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bioconda / bioconda-recipes

Conda recipes for the bioconda channel.
https://bioconda.github.io
MIT License
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Pasta not functional without additional configuration #13892

Open brendanf opened 5 years ago

brendanf commented 5 years ago

Apparently Pasta is looking for the included SATe tools in the wrong location:

(base) $ conda create -n pasta pasta
(base) $ conda activate pasta
(pasta) $ run_pasta.py -i longASV.fasta -d RNA
PASTA INFO: Reading input sequences from 'longASV.fasta'...
PASTA INFO: Configuration written to "/home/brendan/Documents/Uppsala/Projects/oueme-fungi-transect/pastajob6_temp_pasta_config.txt".

PASTA ERROR: PASTA is exiting because of an error:
'/home/brendan/miniconda3/envs/pasta/lib/python3.6/site-packages/bin/mafft' not found. Please install 'mafft' and/or configure its location correctly in '/home/brendan/.pasta/pasta_tool_paths.cfg' 
(pasta) $ whereis mafft
mafft: /usr/bin/mafft /usr/lib/mafft /home/brendan/miniconda3/envs/pasta/bin/mafft /usr/share/man/man1/mafft.1.gz

The issue isn't just with MAFFT, all of the included tools are installed in .../envs/pasta/bin/, but pasta looks for them in .../envs/pasta/lib/python3.6/site-packages/bin/.

Of course I can make it work by following the advice and making .pasta/pasta_tool_paths.cfg in my home directory, but that isn't ideal for distributing a reproducible workflow.

brendanf commented 5 years ago

This works:

PASTA_TOOLS_DEVDIR=$CONDA_PREFIX/bin/ run_pasta.py
gregvonkuster commented 5 years ago

Here is how I use PASTA in a command line for a Galaxy tool https://github.com/gregvonkuster/galaxy_tools/blob/master/tools/phylogenetics/plant_tribes/gene_family_aligner/gene_family_aligner.xml#L19. This approach will work the same outside of Galaxy if you are not using Galaxy.

smirarab commented 5 years ago

I'd be happy to help, but I am finding it difficult to figure out where the recipe is. Can someone put a link here?

PASTA has a three-step installation, which is also platform dependent.

For MAC, we need

git clone https://github.com/smirarab/pasta.git
git clone https://github.com/smirarab/sate-tools-mac.git
cd pasta
python setup.py develop

For Linux, we need:

git clone https://github.com/smirarab/pasta.git
git clone https://github.com/smirarab/sate-tools-linux.git
cd pasta
python setup.py develop

Hope this helps.