[Bioperl-l] How to install 1.6.2

[Scott Cain]

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