Fix #40 for failed container build for SCODE#41
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ibebio wants to merge 5 commits intoMurali-group:masterfrom
Open
Fix #40 for failed container build for SCODE#41ibebio wants to merge 5 commits intoMurali-group:masterfrom
ibebio wants to merge 5 commits intoMurali-group:masterfrom
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apt-get install -y git was failing with the following error: Some packages could not be installed. This may mean that you have requested an impossible situation or if you are using the unstable distribution that some required packages have not yet been created or been moved out of Incoming. The following information may help to resolve the situation: The following packages have unmet dependencies: libc6-dev : Breaks: libgcc-8-dev (< 8.4.0-2~) but 8.3.0-3 is to be installed E: Error, pkgProblemResolver::Resolve generated breaks, this may be caused by held packages. This commit fixes the problem.
ibebio
changed the title
The commit includes necessary modifications to run the containers with Singularity. Dockerfile modficications were added to create missing data/ directories. The .sh scripts were modified to create Singularity images.
Tentative fix for the following error when running algorithms from
ARBORETO container:
INFO: Convert SIF file to sandbox...
Traceback (most recent call last):
File "runArboreto.py", line 43, in <module>
main(sys.argv)
File "runArboreto.py", line 32, in main
network = genie3(inDF, client_or_address = client)
File "/opt/conda/lib/python3.7/site-packages/arboreto/algo.py", line
73, in genie3
limit=limit, seed=seed, verbose=verbose)
File "/opt/conda/lib/python3.7/site-packages/arboreto/algo.py", line
115, in diy
expression_matrix, gene_names, tf_names
= _prepare_input(expression_data, gene_names, tf_names)
File "/opt/conda/lib/python3.7/site-packages/arboreto/algo.py", line
214, in _prepare_input
expression_matrix = expression_data.as_matrix()
File "/opt/conda/lib/python3.7/site-packages/pandas/core/generic.py",
line 5130, in __getattr__
return object.__getattribute__(self, name)
AttributeError: 'DataFrame' object has no attribute 'as_matrix'
The actual source of the error is upstream, since the bioconda recipe does not
specify versions of the packages.
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apt-get install -y gitwas failing with the following error:This commit resolves #40