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blahah / transrate

Understand your transcriptome assembly
http://hibberdlab.com/transrate
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Installing dependencies with version 1.0.3 #194

Closed abshah closed 8 years ago

abshah commented 8 years ago

Hi transrate users/developers,

Recently, I was trying to install transrate version 1.0.3, however, I couldn't get it to install the dependencies. My console output was :

[root@gaiking transrate]# gem install transrate-1.0.3.gem Building native extensions. This could take a while... Successfully installed transrate-1.0.3 Parsing documentation for transrate-1.0.3 Installing ri documentation for transrate-1.0.3 Done installing documentation for transrate after 0 seconds 1 gem installed [root@gaiking transrate]# transrate --install-deps=all Checking dependencies Installing snap (1.0dev.96)... /usr/local/rvm/gems/ruby-2.1.0/gems/transrate-1.0.3/bin/transrate:13:inraise': There was a problem unpacking snap_v1.0dev.96_linux.tar.gz (RuntimeError)

gzip: stdin: not in gzip format tar: Child returned status 1 tar: Error is not recoverable: exiting now from /usr/local/rvm/gems/ruby-2.1.0/gems/bindeps-1.2.1/lib/unpacker.rb:52:in block in unpack' from /usr/local/rvm/rubies/ruby-2.1.0/lib/ruby/2.1.0/tmpdir.rb:88:inmktmpdir' from /usr/local/rvm/gems/ruby-2.1.0/gems/bindeps-1.2.1/lib/unpacker.rb:35:in unpack' from /usr/local/rvm/gems/ruby-2.1.0/gems/bindeps-1.2.1/lib/bindeps.rb:134:inunpack' from /usr/local/rvm/gems/ruby-2.1.0/gems/bindeps-1.2.1/lib/bindeps.rb:86:in install_missing' from /usr/local/rvm/gems/ruby-2.1.0/gems/bindeps-1.2.1/lib/bindeps.rb:29:inblock (3 levels) in require' from /usr/local/rvm/gems/ruby-2.1.0/gems/bindeps-1.2.1/lib/bindeps.rb:20:in each_pair' from /usr/local/rvm/gems/ruby-2.1.0/gems/bindeps-1.2.1/lib/bindeps.rb:20:inblock (2 levels) in require' from /usr/local/rvm/gems/ruby-2.1.0/gems/bindeps-1.2.1/lib/bindeps.rb:19:in chdir' from /usr/local/rvm/gems/ruby-2.1.0/gems/bindeps-1.2.1/lib/bindeps.rb:19:inblock in require' from /usr/local/rvm/rubies/ruby-2.1.0/lib/ruby/2.1.0/tmpdir.rb:88:in mktmpdir' from /usr/local/rvm/gems/ruby-2.1.0/gems/bindeps-1.2.1/lib/bindeps.rb:18:inrequire' from /usr/local/rvm/gems/ruby-2.1.0/gems/transrate-1.0.3/lib/transrate/cmdline.rb:293:in install_missing_dependencies' from /usr/local/rvm/gems/ruby-2.1.0/gems/transrate-1.0.3/lib/transrate/cmdline.rb:258:incheck_dependencies' from /usr/local/rvm/gems/ruby-2.1.0/gems/transrate-1.0.3/lib/transrate/cmdline.rb:164:in check_arguments' from /usr/local/rvm/gems/ruby-2.1.0/gems/transrate-1.0.3/lib/transrate/cmdline.rb:18:ininitialize' from /usr/local/rvm/gems/ruby-2.1.0/gems/transrate-1.0.3/bin/transrate:22:in new' from /usr/local/rvm/gems/ruby-2.1.0/gems/transrate-1.0.3/bin/transrate:22:in<top (required)>' from /usr/local/rvm/gems/ruby-2.1.0/bin/transrate:22:in load' from /usr/local/rvm/gems/ruby-2.1.0/bin/transrate:22:in

' from /usr/local/rvm/gems/ruby-2.1.0/bin/ruby_executable_hooks:15:in eval' from /usr/local/rvm/gems/ruby-2.1.0/bin/ruby_executable_hooks:15:in
'`

blahah commented 8 years ago

Hi @abshah this was probably because v1.0.3 was not released yet, and you were building from an unstable state in master.

The latest release of transrate v1.0.3 now includes the latest version of SNAP and Salmon. Hopefully this will solve the problem - if not please re-open the issue. Many thanks for your patience :)