[mira_talk] Re: Assembly
- From: Sharmista Saha <sharmistasaha@xxxxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Wed, 30 Sep 2009 19:02:45 +0530
say for eg:, if I need to retrieve the A.thaliana gb file, can you direct
me the link for it. I think that will itself illustrate me what I am
hunting.
and thats what I feel is also required for mira running.
Thanks and Regards,
Sharmistha
On Wed, Sep 30, 2009 at 6:46 PM, Sven Klages
<sir.svencelot@xxxxxxxxxxxxxx>wrote:
> I am not sure if I understood correctly, but NCBI always supplies the
> sequences (when saving to file) as sequences.fasta/.gb/.whatever ..
> This is just their default name.
>
> hth,
> Sven
>
> 2009/9/30 Sharmista Saha <sharmistasaha@xxxxxxxxxxxxxx>
>
> one more query, although it is silly, but I can't resist to ask, the gb
>> file which I am downloading, is a particular gene file of a particular
>> species, from the given link.
>> http://www.ncbi.nlm.nih.gov/sites/gquery?itool=toolbar
>>
>> Although what I am saving is a seq.gb but,
>> I think I may be wrong in that also ( may be it does not contain the whole
>> database as required), can anyone suggest me what should be the correct one?
>>
>> Thanks and regards,
>> Sharmistha
>>
>>
>> On Wed, Sep 30, 2009 at 1:40 PM, Sharmista Saha <
>> sharmistasaha@xxxxxxxxxxxxxx> wrote:
>>
>>> Thanks for all the help.
>>> I will try your methods and get back to you.
>>>
>>> Regards,
>>> Sharmistha
>>>
>>> On Wed, Sep 30, 2009 at 1:24 PM, Bastien Chevreux <bach@xxxxxxxxxxxx>wrote:
>>>
>>>> > Subject: [mira_talk] Re: Assembly
>>>> > 3. I ran the respective command you provided, unfortunately, error
>>>> says: bash: mira: command not found.
>>>> > Now can it be easier for you to guide me to the root of my errors?
>>>>
>>>> You obviously did not install the mira executables in a system directory
>>>> (/usr/local/bin comes to mind) or in a private directory which is in your
>>>> PATH variable so that the shell can find it.
>>>>
>>>> Assuming you have no root priviledges and that you don't know how to
>>>> extend the PATH environment for your current shell (bash), the easiest way
>>>> would be to use the fully qualified name of the location where MIRA
>>>> currently resides as command.
>>>>
>>>> So, if the executable is in the directory "/some/where/in/your/system",
>>>> you need to prefix that directory to the mira command and things will run
>>>> fine: "/some/where/in/your/system/mira"
>>>>
>>>> B.
>>>>
>>>> --
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>>>>
>>>
>>>
>>
>
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