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ALE_reconstruction.sh
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ALE_reconstruction.sh
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# clone the nextflow pipeline for running ALE
git clone https://github.com/maxemil/ALE-pipeline.git
# build singularity image of ALE
sudo singularity build ALE.sif ALE-pipeline/Singularity
# create species name abbreviations to use in ALE
python3 ALE-pipeline/bin/create_name_codes.py -i species_names.txt -o species_map.txt
# make sure the names in the species tree are the same as in the clusters,
# otherwise create another mapping file for those, genes_map.txt
# the file fraction_missing.txt should contain completeness estimates,
# e.g 0.2 for 80% complete
# run ALE using ufboots from clusters and small clusters
nextflow ALE-pipeline/main.nf \
--species_tree_files species_trees_input/species.tree \
--input_files "clusters_eurNOG/trees/" \
--input_extension ".ufboot" \
--small_cluster "clusters_eurNOG/faa/cluster_small/*" \
--genes_map genes_map.txt \
--species_map species_map.txt \
--fraction_missing fraction_missing.txt \
--output_ale MGIV-eurNOG \
--output_samples ALE-samples \
--separator ".." \
--outgroup_taxa '["Euryarchaeota_archaeon_JdFR_21","Archaeoglobus_fulgidus_DSM_4304","Archaeoglobi_archaeon_JdFR_42"]' \
--python3 /usr/bin/python \
-resume -qs 8