[Bio-Linux] Trinity added, Mothur and Mira updated

[Carlos Morais]

Anybody else experienced this error? Any ideas?
Thanks
Em 15/10/2015 12:28, "Carlos Morais" <morais at iq.usp.br> escreveu:

> Thanks a lot for the update.
>
> However, it is trying to compile Jellyfish on the go. I'm attaching the
> output. Relevant part:
>
> Trinity version: v2.0.6
> ...
> -------------------------------------------
> ----------- Jellyfish  --------------------
> -- (building a k-mer catalog from reads) --
> -------------------------------------------
>
> Wednesday, October 14, 2015: 13:46:18   CMD: /usr/bin/jellyfish count -t
> 15 -m 25 -s 14446126223  --canonical  both.fa
> mkdir: cannot create directory ‘/usr/bin/.libs’: Permission denied
> /usr/bin/jellyfish: line 202: cd: /build/jellyfish-sMXWdl/jellyfish-2.2.3:
> No such file or directory
> g++: error: sub_commands/jellyfish.o: No such file or directory
> g++: error: sub_commands/count_main.o: No such file or directory
> g++: error: sub_commands/info_main.o: No such file or directory
> g++: error: sub_commands/dump_main.o: No such file or directory
> g++: error: sub_commands/histo_main.o: No such file or directory
> g++: error: sub_commands/stats_main.o: No such file or directory
> g++: error: sub_commands/merge_main.o: No such file or directory
> g++: error: sub_commands/bc_main.o: No such file or directory
> g++: error: sub_commands/query_main.o: No such file or directory
> g++: error: sub_commands/cite_main.o: No such file or directory
> g++: error: sub_commands/mem_main.o: No such file or directory
> g++: error: jellyfish/merge_files.o: No such file or directory
> g++: error: ./.libs/libjellyfish-2.0.so: No such file or directorynError,
> cmd: /usr/bin/jellyfish count -t 15 -m 25 -s 14446126223  --canonical
> both.fa died with ret 256 at /usr/lib/trinityrnaseq/Trinity line 2115.
>
> Trinity run failed. Must investigate error above.
>
> On Mon, Sep 14, 2015 at 10:00 AM, Bishwa Kiran <kirannbishwa01 at gmail.com>
> wrote:
>
>> Thanks for the update !
>>
>> On Mon, Sep 14, 2015 at 6:42 AM, Tim Booth <tbooth at ceh.ac.uk> wrote:
>>
>>> Hi All,
>>>
>>> I've been doing a round of package updates on Bio-Linux 8 over the last
>>> week.  We now have both Mothur and Mira updated to the latest versions:
>>>
>>> mira-assembler package is version 4.9.5
>>> mothur package is version 1.36.1
>>>
>>> Both will be updated by the package updater. If you experience any
>>> problems or regressions with these new packages please let me know.
>>>
>>> I'm also pleased to say that the Trinity RNA-Seq De novo assembler has
>>> been added to the package repository (http://trinityrnaseq.github.io/).
>>> Various modifications have been made to Trinity to make it integrate
>>> nicely with the other packages on the system, so if you have problems
>>> running it please let me know and I'll check if it is maybe something
>>> that got messed up in the packaging.
>>>
>>> trinityrnaseq package is version 2.0.6
>>>
>>> To get it: sudo apt-get install trinityrnaseq
>>> then just type: "Trinity" (with the capital T)
>>>
>>> The credit for all this goes mainly to Michael and Andreas from the
>>> Debian Med project who maintain these packages in Debian.  I've been
>>> able to take what they made and backport it to Bio-Linux for you.
>>>
>>> Cheers,
>>>
>>> TIM
>>>
>>> --
>>> Tim Booth <tbooth at ceh.ac.uk>
>>>
>>> Centre for Ecology and Hydrology
>>> Maclean Bldg, Benson Lane
>>> Crowmarsh Gifford
>>> Wallingford, England
>>> OX10 8BB
>>>
>>> http://environmentalomics.org/bio-linux
>>> +44 1491 69 2297
>>>
>>>
>>> _______________________________________________
>>> Bio-Linux mailing list
>>> Bio-Linux at nebclists.nerc.ac.uk
>>> http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux
>>>
>>
>>
>>
>> --
>> - Bish
>>
>>
>>
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>>
>>
>
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