search

bio-miga / miga

MiGA: Microbial Genomes Atlas
Artistic License 2.0
31 stars 9 forks source link

miga init error, Failed to install pyhmerr #180

Open tryfon opened 4 months ago

tryfon commented 4 months ago

Even though I have installed pyhmmer with the command pip install --break-system-packages pyhmmer pyrodigal as per instructions while running miga init I get the following

Testing sqlite3... yes Testing pyhmmer... no, installing Exception: Command failed with status 1: : OPT: {:stdout=>nil, :stderr=>nil, :dry=>false, :return=>:output, :raise=>true, :show_cmd=>false, :err2out=>true, :env=>{}, :source=>"/home/alexandra/.miga_modules"} CMD: . /home/alexandra/.miga_modules && /home/linuxbrew/.linuxbrew/bin/python3 -m pip install --user pyhmmer

DEBUG: /home/alexandra/.gem/gems/miga-base-1.3.15.6/lib/miga/common/system_call.rb:40:in run_cmd' DEBUG: /home/alexandra/.gem/gems/miga-base-1.3.15.6/lib/miga/cli/action/init.rb:94:inrun_cmd' DEBUG: /home/alexandra/.gem/gems/miga-base-1.3.15.6/lib/miga/cli/action/init.rb:257:in install_library' DEBUG: /home/alexandra/.gem/gems/miga-base-1.3.15.6/lib/miga/cli/action/init.rb:215:incheck_and_install_library' DEBUG: /home/alexandra/.gem/gems/miga-base-1.3.15.6/lib/miga/cli/action/init.rb:203:in block (2 levels) in check_libraries' DEBUG: /home/alexandra/.gem/gems/miga-base-1.3.15.6/lib/miga/cli/action/init.rb:202:ineach' DEBUG: /home/alexandra/.gem/gems/miga-base-1.3.15.6/lib/miga/cli/action/init.rb:202:in block in check_libraries' DEBUG: /home/alexandra/.gem/gems/miga-base-1.3.15.6/lib/miga/cli/action/init.rb:200:ineach' DEBUG: /home/alexandra/.gem/gems/miga-base-1.3.15.6/lib/miga/cli/action/init.rb:200:in check_libraries' DEBUG: /home/alexandra/.gem/gems/miga-base-1.3.15.6/lib/miga/cli/action/init.rb:82:inperform' DEBUG: /home/alexandra/.gem/gems/miga-base-1.3.15.6/lib/miga/cli/action.rb:32:in launch' DEBUG: /home/alexandra/.gem/gems/miga-base-1.3.15.6/lib/miga/cli.rb:182:inlaunch' DEBUG: /home/alexandra/.gem/gems/miga-base-1.3.15.6/bin/miga:12:in <top (required)>' DEBUG: /home/alexandra/.gem/ruby/3.3.0/bin/miga:25:inload' DEBUG: /home/alexandra/.gem/ruby/3.3.0/bin/miga:25:in <main>' /home/alexandra/.gem/gems/miga-base-1.3.15.6/lib/miga/common/system_call.rb:40:inrun_cmd': Command failed with status 1: (MiGA::SystemCallError) : OPT: {:stdout=>nil, :stderr=>nil, :dry=>false, :return=>:output, :raise=>true, :show_cmd=>false, :err2out=>true, :env=>{}, :source=>"/home/alexandra/.miga_modules"} CMD: . /home/alexandra/.miga_modules && /home/linuxbrew/.linuxbrew/bin/python3 -m pip install --user pyhmmer from /home/alexandra/.gem/gems/miga-base-1.3.15.6/lib/miga/cli/action/init.rb:94:in run_cmd' from /home/alexandra/.gem/gems/miga-base-1.3.15.6/lib/miga/cli/action/init.rb:257:ininstall_library' from /home/alexandra/.gem/gems/miga-base-1.3.15.6/lib/miga/cli/action/init.rb:215:in check_and_install_library' from /home/alexandra/.gem/gems/miga-base-1.3.15.6/lib/miga/cli/action/init.rb:203:inblock (2 levels) in check_libraries' from /home/alexandra/.gem/gems/miga-base-1.3.15.6/lib/miga/cli/action/init.rb:202:in each' from /home/alexandra/.gem/gems/miga-base-1.3.15.6/lib/miga/cli/action/init.rb:202:inblock in check_libraries' from /home/alexandra/.gem/gems/miga-base-1.3.15.6/lib/miga/cli/action/init.rb:200:in each' from /home/alexandra/.gem/gems/miga-base-1.3.15.6/lib/miga/cli/action/init.rb:200:incheck_libraries' from /home/alexandra/.gem/gems/miga-base-1.3.15.6/lib/miga/cli/action/init.rb:82:in perform' from /home/alexandra/.gem/gems/miga-base-1.3.15.6/lib/miga/cli/action.rb:32:inlaunch' from /home/alexandra/.gem/gems/miga-base-1.3.15.6/lib/miga/cli.rb:182:in launch' from /home/alexandra/.gem/gems/miga-base-1.3.15.6/bin/miga:12:in<top (required)>' from /home/alexandra/.gem/ruby/3.3.0/bin/miga:25:in load' from /home/alexandra/.gem/ruby/3.3.0/bin/miga:25:in

'

tryfon commented 4 months ago

Fixed it by running /home/linuxbrew/.linuxbrew/bin/python3 -m pip install --user --break-system-packages pyhmmer