: None
jobs_to_start: 1
cloud_environment: False
qiime_scripts_dir: None
denoiser_min_per_core: 50
working_dir: None
python_exe_fp: python
temp_dir: /tmp/
blastall_fp: blastall
seconds_to_sleep: 2
assign_taxonomy_id_to_taxonomy_fp: None
So the Python exe is correct: Python executable: /usr/local/bin/python2.7
However when I run print_qiime_config.py -t I get this result (I only copy the Python message):
test_python_exe_fp (__main__.Qiime_config)
python_exe_fp is set to a working python env ... ok
test_python_supported_version (__main__.Qiime_config)
python is in path and version is supported ... FAIL
It seems to me that QIIME is still using python2.6 lib instead the python2.7.
If I run the all_tests.py i get this error message:
Traceback (most recent call last):
File "all_tests.py", line 10, in <module>
from qiime.util import (parse_command_line_parameters, get_options_lookup,
ImportError: No module named qiime.util
I really don't know how to solve it.....Have you got any suggestions?
Thanks
Giugi