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mrvollger / SDA

Segmental Duplication Assembler (SDA).
MIT License
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Make error #7

Closed lamevan closed 5 years ago

lamevan commented 5 years ago

Hi,when I install SDA it occured this error... Can you explain why it occured?Thanks! ClobberError: This transaction has incompatible packages due to a shared path. packages: defaults::numpy-1.12.1-py27h9378851_1, defaults::numpy-base-1.14.3-py27hdbf6ddf_0 path: 'lib/python2.7/site-packages/numpy/version.pyc'

mrvollger commented 5 years ago

Do you know during which Make rule it broke during?

These are the two most likely candidates:

#
# make conda envs
#
envs/python2.done: 
    source env_conda.cfg && \
        mkdir -p envs && \
        conda env create --force -f envs/python2.yml --prefix $(PWD)/envs/sda-python-2 && \
        touch envs/python2.done

envs/python3.done:
    source env_conda.cfg && \
        mkdir -p envs && \
        conda env create --force -f envs/python3.yml --prefix $(PWD)/envs/sda-python-3 && \
        touch envs/python3.done
lamevan commented 5 years ago

Yes..it broke during env/python2.done make rule

mrvollger commented 5 years ago

Can you try going into envs/python2.yml and remove=py27h9378851_1 from the line containing numpy=.* and =py27hdbf6ddf_0 from the line with numpy-base=.*. After this try making again.

If this does not work then I expect there is a conflict between this and something in your overall python environment. Did you have other versions of python and or numpy loaded in your env while doing this?

lamevan commented 5 years ago

I remove the string you said and it works,thank you!

mrvollger commented 5 years ago

Great. If you end up running the test case please let me know if it works. If so I will push this change.

lamevan commented 5 years ago

Yes,I have run the test and I found that wtdbg.assemblies.fasta is an empty file.. If this a mistake?

mrvollger commented 5 years ago

For small local assemblies wtdbg2 and miniasm are not as good as canu. So you will often find that the wtdgb2 does not have any output assembly. Personally I always use/trust the canu assembly.

mrvollger commented 5 years ago

Fixed with af7126779a712372f788bd4ad4b99cf01f3d3298