Comments (3)
Hello !
I run into the same error installing from the non-recommended bioconda repo. I suggest:
- deleting or adding a warning to the bioconda repo stating that it should not be used,
- or adding a warning in the wiki,
- or fixing the bioconda recipe as installation through conda seems like a desirable feature.
The bioconda recipe uses pip and setup.py to install BiG-SCAPE. It looks like there are two issues with this file:
- the version number is wrong (https://github.com/medema-group/BiG-SCAPE/blob/master/setup.py#L20),
bigscape.py
is exposed (https://github.com/medema-group/BiG-SCAPE/blob/master/setup.py#L25) but datafiles (html_template/
) are not, which causes thedistutils.errors.DistutilsFileError
as BiG-SCAPE assumes the datafiles will be in the script's folder (https://github.com/medema-group/BiG-SCAPE/blob/master/bigscape.py#L2835). You may consider using package_dir or data_files options insetup.py
.
HTH, best
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Hi @AmayAgrawal
Did you install BiG-SCAPE directly from conda? There is indeed an error when installing directly. I haven't had the chance to fix this yet, but I'd recommend the 'traditional' installation for the time being -i.e. installing all the dependencies using conda, then cloning the code, https://github.com/medema-group/BiG-SCAPE/wiki/installation#white_circle-installation-using-conda
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Hi @jorgecnavarrom
Yes I installed it directly from conda and somehow figured out last week only that some of the folders that the software needed to run were missing. So, downloaded it from github and got the code to work. Thanks for your suggestion as well
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Related Issues (20)
- MIBiG 3.1 files have no Biosynthetic Genes HOT 2
- ```NameError: name 'genbankDict' is not defined``` when the input gbk file is not detected with domain. HOT 6
- How to install the latest Bigscape? HOT 4
- index.html network exprot HOT 2
- fix counterintuitive bigscape family number assignments? HOT 2
- Update of the BiG-SCAPE bioconda recipe HOT 3
- bump version number? HOT 3
- BGC_fasta_folder is not defined HOT 3
- Stopped at Hmmalign step HOT 6
- how can i install BiG-SCAPE
- Incorrect number of genomes detected in overview of output HOT 3
- cannot view index.html and tutorial files won't unzip HOT 6
- MIBiG t2pks BGCs not grouping into families HOT 4
- Random BGC families not showing in mixed class HOT 3
- index.html won't finish loading data HOT 6
- Network_Annotations_Full.tsv result HOT 2
- antiSMASH 7 support HOT 1
- ConvergenceWarning: Affinity propagation did not converge, this model will not have any cluster centers. HOT 2
- Package version number needs to be bumped to reflect github release version number HOT 2
- visualizing the singletons HOT 2
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