Error with importing Bio package

[shaman-narayanasamy]

Dear authors,

I am interested in using ccontigs. Everything seems to be working well. However, I am receiving an error regarding the absence of the "Bio" package:

$ ./testcode.sh 
Running test
Downloading Sequences
--2019-07-14 15:56:16--  https://www.ebi.ac.uk/ena/data/view/KF482069,M14428,EF568108,X58839,CU468217,KC821618,KP063541,AB981169,JQ809663,KJ019160,K02718,FJ882854,KJ938717,KP133078,Z24758,GU071086,JQ234922,KF430219,GQ368252,JX051319,KP280063,GU071094,AY954962,EF177456,DQ163914,GU071103,AY500152,KF017927,KM279937,JN699002,FJ848881,KC690136,AJ556162,JF767208,AY526908,KF669652,JX080304,KM067278,KR902979&display=fasta
Resolving www.ebi.ac.uk (www.ebi.ac.uk)... 193.62.193.80
Connecting to www.ebi.ac.uk (www.ebi.ac.uk)|193.62.193.80|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: unspecified [text/plain]
Saving to: ‘./tmpout’

    [                                       <=>                                                                                                ] 2,717,201    297KB/s   in 8.8s   

2019-07-14 15:56:25 (300 KB/s) - ‘./tmpout’ saved [2717201]

Completed
Complete!
>>> PASS: Downloaded and formatted referece fasta
ERROR: LoadError: ArgumentError: Package Bio not found in current path:
- Run `import Pkg; Pkg.add("Bio")` to install the Bio package.

Stacktrace:
 [1] require(::Module, ::Symbol) at ./loading.jl:823
 [2] include at ./boot.jl:326 [inlined]
 [3] include_relative(::Module, ::String) at ./loading.jl:1038
 [4] include(::Module, ::String) at ./sysimg.jl:29
 [5] exec_options(::Base.JLOptions) at ./client.jl:267
 [6] _start() at ./client.jl:436
in expression starting at /mnt/irisgpfs/users/snarayanasamy/repositories/github/ccontigs/ccontigs.jl:6
diff: ./test/juliaout.tsv: No such file or directory
>>> PASS: ccontigs ran properly on reference file
rm: cannot remove ‘./test/juliaout.tsv’: No such file or directory

Is this something to be concerned about? I am attempting to run it in a cluster environment with an existing module of Julia ver. 1.1.1.

Please let me know if this is something to be concerned about, because when I attempt to launch the command, it does not work at all:

$ julia ccontigs.jl -i test/validation.fa -o test.tsv
ERROR: LoadError: ArgumentError: Package Bio not found in current path:
- Run `import Pkg; Pkg.add("Bio")` to install the Bio package.

Stacktrace:
 [1] require(::Module, ::Symbol) at ./loading.jl:823
 [2] include at ./boot.jl:326 [inlined]
 [3] include_relative(::Module, ::String) at ./loading.jl:1038
 [4] include(::Module, ::String) at ./sysimg.jl:29
 [5] exec_options(::Base.JLOptions) at ./client.jl:267
 [6] _start() at ./client.jl:436
in expression starting at /mnt/irisgpfs/users/snarayanasamy/repositories/github/ccontigs/ccontigs.jl:6

Looking forward to hearing from you.

Best regards, Shaman

[Microbiology]

Very strange. I’ve had issues downloading Julia packages on clusters in the past though. Two questions. Can you load in that package when you run a Julia interactive session? Also does it run okay on your laptop or desktop?

[shaman-narayanasamy]

I was running in an interactive session in my attempt. I did not try it on my local machine.

For now, I just followed the instructions of the error and added the following lines to beginning of the ccontigs.jl script:

import Pkg; Pkg.add("ArgParse")
import Pkg; Pkg.add("Bio")

NOTE: The same error for "ArgParse" appeared after I imported the "Bio" package.

It worked both in interactive and batch mode. This is my first time using a Julia based tool, and therefore I am unsure if this is the best solution and may affect runs on other environments. Please let me know if I should try something else.