[Bio-Linux] Trinity added, Mothur and Mira updated - Inchworm problem
Tim Booth
tbooth at ceh.ac.uk
Thu Oct 29 05:59:35 EDT 2015
Hi Carlos,
Thanks for being the first proper tester on the Trinity package. As
with Jellyfish the package was building correctly (hence passing
internal tests) but Inchworm never got packed into the final DEB file.
I've fixed the build rules and the new version is preparing on Launchpad
now. Should appear as an update in about an hour.
Cheers,
TIM
On Wed, 2015-10-28 at 16:34 -0200, Carlos Morais wrote:
> 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
> >
> >
> >
> _______________________________________________
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> > Bio-Linux at nebclists.nerc.ac.uk
> >
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> >
> >
> >
> >
> > --
> > - 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
>
>
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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
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