[Bio-Linux] Trinity added, Mothur and Mira updated - jellyfish problem
Carlos Morais
morais at iq.usp.br
Wed Oct 28 14:34:59 EDT 2015
Thanks a lot, Tim!
This upgrade really fixes the Jellyfish part.
Now it breaks on Inchworm.
Apparently, trinity neither include Inchworm nor depends on another package
providing it. :-(
bash: /usr/lib/trinityrnaseq/Inchworm/bin//inchworm: No such file or
directory
Cheers,
Carlos
On Tue, Oct 27, 2015 at 3:31 PM, Tim Booth <tbooth at ceh.ac.uk> wrote:
> Hi Carlos,
>
> This looks to me like someone (maybe me) stuffed up the jellyfish
> package and installed the wrong file into /usr/bin. It seems to be a
> simple typo in the build script.
>
> I've amended the package and uploaded it to Launchpad. Please look out
> for the updated package 2.2.3-2biolinux2 and see if that sorts it.
>
> Cheers,
>
> TIM
>
> On Mon, 2015-10-26 at 08:41 -0200, Carlos Morais wrote:
> > 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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> > Bio-Linux at nebclists.nerc.ac.uk
> > http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux
> >
> >
> >
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>
> --
> 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
>
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