[imilne]

thanks for the information.

well - the stuff with installing as a normal user is clear. However, it's not only the security issue. You may call me neurotic but I'm simply annoyed if a software creates some ugly folder structures where I don't want them ^^

So you don't like RPMs or apt bundles either then?

Iain

[schmima]

ah - thanks a lot for the information

*edit - as far as I know our lab people, it does not really matter what you give them and how easy you make it (only Win/Apple users)

[arvid]

thanks for the information.

well - the stuff with installing as a normal user is clear. However, it's not only the security issue. You may call me neurotic but I'm simply annoyed if a software creates some ugly folder structures where I don't want them ^^

agreed! I decide on my machine how things should be organized!

YMMV, but the version I installed created a "Tablet" folder in my home directory (where all the stuff goes), and asked me where a good place for a symlink to the start script would be (I have ~/bin/ in PATH, so I selected that)... You can move that around as you like.
I think they do the installer thing to keep the entry barrier really low for lab folks, not to clog up your file system.

[schmima]

thanks for the information.

well - the stuff with installing as a normal user is clear. However, it's not only the security issue. You may call me neurotic but I'm simply annoyed if a software creates some ugly folder structures where I don't want them ^^

[arvid]

hm - interesting viewer. However - I did not install it yet as I generally don't like to execute some kind of installer where I have no clue what it does where. I wonder if there are any command-line options that may be of interest to me or if I can find somewhere some information about it?

If you install it as a normal user (which works fine with Tablet for me) you don't have to worry - there is an uninstaller as well. I wouldn't install any unknown software as root, agreed!

[schmima]

Ups - I'm sorry. With the "interesting viewer" I was referring to tablet - not samscope.

[Crypticfortune]

hm - interesting viewer. However - I did not install it yet as I generally don't like to execute some kind of installer where I have no clue what it does where. I wonder if there are any command-line options that may be of interest to me or if I can find somewhere some information about it?

*Edit* Doh, that question was from a different user, not zlu. Totally embarassing. Sorry!

I don't want to hijack this Tablet thread over another viewer, so feel free to contact me directly or use the samscope sourceforge site, or start another thread here or something, if you have questions. But for now, you can use "scons --dry-run" to show what any scons command *would* do without actually doing it (like "scons install --dry-run"). Or you can just run it from the build directory without installing it. The samscope wiki has some more details on building and installing.

[schmima]

hm - interesting viewer. However - I did not install it yet as I generally don't like to execute some kind of installer where I have no clue what it does where. I wonder if there are any command-line options that may be of interest to me or if I can find somewhere some information about it?

[Crypticfortune]

By the way, does anyone know of a "simple window-based" program (for the lab people ) that is capable of calculating the consensus from a mapping project?

As long as by "window-based" you mean a GUI and not MS Windows I'd recommend you try out Samscope. It will show you an "estimated" consensus for the bases you're looking at. I say "estimate" because if you have more reads than pixels on a given base, it might ignore some of them in said estimate (if you scroll around and display all of them at least once, they will all be included). This isn't really the point of Samscope, so I figure an estimate is good enough, but if there's actually demand for this sort of thing, it wouldn't be too hard to force exact calculation, on say mouse over or something. So easy, I think I'll go add that feature now in fact...

[zlu]

...
i.e. There isn't a "consensus" track in Tablet.

That's what I thought. Thanks for the clarification.

By the way, does anyone know of a "simple window-based" program (for the lab people ) that is capable of calculating the consensus from a mapping project?

[maubp]

When I select the copy-to-clipboard option, the sequence that gets copied is in fact the reference sequence. So is the consensus here not referring to the real consensus of the mapping? In the attached screen-shot, I'll say the highlighted T should be the consensus but not the C that shows up in the "consensus" track. Or am I doing something wrong here?

I don't think Tablet attempts to calculate a "consensus" from the reads, it just shows you the reference sequence they are mapped against.

If you are looking at a de novo assembly file, then this "reference" would be the consensus as calculated by the assembly tool.

i.e. There isn't a "consensus" track in Tablet.

[zlu]

It already can. Just right-click the consensus sequence and select a copy-to-clipboard option.

Iain

When I select the copy-to-clipboard option, the sequence that gets copied is in fact the reference sequence. So is the consensus here not referring to the real consensus of the mapping? In the attached screen-shot, I'll say the highlighted T should be the consensus but not the C that shows up in the "consensus" track. Or am I doing something wrong here?

[GStephen]

We've released a new version of Tablet today. People with Tablet already installed should see the update prompt the next time they open Tablet.

You can download Tablet from our website where there is also a listing of the changes to Tablet since the last release.

Gordon

[phatjoe]

That sounds like you're out of disk space rather than memory. Go into Tablet Options and change the location of its cache directory to somewhere with plenty of free space. If you also convert the sam file to bam, then Tablet won't need much working space either.

Iain

You are right! Thanks for the speedy reply!

[imilne]

Hi,
I am new to tablet and I've encountered this problem.

error: java.io.IOException: No space left on device

That sounds like you're out of disk space rather than memory. Go into Tablet Options and change the location of its cache directory to somewhere with plenty of free space. If you also convert the sam file to bam, then Tablet won't need much working space either.

Iain