[Bioperl-l] How to install 1.6.2

[Minh Bui]

I install the version you sent.

and it works.

Thank you very much, Scott.


On Fri, Feb 4, 2011 at 11:33 AM, Scott Cain <scott at scottcain.net> wrote:

> OK, the seqfeature_load script in that branch has the summary feature
> option in it.  Are you sure that the script you have doesn't?
>
> Scott
>
>
> On Fri, Feb 4, 2011 at 11:27 AM, Minh Bui <buiduyminh at gmail.com> wrote:
> > 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.
> >
>
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain dot
> net
> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> Ontario Institute for Cancer Research
>



-- 
Minh Bui.