installation: Fatal error: local()

[idot]

When installing I first get warnings and then an error. I am also wondering about the python version bcbio uses. Shouldn't it use its own version even during installation, because the log says it uses: "/biosw/debian5-x86_64/python/2.7.3/lib/python2.7/subprocess.py", which is what I called the install script with. Is there a discussion group or forum for bcbio?

Warning: Could not tap chapmanb/cbl/samtools over homebrew/science/samtools
Warning: Could not tap chapmanb/cbl/htslib over homebrew/science/htslib
Tapped 217 formula
Error: Input/output error - /home/imba/tamir/.cache/Homebrew/Formula/cpanminus.brewing

Fatal error: local() encountered an error (return code 1) while executing 'export CC=${CC:-`which gcc`} && export CXX=${CXX:-`which g++`} && export PERL5LIB=/groups/csf-ngs/bin/workflow/bcbio/lib/perl5:${PERL5LIB} && /groups/csf-ngs/bin/workflow/bcbio/bin/brew install --env=inherit cpanminus'

Aborting.
Upgrading third party tools to latest versions
Setting up virtual machine
[localhost] local: lsb_release -a | grep Codename | cut -f 2
[localhost] local: cat /proc/version
[localhost] local: echo $HOME
[localhost] local: uname -m
[localhost] local: ls /groups/csf-ngs/bin/workflow/bcbio/share/java/picard-1.96
[localhost] local: ls /groups/csf-ngs/bin/workflow/bcbio/share/java/RNA-SeQC-1.1.7
[localhost] local: ls /groups/csf-ngs/bin/workflow/bcbio/share/java/bcbio_variation-0.1.3
[localhost] local: ls /groups/csf-ngs/bin/workflow/bcbio/share/java/gatk-2.3-9-gdcdccbb
[localhost] local: ls /groups/csf-ngs/bin/workflow/bcbio/share/java/mutect-1.1.5
[localhost] local: ls /groups/csf-ngs/bin/workflow/bcbio/share/java/snpeff-3_4
[localhost] local: ls /groups/csf-ngs/bin/workflow/bcbio/share/java/varscan-2.3.6
[localhost] local: echo $HOME
[localhost] local: uname -m
[localhost] local: /groups/csf-ngs/bin/workflow/bcbio/bin/brew tap
[localhost] local: /groups/csf-ngs/bin/workflow/bcbio/bin/brew update
[localhost] local: /groups/csf-ngs/bin/workflow/bcbio/bin/brew tap --repair
[localhost] local: /groups/csf-ngs/bin/workflow/bcbio/bin/brew outdated
[localhost] local: export CC=${CC:-`which gcc`} && export CXX=${CXX:-`which g++`} && export PERL5LIB=/groups/csf-ngs/bin/workflow/bcbio/lib/perl5:${PERL5LIB} && /groups/csf-ngs/bin/workflow/bcbio/bin/brew install --env=inherit cpanminus
Checking required dependencies
Installing isolated base python installation
Installing bcbio-nextgen
Installing data and third party dependencies
Traceback (most recent call last):
  File "/groups/csf-ngs/bin/workflow/bcbio/scripts/bcbio_nextgen_install.py", line 232, in <module>
    main(parser.parse_args(), sys.argv[1:])
  File "/groups/csf-ngs/bin/workflow/bcbio/scripts/bcbio_nextgen_install.py", line 37, in main
    subprocess.check_call([bcbio["bcbio_nextgen.py"], "upgrade"] + _clean_args(sys_argv, args, bcbio))
  File "/biosw/debian5-x86_64/python/2.7.3/lib/python2.7/subprocess.py", line 511, in check_call
    raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '['/groups/csf-ngs/bin/workflow/bcbio/anaconda/bin/bcbio_nextgen.py', 'upgrade', '--tooldir=/groups/csf-ngs/bin/workflow/bcbio', '--nosudo', '--isolate', '--distribution', 'debian', '--data']' returned non-zero exit status 1

[chapmanb]

Ido; The install failure is from brew not having the ability to access /home/imba/tamir/.cache/Homebrew/Formula/cpanminus.brewing. I'm still not sure what happened with your brew installation but you might try manually removing the cache directory and restarting: rm -rf /home/imba/tamir/.cache/Homebrew. Hopefully that will get things working again.

The error traceback you see is from calling the bcbio_nextgen_install.py script, so you'll see references to the python you used to start this. Internally within the bcbio_nextgen.py upgrade command, it is using it's own installed local python. Everything appears normal on that side.

Happy to also help with issues on the biovalidation mailing list: https://github.com/chapmanb/bcbio-nextgen#documentation.

Thanks for all the patience getting this upgraded.

[idot]

This is I think due to some undefinable NAS issue. Is it possible to change the .cache location to another path?

[chapmanb]

You can set the cache with:

export HOMEBREW_CACHE=/path/to/cachedir

If this seems to clear it up I'll add the tip to the documentation as well. Thanks much for the help debugging.

[idot]

Thank you very very much for both this system and the quick help. I have the feeling we getting there, only 1/4 of all the world bioinformatic programs left to download compile and install.

Now I am stuck with: ==> make

• linking smithwaterman make[2]: Leaving directory /tmp/glia-HhRE/vcflib/smithwaterman' make[2]: Leaving directory/tmp/glia-HhRE/vcflib/fastahack' make[1]: Leaving directory /tmp/glia-HhRE/vcflib' make: *** [vcflib/src/Variant.o] Error 2 /usr/lib/ruby/1.8/open-uri.rb:277:inopen_http': 404 Not Found (OpenURI::HTTPError) from /usr/lib/ruby/1.8/open-uri.rb:616:in buffer_open' from /usr/lib/ruby/1.8/open-uri.rb:164:inopen_loop' from /usr/lib/ruby/1.8/open-uri.rb:162:in catch' from /usr/lib/ruby/1.8/open-uri.rb:162:inopen_loop' from /usr/lib/ruby/1.8/open-uri.rb:132:in open_uri' from /usr/lib/ruby/1.8/open-uri.rb:518:inopen' from /usr/lib/ruby/1.8/open-uri.rb:26:in open' from /groups/csf-ngs/bin/workflow/bcbio/Library/Homebrew/utils.rb:265:inopen' from /groups/csf-ngs/bin/workflow/bcbio/Library/Homebrew/utils.rb:282:in each_issue_matching' from /groups/csf-ngs/bin/workflow/bcbio/Library/Homebrew/utils.rb:294:inissues_for_formula' from /groups/csf-ngs/bin/workflow/bcbio/Library/Homebrew/exceptions.rb:178:in issues' from /groups/csf-ngs/bin/workflow/bcbio/Library/Homebrew/exceptions.rb:212:indump' from /groups/csf-ngs/bin/workflow/bcbio/Library/brew.rb:118

I managed to compile vcflib manually by going into /clustertmp/csfs/ido/homebrew/glia--git applying this fix:http://www.langebio.cinvestav.mx/bioinformatica/jacob/?p=1116 (adding som_network_t_record to one unnamed struct)

But of course restarting the bcbio installer does not have the fix.

[chapmanb]

Ido; It would be good to report this upstream to Erik to get a proper fix in. There is already a workaround in fsom for patching this on Apple, but I guess it needs to be extended to some other cases. What version of gcc do you have that triggers this?

[chapmanb]

Closing old bugs. Please respond and we can re-open if this is still an issue.