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MIGA Intallation error

March 9, 2020 at 12:13pm

MIGA Intallation error

March 9, 2020 at 12:13pm
Hi! I am trying to install MIGA using conda. Everything goes nicely but when I do miga init i got an error:
Testing Ruby (Required version: 2.1+)... sh: 2: /home/jg/.miga_modules: source: not found
/usr/bin
Testing Python... sh: 2: /home/jg/.miga_modules: source: not found
/home/jg/anaconda3/bin
Testing R... sh: 2: /home/jg/.miga_modules: source: not found
/usr/bin
Testing SQLite3... sh: 2: /home/jg/.miga_modules: source: not found
/home/jg/anaconda3/bin
Testing NCBI BLAST+... sh: 2: /home/jg/.miga_modules: source: not found
Where can I find it? [.] >
I cannot find blastp sh: 2: /home/jg/.miga_modules: source: not found
Where can I find it? [.] >
I cannot find blastp sh: 2: /home/jg/.miga_modules: source: not found
Where can I find it? [.] > /home/jg/ncbi-blast/
I cannot find blastp sh: 2: /home/jg/.miga_modules: source: not found
Where can I find it? [.] > /home/jg/ncbi-blast/bin
Exception: undefined local variable or method `rc_fh' for #<MiGA::Cli::Action::Init:0x000055c3bf721248>
DEBUG: /var/lib/gems/2.5.0/gems/miga-base-0.6.0.0/lib/miga/cli/action/init.rb:191:in `block in find_software'
DEBUG: /var/lib/gems/2.5.0/gems/miga-base-0.6.0.0/lib/miga/cli/action/init.rb:181:in `loop'
DEBUG: /var/lib/gems/2.5.0/gems/miga-base-0.6.0.0/lib/miga/cli/action/init.rb:181:in `find_software'
DEBUG: /var/lib/gems/2.5.0/gems/miga-base-0.6.0.0/lib/miga/cli/action/init.rb:160:in `block (2 levels) in check_software_requirements'
DEBUG: /var/lib/gems/2.5.0/gems/miga-base-0.6.0.0/lib/miga/cli/action/init.rb:155:in `each_line'
DEBUG: /var/lib/gems/2.5.0/gems/miga-base-0.6.0.0/lib/miga/cli/action/init.rb:155:in `block in check_software_requirements'
DEBUG: /var/lib/gems/2.5.0/gems/miga-base-0.6.0.0/lib/miga/cli/action/init.rb:154:in `open'
DEBUG: /var/lib/gems/2.5.0/gems/miga-base-0.6.0.0/lib/miga/cli/action/init.rb:154:in `check_software_requirements'
DEBUG: /var/lib/gems/2.5.0/gems/miga-base-0.6.0.0/lib/miga/cli/action/init.rb:51:in `perform'
DEBUG: /var/lib/gems/2.5.0/gems/miga-base-0.6.0.0/lib/miga/cli/action.rb:33:in `launch'
DEBUG: /var/lib/gems/2.5.0/gems/miga-base-0.6.0.0/lib/miga/cli.rb:197:in `launch'
DEBUG: /var/lib/gems/2.5.0/gems/miga-base-0.6.0.0/bin/miga:10:in `<top (required)>'
DEBUG: /usr/local/bin/miga:23:in `load'
DEBUG: /usr/local/bin/miga:23:in `<main>'
Any ideas?

March 9, 2020 at 6:05pm
Hello I was actually revisiting this exact point in the documentation. Please try running this:
echo 'conda activate miga' > ~/.miga_modules
And then rerun miga init
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Quick question: Is conda in your environment?
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I did what you mentioned but the error persists. What do you mean by conda in my environment?
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March 11, 2020 at 5:09pm
If you run conda by itself in the command line, do you get an error that the command doesn't exist or the conda help message?
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