I am getting following error while running TransRate,
Dependencies are missing:
So, I git cloned the patch you have distributed above. I am getting following error while running command $ gem build transrate.gemspec
ERROR: While executing gem ... (Gem::InvalidSpecificationException)
duplicate dependency on bindeps (>= 1.2.1, ~> 1.2, development), (>= 1.2.1, ~> 1.2) use:
add_runtime_dependency 'bindeps', '>= 1.2.1, ~> 1.2', '>= 1.2.1, ~> 1.2'
/usr/lib64/ruby/2.1.0/rubygems/specification.rb:2608:in block in validate_dependencies'
/usr/lib64/ruby/2.1.0/rubygems/specification.rb:2606:in
each'
/usr/lib64/ruby/2.1.0/rubygems/specification.rb:2606:in validate_dependencies'
/usr/lib64/ruby/2.1.0/rubygems/specification.rb:2589:in
validate'
/usr/lib64/ruby/2.1.0/rubygems/package.rb:230:in build'
/usr/lib64/ruby/2.1.0/rubygems/package.rb:114:in
build'
/usr/lib64/ruby/2.1.0/rubygems/commands/build_command.rb:48:in execute'
/usr/lib64/ruby/2.1.0/rubygems/command.rb:305:in
invoke_with_build_args'
/usr/lib64/ruby/2.1.0/rubygems/command_manager.rb:167:in process_args'
/usr/lib64/ruby/2.1.0/rubygems/command_manager.rb:137:in
run'
/usr/lib64/ruby/2.1.0/rubygems/gem_runner.rb:54:in run'
/usr/bin/gem:21:in
<main>'
And if I try to run tranrate without building it, I get this error:
/usr/lib64/ruby/2.1.0/rubygems/core_ext/kernel_require.rb:55:in require': cannot load such file -- transrate (LoadError)
from /usr/lib64/ruby/2.1.0/rubygems/core_ext/kernel_require.rb:55:in
require'
from /work/03125/bikash/phylogenomic/transrate/bin/transrate:2:in `<main>'
Any help/suggestions is greatly appreciated.
Thanks!
Hi, I have tried to install transrate via conda using " conda install -c bioconda transrate" but i received the following error message:
UnsatisfiableError: The following specifications were found to be incompatible with your system:
Your installed version is: 2.31.
I am new to transcriptome assembly and I am not sure how I can fix this error. I wanted to download via the link provided on the transrate website but it seems to be no longer valid. I would like to know how to either rectify this error or other ways to download transrate other than using ruby. Thank you so much!