[Bioperl-l] How to install 1.6.2

[Scott Cain]

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