configure.json

{"orf": {"conda": "envs/transdecoder.yaml", "shell": "\n        TransDecoder.LongOrfs -t {input}  -m 30\n        TransDecoder.Predict -t {input} --single_best_orf\n        "}, "blast": {"conda": "envs/diamond.yaml", "shell": "\n        diamond makedb --in {input} --out {input}.seq.db -d {input}\n        diamond blastp -d {input} -d {input}.dmnd -q {input} -o {output} -p {threads} -e 1E-5\n        "}, "clust": {"shell": "silix -r 0.9 {input.sequence_file} {input.blast_file} > {output} || true"}, "align": {"conda": "envs/mafft.yaml", "shell": "mafft --auto --thread -1 {input} > {output}"}, "tree": {"conda": "envs/fasttree.yaml", "shell": "fasttree  -nosupport {input} > {output} || true"}, "model": {"shell": "(echo 1; echo 1;echo srcdir(\"{input.align}\"); echo srcdir(\"{input.tree}\"); echo 20;echo 5; echo 2000000; echo 1000000;echo 100;echo 0.5 )|HYPHYMP /home/usr/hyphy/res/TemplateBatchFiles/FUBAR.bf"}}