Docker-in-Docker (DinD) capabilities of public runners deactivated. More info

Commit 927ad8f5 authored by Carine Rey's avatar Carine Rey
Browse files

add a new workflow: fna2faa

parent c0acc5c5
......@@ -9,7 +9,7 @@ let env = docker_image ~account:"carinerey" ~name:"bppsuite:06182018" ()
let assign k v =
seq ~sep:"=" [ string k ; v ]
let conf_file ~tree ~nb_sites =
let conf_file_bppseqgen ~tree ~nb_sites =
seq ~sep:"\n" [
assign "input.tree.file" (dep tree) ;
assign "output.sequence.file" dest ;
......@@ -30,6 +30,25 @@ let conf_file ~tree ~nb_sites =
let bppseqgen ~nb_sites ~tree : nucleotide_fasta workflow =
workflow ~descr:"bppsuite.bppseqgen" [
cmd "bppseqgen" ~env [
assign "param" (file_dump (conf_file ~tree ~nb_sites)) ;
assign "param" (file_dump (conf_file_bppseqgen ~tree ~nb_sites)) ;
]
]
let conf_file_bppseqman ~fna =
seq ~sep:"\n" [
assign "input.sequence.file" (dep fna) ;
assign "output.sequence.file" dest ;
string {|alphabet=Codon(letter=DNA)
genetic_code = Standard
input.alignment = true
sequence.manip = Translate
|}
]
let fna2faa ~(fna:nucleotide_fasta workflow) : aminoacid_fasta workflow =
workflow ~descr:"bppsuite.fna2faa" [
cmd "bppseqman" ~env [
assign "param" (file_dump (conf_file_bppseqman ~fna)) ;
]
]
......@@ -6,3 +6,7 @@ val bppseqgen :
nb_sites:int ->
tree:nhx workflow ->
nucleotide_fasta workflow
val fna2faa :
fna:nucleotide_fasta workflow ->
aminoacid_fasta workflow
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