Help for option usage

[julie]

Hi all,
After lot of failed tests, I need help to run rseg with options.
Sorry in advance for this trivial ask.

First, one classical use; I'm in a directory named RSEG and I write in terminal this command :

../rseg/bin/rseg -c mouse-mm9-size.bed -i 20 -v H3K36me3_3col.sorted.bed

The result with enriched domains is wrote on my terminal! and no file is created.
So, I write this command :

../rseg/bin/rseg -c mouse-mm9-size.bed -i 20 -o $PWD H3K36me3_3col.sorted.bed
And I have the same result! just it says me :

write_bed_file : cannot open /home/utilisateur/RSEG (which is my current directory)

So this command run correctly AND write the results in bed file only if I precise the file name of output and not just the directory, like this : "-o $PWD/myfileoutput.bed"

And this problem appears too with options : -boundary, -read-counts-requested, -track, if no file name is specified for each option, it canoot write the result files!

I have tried the option -o MY_File_Path and the option -name My_prefix_of_all_outputs but it doesn't work.

Finally I have noticed that often, the options must be write after the input file because if I write these options before the input file, it cannot recognize my input and considers one of this option like my input file.

What do I do bad? How can use all of this options and write the results in a directory with the same prefix for all? Must I specifie the output file for all options ?

Thanks in advance.

Julie

[Song, Qiang]

Yes, the new version requires you specify each output file name that you want.

This is different from the previous version in order to integrate to Galaxy.

Sorry if I have not made it clear in the manual.

Each of the following options require a file name.

  -o, -out               domain output file 

      -score             Posterior scores file 

      -readcount         readcounts file 

      -boundary          domain boundary file 

      -boundary-score    boundary transition scores file 

[julie]

Thanks, I've seen it when I try the command rseg -help in a terminal.


And for galaxy, is your version publicly available ? Because it's referenced in the web toolshed but not accessible from my local instance of galaxy.
Thanks.
Julie

[Song, Qiang]

Our galaxy website with rseg is not publicly available at this time.