<div dir="ltr"><div><div><div><div><div>Thanks a lot, Tim!<br></div>This upgrade really fixes the Jellyfish part.<br></div>Now it breaks on Inchworm.<br></div>Apparently, trinity neither include Inchworm nor depends on another package providing it. :-(<br><br><span style="font-family:monospace,monospace">bash: /usr/lib/trinityrnaseq/</span><span style="font-family:monospace,monospace">Inchworm/bin//inchworm: No such file or directory</span><br><br></div>Cheers,<br></div> Carlos<br></div><div class="gmail_extra"><br><div class="gmail_quote">On Tue, Oct 27, 2015 at 3:31 PM, Tim Booth <span dir="ltr"><<a href="mailto:tbooth@ceh.ac.uk" target="_blank">tbooth@ceh.ac.uk</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi Carlos,<br>
<br>
This looks to me like someone (maybe me) stuffed up the jellyfish<br>
package and installed the wrong file into /usr/bin. It seems to be a<br>
simple typo in the build script.<br>
<br>
I've amended the package and uploaded it to Launchpad. Please look out<br>
for the updated package 2.2.3-2biolinux2 and see if that sorts it.<br>
<br>
Cheers,<br>
<br>
TIM<br>
<br>
On Mon, 2015-10-26 at 08:41 -0200, Carlos Morais wrote:<br>
> Anybody else experienced this error? Any ideas?<br>
> Thanks<br>
><br>
> Em 15/10/2015 12:28, "Carlos Morais" <<a href="mailto:morais@iq.usp.br">morais@iq.usp.br</a>> escreveu:<br>
> Thanks a lot for the update.<br>
><br>
><br>
> However, it is trying to compile Jellyfish on the go. I'm<br>
> attaching the output. Relevant part:<br>
><br>
> Trinity version: v2.0.6<br>
> ...<br>
> -------------------------------------------<br>
> ----------- Jellyfish --------------------<br>
> -- (building a k-mer catalog from reads) --<br>
> -------------------------------------------<br>
><br>
> Wednesday, October 14, 2015: 13:46:18<br>
> CMD: /usr/bin/jellyfish count -t 15 -m 25 -s 14446126223<br>
> --canonical both.fa<br>
> mkdir: cannot create directory ‘/usr/bin/.libs’: Permission<br>
> denied<br>
> /usr/bin/jellyfish: line 202:<br>
> cd: /build/jellyfish-sMXWdl/jellyfish-2.2.3: No such file or<br>
> directory<br>
> g++: error: sub_commands/jellyfish.o: No such file or<br>
> directory<br>
> g++: error: sub_commands/count_main.o: No such file or<br>
> directory<br>
> g++: error: sub_commands/info_main.o: No such file or<br>
> directory<br>
> g++: error: sub_commands/dump_main.o: No such file or<br>
> directory<br>
> g++: error: sub_commands/histo_main.o: No such file or<br>
> directory<br>
> g++: error: sub_commands/stats_main.o: No such file or<br>
> directory<br>
> g++: error: sub_commands/merge_main.o: No such file or<br>
> directory<br>
> g++: error: sub_commands/bc_main.o: No such file or directory<br>
> g++: error: sub_commands/query_main.o: No such file or<br>
> directory<br>
> g++: error: sub_commands/cite_main.o: No such file or<br>
> directory<br>
> g++: error: sub_commands/mem_main.o: No such file or directory<br>
> g++: error: jellyfish/merge_files.o: No such file or directory<br>
> g++: error: ./.libs/<a href="http://libjellyfish-2.0.so" rel="noreferrer" target="_blank">libjellyfish-2.0.so</a>: No such file or<br>
> directorynError, cmd: /usr/bin/jellyfish count -t 15 -m 25 -s<br>
> 14446126223 --canonical both.fa died with ret 256<br>
> at /usr/lib/trinityrnaseq/Trinity line 2115.<br>
><br>
> Trinity run failed. Must investigate error above.<br>
><br>
><br>
> On Mon, Sep 14, 2015 at 10:00 AM, Bishwa Kiran<br>
> <<a href="mailto:kirannbishwa01@gmail.com">kirannbishwa01@gmail.com</a>> wrote:<br>
> Thanks for the update !<br>
><br>
> On Mon, Sep 14, 2015 at 6:42 AM, Tim Booth<br>
> <<a href="mailto:tbooth@ceh.ac.uk">tbooth@ceh.ac.uk</a>> wrote:<br>
> Hi All,<br>
><br>
> I've been doing a round of package updates on<br>
> Bio-Linux 8 over the last<br>
> week. We now have both Mothur and Mira<br>
> updated to the latest versions:<br>
><br>
> mira-assembler package is version 4.9.5<br>
> mothur package is version 1.36.1<br>
><br>
> Both will be updated by the package updater.<br>
> If you experience any<br>
> problems or regressions with these new<br>
> packages please let me know.<br>
><br>
> I'm also pleased to say that the Trinity<br>
> RNA-Seq De novo assembler has<br>
> been added to the package repository<br>
> (<a href="http://trinityrnaseq.github.io/" rel="noreferrer" target="_blank">http://trinityrnaseq.github.io/</a>).<br>
> Various modifications have been made to<br>
> Trinity to make it integrate<br>
> nicely with the other packages on the system,<br>
> so if you have problems<br>
> running it please let me know and I'll check<br>
> if it is maybe something<br>
> that got messed up in the packaging.<br>
><br>
> trinityrnaseq package is version 2.0.6<br>
><br>
> To get it: sudo apt-get install trinityrnaseq<br>
> then just type: "Trinity" (with the capital T)<br>
><br>
> The credit for all this goes mainly to Michael<br>
> and Andreas from the<br>
> Debian Med project who maintain these packages<br>
> in Debian. I've been<br>
> able to take what they made and backport it to<br>
> Bio-Linux for you.<br>
><br>
> Cheers,<br>
><br>
> TIM<br>
><br>
> --<br>
> Tim Booth <<a href="mailto:tbooth@ceh.ac.uk">tbooth@ceh.ac.uk</a>><br>
><br>
> Centre for Ecology and Hydrology<br>
> Maclean Bldg, Benson Lane<br>
> Crowmarsh Gifford<br>
> Wallingford, England<br>
> OX10 8BB<br>
><br>
> <a href="http://environmentalomics.org/bio-linux" rel="noreferrer" target="_blank">http://environmentalomics.org/bio-linux</a><br>
> <a href="tel:%2B44%201491%2069%202297" value="+441491692297">+44 1491 69 2297</a><br>
><br>
><br>
> _______________________________________________<br>
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><br>
><br>
><br>
><br>
> --<br>
> - Bish<br>
><br>
><br>
><br>
><br>
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<br>
--<br>
Tim Booth <<a href="mailto:tbooth@ceh.ac.uk">tbooth@ceh.ac.uk</a>><br>
<br>
Centre for Ecology and Hydrology<br>
Maclean Bldg, Benson Lane<br>
Crowmarsh Gifford<br>
Wallingford, England<br>
OX10 8BB<br>
<br>
<a href="http://environmentalomics.org/bio-linux" rel="noreferrer" target="_blank">http://environmentalomics.org/bio-linux</a><br>
<a href="tel:%2B44%201491%2069%202297" value="+441491692297">+44 1491 69 2297</a><br>
<br>
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</blockquote></div><br></div>