<div dir="ltr">Thanks again for the upgrade. I'm already running Trinity for 2 hours, and it is now on Chrysalis phase. So, I'm assuming Inchworm part is now OK. I'll let you know if it stumbles on another point.<br></div><div class="gmail_extra"><br><div class="gmail_quote">On Thu, Oct 29, 2015 at 7:59 AM, 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>
Thanks for being the first proper tester on the Trinity package. As<br>
with Jellyfish the package was building correctly (hence passing<br>
internal tests) but Inchworm never got packed into the final DEB file.<br>
I've fixed the build rules and the new version is preparing on Launchpad<br>
now. Should appear as an update in about an hour.<br>
<br>
Cheers,<br>
<br>
TIM<br>
<br>
On Wed, 2015-10-28 at 16:34 -0200, Carlos Morais wrote:<br>
> Thanks a lot, Tim!<br>
><br>
> This upgrade really fixes the Jellyfish part.<br>
><br>
> Now it breaks on Inchworm.<br>
><br>
> Apparently, trinity neither include Inchworm nor depends on another<br>
> package providing it. :-(<br>
><br>
> bash: /usr/lib/trinityrnaseq/Inchworm/bin//inchworm: No such file or<br>
> directory<br>
><br>
><br>
> Cheers,<br>
><br>
> Carlos<br>
><br>
><br>
> On Tue, Oct 27, 2015 at 3:31 PM, Tim Booth <<a href="mailto:tbooth@ceh.ac.uk">tbooth@ceh.ac.uk</a>> wrote:<br>
> Hi Carlos,<br>
><br>
> This looks to me like someone (maybe me) stuffed up the<br>
> jellyfish<br>
> package and installed the wrong file into /usr/bin. It seems<br>
> to be a<br>
> simple typo in the build script.<br>
><br>
> I've amended the package and uploaded it to Launchpad. Please<br>
> look out<br>
> for the updated package 2.2.3-2biolinux2 and see if that sorts<br>
> 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>><br>
> escreveu:<br>
> > Thanks a lot for the update.<br>
> ><br>
> ><br>
> > However, it is trying to compile Jellyfish on the<br>
> 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<br>
> 14446126223<br>
> > --canonical both.fa<br>
> > mkdir: cannot create directory ‘/usr/bin/.libs’:<br>
> Permission<br>
> > denied<br>
> > /usr/bin/jellyfish: line 202:<br>
> > cd: /build/jellyfish-sMXWdl/jellyfish-2.2.3: No such<br>
> file or<br>
> > directory<br>
> > g++: error: sub_commands/jellyfish.o: No such file<br>
> or<br>
> > directory<br>
> > g++: error: sub_commands/count_main.o: No such file<br>
> or<br>
> > directory<br>
> > g++: error: sub_commands/info_main.o: No such file<br>
> or<br>
> > directory<br>
> > g++: error: sub_commands/dump_main.o: No such file<br>
> or<br>
> > directory<br>
> > g++: error: sub_commands/histo_main.o: No such file<br>
> or<br>
> > directory<br>
> > g++: error: sub_commands/stats_main.o: No such file<br>
> or<br>
> > directory<br>
> > g++: error: sub_commands/merge_main.o: No such file<br>
> or<br>
> > directory<br>
> > g++: error: sub_commands/bc_main.o: No such file or<br>
> directory<br>
> > g++: error: sub_commands/query_main.o: No such file<br>
> or<br>
> > directory<br>
> > g++: error: sub_commands/cite_main.o: No such file<br>
> or<br>
> > directory<br>
> > g++: error: sub_commands/mem_main.o: No such file or<br>
> directory<br>
> > g++: error: jellyfish/merge_files.o: No such file or<br>
> directory<br>
> > g++: error: ./.libs/<a href="http://libjellyfish-2.0.so" rel="noreferrer" target="_blank">libjellyfish-2.0.so</a>: No such<br>
> file or<br>
> > directorynError, cmd: /usr/bin/jellyfish count -t 15<br>
> -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<br>
> updates on<br>
> > Bio-Linux 8 over the last<br>
> > week. We now have both Mothur and<br>
> Mira<br>
> > updated to the latest versions:<br>
> ><br>
> > mira-assembler package is version<br>
> 4.9.5<br>
> > mothur package is version 1.36.1<br>
> ><br>
> > Both will be updated by the package<br>
> updater.<br>
> > If you experience any<br>
> > problems or regressions with these<br>
> new<br>
> > packages please let me know.<br>
> ><br>
> > I'm also pleased to say that the<br>
> 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<br>
> to<br>
> > Trinity to make it integrate<br>
> > nicely with the other packages on<br>
> the system,<br>
> > so if you have problems<br>
> > running it please let me know and<br>
> I'll check<br>
> > if it is maybe something<br>
> > that got messed up in the packaging.<br>
> ><br>
> > trinityrnaseq package is version<br>
> 2.0.6<br>
> ><br>
> > To get it: sudo apt-get install<br>
> trinityrnaseq<br>
> > then just type: "Trinity" (with the<br>
> capital T)<br>
> ><br>
> > The credit for all this goes mainly<br>
> to Michael<br>
> > and Andreas from the<br>
> > Debian Med project who maintain<br>
> these packages<br>
> > in Debian. I've been<br>
> > able to take what they made and<br>
> 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>
> ><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>
> _______________________________________________<br>
> > Bio-Linux mailing list<br>
> > <a href="mailto:Bio-Linux@nebclists.nerc.ac.uk">Bio-Linux@nebclists.nerc.ac.uk</a><br>
> ><br>
> <a href="http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux" rel="noreferrer" target="_blank">http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux</a><br>
> ><br>
> ><br>
> ><br>
> ><br>
> > --<br>
> > - Bish<br>
> ><br>
> ><br>
> ><br>
> ><br>
> ><br>
> _______________________________________________<br>
> > Bio-Linux mailing list<br>
> > <a href="mailto:Bio-Linux@nebclists.nerc.ac.uk">Bio-Linux@nebclists.nerc.ac.uk</a><br>
> ><br>
> <a href="http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux" rel="noreferrer" target="_blank">http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux</a><br>
> ><br>
> ><br>
> ><br>
> > _______________________________________________<br>
> > Bio-Linux mailing list<br>
> > <a href="mailto:Bio-Linux@nebclists.nerc.ac.uk">Bio-Linux@nebclists.nerc.ac.uk</a><br>
> > <a href="http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux" rel="noreferrer" target="_blank">http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux</a><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>
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> <a href="mailto:Bio-Linux@nebclists.nerc.ac.uk">Bio-Linux@nebclists.nerc.ac.uk</a><br>
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><br>
><br>
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> <a href="mailto:Bio-Linux@nebclists.nerc.ac.uk">Bio-Linux@nebclists.nerc.ac.uk</a><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>
<br>
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</blockquote></div><br></div>