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

[Carlos Morais]

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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