Issue installing slamdunk

[airiskic]

Hi,

I'm doing metabolic labelling and have run the pipeline in Nextflow and now have to use slamdunk. However, I stumble on the issue that when installing with bioconda (1) it keeps solving the environment and when I download it with pip(2) it gives me an error that it can't locate my files. I have tried all the suggested solutions under issues (69, 29, and 92) but none of the seem to solve the issue. Also, I have tired running the commands on two HPC's that I have access through and I run into the same issues.

(1)The code I have run with conda: conda config --add channels defaults conda config --add channels bioconda conda config --add channels conda-forge conda config --set channel_priority strict

conda create -n slam2 -c conda-forge -c bioconda slamdunk

Output is: Collecting package metadata (current_repodata.json): done Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source. Collecting package metadata (repodata.json): done Solving environment:

(2)The code run with pip slamdunk all -r Downloads/Homo_sapiens.GRCh38.cdna.all.fa -b Desktop/slam/ref/GRCh38_109.bed -o Desktop/slam -5 12 -n 100 -t 1 -m -rl 100 --skip-sam files Desktop/data_path.txt

Output is: raise RuntimeError("One or more input files don't exist: " + str(inFiles)) RuntimeError: One or more input files don't exist: ['Downloads/Homo_sapiens.GRCh38.cdna.all.fa', 'files']

All help would be appreciated. Thanks in advance. /Amila

[airiskic]

solved simply by using pip install on HPC