[aimc]

Hello.
I am running gap5 ( staden-2.0.0b9.i686 ) . I created an g5d and g5x with tg_index

But when i run gap5, i cannot map reads to the sequences.
The graphical user interface won't let me browse , or even write into the Entry box, to select the reads.

(attaching image)


I'm running Ubuntu 64-bit 14.04

I would appreciate some help with this issue, i just want to use it to explore a map of reads to contigs.

[jkbonfield]

Do the other dialogues work for you, for example Find Internal Joins? I haven't see cases before where you cannot type into a dialogue box. Which window manager are you using? Is this a genuine ubuntu box or running inside some VM? Is the X11 server the same machine, or an emulated X on, say, MS Windows?

As far as working around the problem, what this dialogue is doing behind the scenes is:
1) Export the consensus in depadded form.
2) Build a bwa index of the consensus and use bwa to align against it, yielding a bam file.
3) Run tg_index -a -g on the BAM file to import the alignments back again. The -g flag tells it to reinsert pads that were stripped out in part 1 above, to insure the padded form is all still in alignment (gap5 internally uses padded coordinates rather than depadded reference coordinates).

[aimc]

Hi again and thanks for your quick response !

As you said it should work, i tried again with no luck.
I tried a second time with sudo bash, so executing gap5 with super user permissions; this time it would let me write into the Entry box.

(image attached)

This issue is sure weird but i replicated it many times , just to be sure that using sudo is a(n ugly) workaround.

Using Ubuntu 14.04.1:
Linux ubuntu 3.13.0-40-generic #69-Ubuntu SMP Thu Nov 13 17:53:56 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux

HP Laptop ( Not a VM ) ; Ubuntu installed with Wubi

Tk:
Tkinter.__version__
$Revision: 81008 $

[rittza]

Hi everyone
I am trying to use GAP5 to work on my NGS data, and I came across a problem while installing. I have found no records of anything similar on the internet, so as a last resort I decided to ask here.

I have installed the 2.0.0b10 staden package from http://sourceforge.net/projects/staden/and installed GAP5 in windows 7.

While trying to convert my SAM files to the gap5 database format, I always get

Sorry, database busy
Unable to lock and/or open database
gio_open: No error

I figured this could be due to the folder properties and changed them in the cmd line, using

attrib -s +r

But the folder's properties are unchanged.

Has anyone come across this problem in windows?

Thanks in advance