[Bioperl-l] How to install 1.6.2
Minh Bui
buiduyminh at gmail.com
Fri Feb 4 17:52:21 UTC 2011
Thank you so much for your help and clarification.
Minh.
On Fri, Feb 4, 2011 at 11:50 AM, Chris Fields <cjfields at illinois.edu> wrote:
> Note that is a branch, not a tagged release. We created a new branch for
> the eventual 1.6.2 release due to problems cherry-picking commits over the
> last year or so. It's not really different from master, with the exception
> that we'll be merging code in from the recent evo hackathon soon to master
> and NOT to the release.
>
> chris
>
> On Feb 4, 2011, at 10:33 AM, Scott Cain 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
> >
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>
--
Minh Bui.
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