search

glennhickey / progressiveCactus

Distribution package for the Prgressive Cactus multiple genome aligner. Dependencies are linked as submodules
Other
80 stars 26 forks source link

environment must add biopython to PYTHONPATH but does not #83

Closed malcook closed 6 years ago

malcook commented 6 years ago

i've successfully installed and run the blanchette00 test as

bin/runProgressiveCactus.sh examples/blanchette00.txt ./work ./work/b00.hal

However, trying to create a hub:

submodules/hal/bin/hal2assemblyHub.py --gcContent --maxThreads=4 --defaultMemory=10000000000 ./work/b00.hal ./work/b00.hub

fails producing: Traceback (most recent call last): File "submodules/hal/bin/hal2assemblyHub.py", line 28, in <module> from hal.assemblyHub.prepareHubFiles import * File "/n/core/Bioinformatics/analysis/Sanchez/wew/cbio.wew.100/progressiveCactus/submodules/hal/assemblyHub/prepareHubFiles.py", line 16, in <module> from Bio import Phylo ImportError: No module named Bio

examining the environment file, I see this line:

export PYTHONPATH=/path/to/installation/progressiveCactus/submodules:$PYTHONPATH Bio::Phylo is found after I additionally add

export PYTHONPATH=/path/to/installation/progressiveCactus/submodules/biopython:$PYTHONPATH

Provision for this should probably have been done as part of eab16d26f59de58aae0e42d2c1c5a9065da5b238

By the way, to protect against whitespace issues, you should probably write the above with quotes, as:

export PYTHONPATH="/path/to/installation/progressiveCactus/submodules/biopython":"${PYTHONPATH}"

malcook commented 6 years ago

Hi - by my sights this appears to have been resolved.