the gen_fusion_file.jl script does not work because OpenGene can not be installed

[yahiaBioinfo]

Hi !

I would like to run the julia script on a list of genes to get the file fusion.csv but I have not managed to install OpenGene, here is the error returned

julia> Pkg.add("OpenGene")
   Cloning default registries into /root/.julia/registries
   Cloning registry General from "https://github.com/JuliaRegistries/General.git"
  Updating registry at `~/.julia/registries/General`
  Updating git-repo `https://github.com/JuliaRegistries/General.git`
 Resolving package versions...
ERROR: Unsatisfiable requirements detected for package OpenGene [63bcc5cb]:
 OpenGene [63bcc5cb] log:
 ├─possible versions are: 0.1.0-0.1.11 or uninstalled
 ├─restricted to versions * by an explicit requirement, leaving only versions 0.1.0-0.1.11
 └─restricted by julia compatibility requirements to versions: uninstalled — no versions left
Stacktrace:
 [1] #propagate_constraints!#61(::Bool, ::Function, ::Pkg.GraphType.Graph, ::Set{Int64}) at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.0/Pkg/src/GraphType.jl:1005
 [2] propagate_constraints! at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.0/Pkg/src/GraphType.jl:946 [inlined]
 [3] #simplify_graph!#121(::Bool, ::Function, ::Pkg.GraphType.Graph, ::Set{Int64}) at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.0/Pkg/src/GraphType.jl:1460
 [4] simplify_graph! at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.0/Pkg/src/GraphType.jl:1460 [inlined]
 [5] macro expansion at ./logging.jl:319 [inlined]
 [6] resolve_versions!(::Pkg.Types.Context, ::Array{Pkg.Types.PackageSpec,1}) at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.0/Pkg/src/Operations.jl:338
 [7] #add_or_develop#58(::Array{Base.UUID,1}, ::Function, ::Pkg.Types.Context, ::Array{Pkg.Types.PackageSpec,1}) at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.0/Pkg/src/Operations.jl:1164
 [8] #add_or_develop at ./none:0 [inlined]
 [9] #add_or_develop#13(::Symbol, ::Bool, ::Base.Iterators.Pairs{Union{},Union{},Tuple{},NamedTuple{(),Tuple{}}}, ::Function, ::Pkg.Types.Context, ::Array{Pkg.Types.PackageSpec,1}) at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.0/Pkg/src/API.jl:64
 [10] #add_or_develop at ./none:0 [inlined]
 [11] #add_or_develop#12 at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.0/Pkg/src/API.jl:29 [inlined]
 [12] #add_or_develop at ./none:0 [inlined]
 [13] #add_or_develop#11 at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.0/Pkg/src/API.jl:28 [inlined]
 [14] #add_or_develop at ./none:0 [inlined]
 [15] #add_or_develop#10 at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.0/Pkg/src/API.jl:27 [inlined]
 [16] #add_or_develop at ./none:0 [inlined]
 [17] #add#18 at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.0/Pkg/src/API.jl:69 [inlined]
 [18] add(::String) at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.0/Pkg/src/API.jl:69 
 [19] top-level scope at none:0

here my geneList (iI working with hg19), I would be happy if you can help me ()

CAMTA1
CCNB3
CIC
EPC1
EWSR1
FOXO1
FUS
GLI1
HMGA2
JAZF1
MEAF6
MKL2
NCOA2
NTRK3
PDGFB
PLAG1
ROS1
SS18
STAT6
TAF15
TCF12
TFE3
TFG
USP6
YWHAE

Thank you

[sfchen]

Currently I have no time to make OpenGene adapt to Julia 1.0.

But you can give me your gene list, then I can generate the fusion file for you.

[sfchen]

You can paste or upload your gene list here, or send to me by email: [email protected]

[yahiaBioinfo]

Thank you for your help, here my gene list (I need the fusion on hg19) ;

ALK
CAMTA1
CCNB3
CIC
EPC1
EWSR1
FOXO1
FUS
GLI1
HMGA2
JAZF1
MEAF6
MKL2
NCOA2
NTRK3
PDGFB
PLAG1
ROS1
SS18
STAT6
TAF15
TCF12
TFE3
TFG
USP6
YWHAE

thanks

[sfchen]

Just sent u by email.