[maker-devel] Help on Maker

[Michael Campbell]

Hi Huda,

I'm forwarding this to the MAKER dev list to get some more eyes on it. The
link to the Korf website works for me. Where are you trying to connect form?

Mike

On Sun, Feb 10, 2013 at 10:10 PM, Hud Hud <hudarul at yahoo.com> wrote:

> Hi Mike,
> Thnks 4 ur reply..ive tried the ./Build blast command..I prtscrn the last
> part of the configuration as attached. Is there anything that I've
> missed?....And for the SNAP, I tried to download manually from the website,
> but i cant get access to the korflab.ucdavis.edu/software website..
>
> Thanks..
>   ------------------------------
> *From:* Michael Campbell <michael.s.campbell1 at gmail.com>
> *To:* "李青 Li, Qing" <liqing850104 at gmail.com>
> *Cc:* Hud Hud <hudarul at yahoo.com>
> *Sent:* Monday, February 11, 2013 11:42 AM
> *Subject:* Re: Help on Maker
>
> Hi Huda,
>
> If you have unpacked the maker tar ball and moved to the src directory and
> have run the "perl Build.PL <http://build.pl/>" command you can run the
> next command "./Build status" and that should give a report that looks like
> this.
>
>
> ==============================================================================
> STATUS MAKER 2.25
>
> ==============================================================================
> PERL Dependencies: VERIFIED
> External Programs: VERIFIED
> External C Libraries: VERIFIED
> MPI SUPPORT: DISABLED
> MWAS Web Interface: DISABLED
> MAKER PACKAGE: CONFIGURATION OK
>
>
> Important Commands:
> ./Build installdeps #installs missing PERL dependencies
>  ./Build installexes #installs all missing external programs
> ./Build install #installs MAKER
>  ./Build status #Shows this status menu
>
> Other Commands:
> ./Build repeatmasker #installs RepeatMasker (asks for RepBase)
>  ./Build blast #installs BLAST (NCBI BLAST+)
>  ./Build exonerate #installs Exonerate (v2 on UNIX / v1 on Mac OSX)
> ./Build snap #installs SNAP
>  ./Build augustus #installs Augustus
> ./Build apollo #installs Apollo
>  ./Build gbrowse #installs GBrowse (must be root)
> ./Build jbrowse #installs JBrowse (MAKER copy, not web accecible)
>  ./Build mpich2 #installs MPICH2 (but manual install recommended)
>
>
> I've highlighted the commands above that you can run to have MAKER install
> snap and blast for you. Here is a url for a gmod tutorial for installing
> and running MAKER http://gmod.org/wiki/MAKER_Tutorial_2012.
>
> I haven't actually used cygwin so I am interested in hearing how MAKER
> runs in that environment. I will ask a few other people and see if they
> have any experience with cygwin.
>
> Let me know if you get stuck or have any more questions,
> Mike
>
>
> On Sun, Feb 10, 2013 at 6:52 PM, 李青 Li, Qing <liqing850104 at gmail.com>wrote:
>
> Hello Huda,
> No worries:) I am cp your question to the expert maker usr in our group!
>
> Mike, would you think you could answer Huda's question and help him, or
> would you think we need to ask Carlson for help?
> Best,
> Qing
>
>
> 2013/2/10 Hud Hud <hudarul at yahoo.com>
>
> Hello Hi, Im Huda...Im having problem during the installation of
> MAKER...I'm not sure whether im asking the right person, I just pick anyone
> from the list of Yandell People page...Hofefully im not troubling u with
> this email...
> Back to the problem...I try to install Maker but I've noticed that im
> missing some external program that are Blast and SNAP...how to solve this
> problem. FYI im very new in this field and not very familiar with
> programming or scripting. Im using cygwin. Thanks for your help
>
>
>
>
>
> --
> Michael Campbell MS, RD.
> Graduate Student
> Eccles Institute of Human Genetics
> University of Utah
> 15 North 2030 East, Room 2100
> Salt Lake City, UT 84112-5330
> ph:585-3543
>
>
>
>


-- 
Michael Campbell MS, RD.
Graduate Student
Eccles Institute of Human Genetics
University of Utah
15 North 2030 East, Room 2100
Salt Lake City, UT 84112-5330
ph:585-3543
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