Maf Format - Bx_Python Missing In Local Galaxy Install?

Question: Maf Format - Bx_Python Missing In Local Galaxy Install?

9.7 years ago by

Hello, When importing MAF file, local galaxy install loads the data but shows an error: No data: global name 'bx' is not defined When I tried to convert maf to fasta, I got the following error: Traceback (most recent call last): File "/home/rochak/galaxy_latest/lib/galaxy/datatypes/converters/maf _to_fasta_converter.py", line 7, in import bx.align.maf File "/home/rochak/galaxy_latest/eggs/py2.5-linux- x86_64-ucs2/bx_python-0.5.0_dev_r459-py2.5-linux- x86_64.egg/bx/align/__init__.py", line 7, in File "/home/rochak/galaxy_latest/eggs/py2.5-linux- x86_64-ucs2/bx_python-0.5.0_dev_r459-py2.5-linux- x86_64.egg/bx/align/core.py", line 8, in File "/home/rochak/galaxy_latest/eggs/py2.5-linux- x86_64-ucs2/bx_python-0.5.0_dev_r459-py2.5-linux- x86_64.egg/bx/misc/__init__.py", line 5, in ImportError: No module named bz2 Does galaxy install bx_python in its initial setup? /home/rochak/galaxy_latest/eggs/py2.5-linux- x86_64-ucs2/bx_python-0.5.0_dev_r459-py2.5-linux-x86_64.egg is a file, not a directory. How should I proceed forward to fix this? Thanks, Rochak

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modified 9.7 years ago • written 9.7 years ago by Rochak Neupane • 60

9.7 years ago by

Rochak Neupane • 60

Rochak Neupane • 60 wrote:

Oh, I forgot to mention, but on the loaded data, the following is displayed below "AutoDetect" button when I click on the pencil. " This will inspect the dataset and attempt to correct the above column values if they are not accurate. Required metadata values are missing. Some of these values may not be editable by the user. Selecting "Auto-detect" will attempt to fix these values." Error after clicking "Auto-Detect". Traceback below. File '/home/rochak/galaxy_latest/eggs/py2.5-noplatform/WebError-0.8a- py2.5.egg/weberror/evalexception/middleware.py', line 364 in respond File '/home/rochak/galaxy_latest/eggs/py2.5-noplatform/Paste-1.5.1-py2 .5.egg/paste/debug/prints.py', line 98 in __call__ File '/home/rochak/galaxy_latest/eggs/py2.5-noplatform/Paste-1.5.1-py2 .5.egg/paste/wsgilib.py', line 539 in intercept_output File '/home/rochak/galaxy_latest/eggs/py2.5-noplatform/Beaker-0.5-py2. 5.egg/beaker/session.py', line 103 in __call__ File '/home/rochak/galaxy_latest/eggs/py2.5-noplatform/Paste-1.5.1-py2 .5.egg/paste/recursive.py', line 80 in __call__ File '/home/rochak/galaxy_latest/eggs/py2.5-noplatform/Paste-1.5.1-py2 .5.egg/paste/httpexceptions.py', line 632 in __call__ File '/home/rochak/galaxy_latest/lib/galaxy/web/framework/base.py', line 124 in __call__ body = method( trans, **kwargs ) File '/home/rochak/galaxy_latest/lib/galaxy/web/controllers/root.py', line 266 in edit data.datatype.set_meta( data ) File '/home/rochak/galaxy_latest/lib/galaxy/datatypes/sequence.py', line 216 in set_meta indexes = bx.interval_index_file.Indexes() NameError: global name 'bx' is not defined sequence.py 212 #these metadata values are not accessable by users, always overwrite 213 214 species = [] 215 species_chromosomes = {} 216 indexes = bx.interval_index_file.Indexes() clearly bx is not installed. Thought it was installed when running setup.sh?

ADD COMMENT • link written 9.7 years ago by Rochak Neupane • 60

Hi Rochak, From your original email, it appears that the bx import is failing because your Python does not have the bz2 module. This is a standard module but will only be built if the Python build scripts locate bz2 libraries and headers at compile time. --nate

ADD REPLY • link written 9.7 years ago by Nate Coraor ♦ 3.2k

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