Installation fails: ResolvePackageNotFound for gxx, gfortran, gcc, libgfortran

farhat-lab / gentb-snakemake

From FASTQ file to antibiotic resistance prediction using RandomForest - the GenTB pipeline wrapped in snakemake

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Installation fails: ResolvePackageNotFound for gxx, gfortran, gcc, libgfortran #2

Closed klaasdewaele closed 2 years ago

klaasdewaele commented 2 years ago

Hi,

I'd like to test the GenTB pipeline for some files I have. However, during installation using Conda I get the below error:

ResolvePackageNotFound: 
- gxx_impl_linux-64==7.5.0=hdf63c60_6 
- gfortran_impl_linux-64==7.5.0=hdf63c60_6 
- gcc_impl_linux-64==7.5.0=hd420e75_6 
- libgfortran-ng==7.5.0=hdf63c60_6

Any ideas on what's wrong here? Thanks in advance!

best, Klaas

klaasdewaele commented 2 years ago

Installation on Debian 4.19 worked after removal of build strings from some packages in the snakemake-gentb.yml file:

binutils_impl_linux-64=2.34
binutils_linux-64=2.34
gcc_impl_linux-64=7.5.0
gcc_linux-64=7.5.0
gfortran_impl_linux-64=7.5.0
gfortran_linux-64=7.5.0
gxx_impl_linux-64=7.5.0
gxx_linux-64=7.5.0
libgfortran-ng=7.5.0
ld_impl_linux-64=2.34

Execution of the pipeline then failed due to an indentation error in line 382 of varMatchUnk.py. After correction the pipeline worked!