[mira_talk] Re: can't find miraconvert
- From: Robert Bruccoleri <bruc@xxxxxxxxxxxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Sun, 13 Apr 2014 22:11:24 -0400
Dear Theo,
You haven't installed mira and it's symbolic links correctly.
When you unpack the mira binaries, the 'bin' directory looks like this:
[root@liberty bin]# pwd
/vm/local/src/mira_4.0.1_linux-gnu_x86_64_static/bin
[root@liberty bin]# ls -la
total 5880
drwxr-xr-x 2 1000 1000 4096 Apr 9 14:39 .
drwxr-xr-x 6 1000 1000 4096 Apr 9 14:39 ..
-rwxr-xr-x 1 1000 1000 5974184 Apr 9 14:39 mira
lrwxrwxrwx 1 1000 1000 4 Apr 13 22:03 mirabait -> mira
lrwxrwxrwx 1 1000 1000 4 Apr 13 22:03 miraconvert -> mira
lrwxrwxrwx 1 1000 1000 4 Apr 13 22:03 miramem -> mira
In order to use all the features of mira, you must put this bin
directory in your shell path. I don't know zsh very well, but I think
it's similar to the Bourne shell or the Born Again Shell, so you would
put this command in your .zshrc file:
export PATH=<absolute location of mira bin directory>:$PATH
where you substitute the location of the mira bin directory accordingly.
(BTW, I just tried it myself, and it works). It will not work correctly
just to move the binary around. You could move the binary, but you also
have to define the symbolic links that Mira depends upon.
Bob
On 04/13/2014 09:58 PM, Theo.Allnutt@xxxxxxxx wrote:
Hi,
just get
zsh: command not found: miraconvert
there was no binary for miraconvert in the install instructions - just
dragged 'mira' to the /bin directories.
*From:*mira_talk-bounce@xxxxxxxxxxxxx
[mailto:mira_talk-bounce@xxxxxxxxxxxxx] *On Behalf Of *Juan Daniel
Montenegro Cabrera
*Sent:* Monday, 14 April 2014 11:57 AM
*To:* mira_talk@xxxxxxxxxxxxx
*Subject:* [mira_talk] Re: can't find miraconvert
Sure,
You need to use
miraconvert -f caf -t ace your.caf your.ace
and it does the magic. You can apply as many filters as you want. For
all available filters and options:
miraconvert -h
Cheers,
Juan Montenegro
2014-04-14 11:50 GMT+10:00 <Theo.Allnutt@xxxxxxxx
<mailto:Theo.Allnutt@xxxxxxxx>>:
Hi,
I finally got Mira 4 to run, but got a message that the large contigs
could not be converted and to run ' extractLargeContigs.sh'
which I did but then got this in the log:
./extractLargeContigs.sh: 16: ./extractLargeContigs.sh: miraconvert:
not found
Also, the TCS file only has this in it:
"TCS output currently not available, please contact the author."
My CAF file is 1.6GB but will not open in Tablet, my usual viewer
(Consed won't install on my system). Is there a way to convert it to
ACE in Mira 4? The Reference Manual does not give an example of the
syntax for the parameter.
Thanks.
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fn:Robert Bruccoleri
n:Bruccoleri;Robert
org:Audacious Energy, LLC and Congenomics, LLC
adr:;;;;;;USA
email;internet:bruc@xxxxxxx
title:President
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