[Bioperl-l] How to install 1.6.2

[Minh Bui]

I got it from here
https://github.com/bioperl/bioperl-live/tree/release-1-6-2



On Fri, Feb 4, 2011 at 11:23 AM, Scott Cain <scott at scottcain.net> wrote:

> Hi Minh,
>
> Where did you get BioPerl 1.6.2 from?  It hasn't been released yet.
> You need to be BioPerl from git hub to use summary features:
>
>  https://github.com/bioperl/bioperl-live
>
> and click the download link on the right and select either tar.gz or
> zip file to download.
>
> Scott
>
>
> On Fri, Feb 4, 2011 at 11:14 AM, Minh Bui <buiduyminh at gmail.com> wrote:
> > HI Scott,
> >
> > I installed it anyway but the terminal (i am using Ubuntu 10.10) and it
> says
> > that bp_seqfeature_load.pl (unchanged) --> I still can't use --summary
> > feature.
> >
> > Is there other way to use this feature?
> >
> >
> >
> >
> > On Fri, Feb 4, 2011 at 11:09 AM, Scott Cain <scott at scottcain.net> wrote:
> >>
> >> Hi Minh,
> >>
> >> I don't know why that test failed, but if you don't need to parse or
> >> produce EMBL files, it doesn't matter (and even if you do, it still
> >> may not matter, depending on what the test was).  I suggest
> >> installing.
> >>
> >> Scott
> >>
> >>
> >> On Fri, Feb 4, 2011 at 11:05 AM, Minh Bui <buiduyminh at gmail.com> wrote:
> >> > Oh
> >> > One more thing, I just downloaded Bioperl 1.6.2 and
> >> >
> >> > When I tried to run perl Build.PL, i got this message.
> >> > *
> >> > Checking whether your kit is complete...
> >> > WARNING: the following files are missing in your kit:
> >> >    .shipit
> >> > Please inform the author.
> >> >
> >> > Checking prerequisites...
> >> > Install [a]ll optional external modules, [n]one, or choose
> >> > [i]nteractively?
> >> > [n]
> >> > *
> >> >
> >> > Then I ran ./Build test but it failed.
> >> >
> >> > Test Summary Report
> >> > -------------------
> >> > t/SeqIO/embl.t                             (Wstat: 512 Tests: 85
> Failed:
> >> > 0)
> >> >  Non-zero exit status: 2
> >> >  Parse errors: Bad plan.  You planned 95 tests but ran 85.
> >> > Files=350, Tests=22459, 96 wallclock secs ( 2.78 usr  0.66 sys + 79.46
> >> > cusr
> >> > 4.21 csys = 87.11 CPU)
> >> > Result: FAIL
> >> > Failed 1/350 test programs. 0/22459 subtests failed.
> >> >
> >> > Is there anyway to install 1.6.2 because I really need it. Thank you
> for
> >> > your help.
> >> >
> >> > On Fri, Feb 4, 2011 at 10:44 AM, Minh Bui <buiduyminh at gmail.com>
> wrote:
> >> >
> >> >> Hi,
> >> >>
> >> >> I am trying to use the "summary" feature in  bp_seqfeature_load.pl(for
> >> >> Gbrowse) but it requires Bioperl 1.6.2. I have been trying to install
> >> >> 1.6.2 but no luck.
> >> >>
> >> >> First, I used GIT :
> >> >>
> >> >> git clone git://github.com/bioperl/bioperl-live.git
> >> >>
> >> >> and I got this error:
> >> >> *
> >> >> "github.com[0: 207.97.227.239]: errno=Connection timed out
> >> >> fatal: unable to connect a socket (Connection timed out)"
> >> >>
> >> >> *
> >> >> Then, I downloaded snapshot Core Modules on this page
> >> >> http://www.bioperl.org/wiki/Getting_BioPerl but it doesn't work
> either.
> >> >>
> >> >>
> >> >> could someone please show me how to install 1.6.2 or if there is
> anyway
> >> >> to use summary feature, please let me know.
> >> >>
> >> >> Thank you very much,
> >> >>
> >> >>
> >> >> --
> >> >> Minh Bui.
> >> >>
> >> >
> >> >
> >> >
> >> > --
> >> > Minh Bui.
> >> > _______________________________________________
> >> > Bioperl-l mailing list
> >> > Bioperl-l at lists.open-bio.org
> >> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >> >
> >>
> >>
> >>
> >> --
> >> ------------------------------------------------------------------------
> >> Scott Cain, Ph. D.                                   scott at scottcain
> >> dot net
> >> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> >> Ontario Institute for Cancer Research
> >
> >
> >
> > --
> > Minh Bui.
> >
>
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain dot
> net
> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> Ontario Institute for Cancer Research
>



-- 
Minh Bui.