[Bio-Linux] Trinity added, Mothur and Mira updated - jellyfish problem
Tim Booth
tbooth at ceh.ac.uk
Tue Oct 27 13:31:19 EDT 2015
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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>
>
>
>
> --
> - Bish
>
>
>
>
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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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