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timbitz / Whippet.jl

Lightweight and Fast; RNA-seq quantification at the event-level
MIT License
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Issue with ArgParse #133

Closed zoescherzer0318 closed 1 year ago

zoescherzer0318 commented 1 year ago

I cannot seem to get Whippet to work, and it keeps outputting an error saying it cannot access ArgParse even though I made sure this module is in my .julia/v0.6 directory. I opened the julia RPL within the .julia/v0.6 directory and did Pkg.add("ArgParse") just to make sure, yet the same error is still being thrown (below).

Tue Aug 16 15:22:25 EDT 2022 Working directory is /blue/ewang/zoejstar/libZJS module add julia/0.6.4 cd /blue/ewang/zoejstar/.julia/v0.6/Whippet/ julia /blue/ewang/zoejstar/.julia/v0.6/Whippet/bin/whippet-quant.jl /blue/ewang/zoejstar/NIH3T3/fasta_files/SRR1816794_1.fastq.gz -o /blue/ewang/zoejstar/NIH3T3/whippet_output/3T3_1 -x /blue/ewang/zoejstar/.julia/v0.6/Whippet/index/mm10.jls Whippet v0.11.1 loading and compiling... ERROR: LoadError: ArgumentError: Module ArgParse not found in current path. Run Pkg.add("ArgParse") to install the ArgParse package. Stacktrace: [1] _require(::Symbol) at ./loading.jl:435 [2] require(::Symbol) at ./loading.jl:405 [3] include_from_node1(::String) at ./loading.jl:576 [4] include(::String) at ./sysimg.jl:14 [5] process_options(::Base.JLOptions) at ./client.jl:305 [6] _start() at ./client.jl:371 while loading /blue/ewang/zoejstar/.julia/v0.6/Whippet/bin/whippet-quant.jl, in expression starting on line 10 ===== module add julia/0.6.4 cd /blue/ewang/zoejstar/.julia/v0.6/Whippet/ julia /blue/ewang/zoejstar/.julia/v0.6/Whippet/bin/whippet-quant.jl /blue/ewang/zoejstar/NIH3T3/fasta_files/SRR1816794_1.fastq.gz -o /blue/ewang/zoejstar/NIH3T3/whippet_output/3T3_1 -x /blue/ewang/zoejstar/.julia/v0.6/Whippet/index/mm10.jls finished ===== runWhippet.30757.1660677721.7399876.out (END)

timbitz commented 1 year ago

Hi @zoescherzer0318 -- This looks like it could be an issue with your cluster and module loading. Did you try opening the REPL and typing 'using ArgParse' or 'using Whippet' ?

timbitz commented 1 year ago

Also I just noticed you're using Julia 0.6.4 and Whippet v0.11.1-- which is no longer a supported version for this package anymore. Please use the Julia Long term support release 1.6.7

timbitz commented 1 year ago

And you should be using Whippet version 1.6. I'm going to close this issue, as I'm not going to debug a long-deprecated release.