I use it on Ubuntu and Red Hat frequently. The latest version combination I
have is Ubuntu 15.04 with Staden 2.0.0b10, and it works perfectly. How did
you install the Staden package?
On Thu, Dec 17, 2015 at 2:10 AM, Andrej Benjak <abenjak@xxxxxxxxx> wrote:
GAP5 editing worked on Linux for me. But I haven't used it much, so I
don't know about shortcuts, or what your error message means, sorry.
Can you load the same database on another computer with a different OS,
just in case?
Andrej
On 17-Dec-15 07:21, Chitra P wrote:
Hi,
Thanks for your reply. Yes both the .g5d and .g5x are in the same folder.
Has someone who has a linux system tried editing on GAP5? I am wondering
if the keyboard shortcuts are different for linux?
Thanks
Chitra
On Wed, Dec 16, 2015 at 11:22 PM, Rameez Mj < <rameez03online@xxxxxxxxx>
rameez03online@xxxxxxxxx> wrote:
Make sure the "databasename .g5x" (which is created along with
database.g5d while using tg_index on .caf file) is also present in the
same folder.
On 14 December 2015 at 13:50, Chitra P < <pattabiraman.chitra@xxxxxxxxx>
pattabiraman.chitra@xxxxxxxxx> wrote:
Hi,
Thank you for the reply.I just tried using the CAF file as the input for
tg_index however I am still unable edit (or see the effect of my editing?).
Is there some other file I need to load into gap5 other than the .g5d ?
Thanks,
Chitra
On Mon, Dec 14, 2015 at 1:29 PM, Andrej Benjak < <abenjak@xxxxxxxxx>
abenjak@xxxxxxxxx> wrote:
I used to use tg_index on the original CAF file and have never had
problems. Could you try?
cheers,
Andrej
On 12/13/2015 06:58 AM, Chitra P wrote:
Hi,
I know this is slightly off-topic for the MIRA list, but I would be
grateful for any help with this.
I want to edit a MIRA assembly with gap5 ( I have installed
staden-2.0.0b9.i686 on a Ubuntu 14.04). At present, I am able to load but
unable to edit the sequences.
This is what I did :
I converted the MIRA maf and fasta files to sam
then used tg_index to convert it to a gap5 database
I am able to view the sequences but unable to edit the sequence. In my
terminal get the following error message when I try editing
*'D8YB9:08803:07440': couldn't open*
Thanks,
PC
