siwolf/score

SCORE - a consensus tool for detecting differentially expressed genes in bacteria

score's Issues

Conda not able to install packages labeled 'broken'

Thanks for the nice software!

When installing the dependencies through Snakemake + Conda, some YAML files refer to packages labeled 'broken'. To the best of my knowledge, these cannot be installed through Snakemake (however manually you can set e.g. -c bioconda/labels/broken to include them, but I haven't seen an option with Snakemake to do this).

AFAIK this only concerns score_deg_environment.yml. The error message is:

Creating conda environment libraries/env/score_deg_environment.yml...
Downloading remote packages.
CreateCondaEnvironmentException:
Could not create conda environment from /project/vdputten/Kees/RM/SCORE-1.0.1/libraries/env/score_deg_environment.yml:
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... failed

ResolvePackageNotFound:
  - libgfortran-ng==7.5.0=hdf63c60_6
  - 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

Replacing the tags with tags from the same version but a different build might work

error running

Hi @SiWolf

I am trying to run this pipeline but unfortunately I get an error. Any idea how to solve it? I have already added my fasta and gff files to the reference folder and I have updated the metadata file. But i keep getting the same error.

`(score) sam@bioinf-pc:~/Downloads/SCORE$ bash run-SCORE.sh 2 PE
rm: cannot remove '.gz': No such file or directory
rm: cannot remove '.idx': No such file or directory
rm: cannot remove 'kallisto/sample*': No such file or directory
rm: cannot remove '.rda': No such file or directory
rm: cannot remove '.txt': No such file or directory
rm: cannot remove 'consensus*': No such file or directory
rm: cannot remove 'deg*': No such file or directory
rm: cannot remove 'diffexpr*': No such file or directory
rm: cannot remove 'filtered*': No such file or directory
rm: cannot remove 'genes*': No such file or directory
rm: cannot remove 'hmmer*': No such file or directory
rm: cannot remove 'pathway*': No such file or directory
rm: cannot remove 'proteins*': No such file or directory
rm: cannot remove 'transcript*': No such file or directory
rm: cannot remove 'summary*': No such file or directory
rm: cannot remove 'benchmarking*': No such file or directory
rm: cannot remove 'log.txt': No such file or directory
rm: cannot remove 'references/.tmp': No such file or directory
rm: cannot remove '': No such file or directory
rm: cannot remove '': No such file or directory
rm: cannot remove '.sam': No such file or directory
rm: cannot remove '': No such file or directory
rm: cannot remove '': No such file or directory
FileNotFoundError in line 203 of /home/sam/Downloads/SCORE/SCORE_PE.snk:
[Errno 2] No such file or directory: 'references/027-annot.gff'
File "/home/sam/Downloads/SCORE/SCORE_PE.snk", line 218, in
File "/home/sam/Downloads/SCORE/SCORE_PE.snk", line 203, in verfify_id_combination
FileNotFoundError in line 203 of /home/sam/Downloads/SCORE/SCORE_PE.snk:
[Errno 2] No such file or directory: 'references/027-annot.gff'
File "/home/sam/Downloads/SCORE/SCORE_PE.snk", line 218, in
File "/home/sam/Downloads/SCORE/SCORE_PE.snk", line 203, in verfify_id_combination

real 0m0,157s
user 0m0,133s
sys 0m0,025s
`

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