PseudoPipe is very hassle to configure

Question

[Kumar]

Hi,

I tried PseudoPipe. It is very hassle to configure, even with its example data itself. there is no any README and Manual file to take help. How much such a difficult pipeline to simple run?

Is anybody have any experience to run, please send me the process. I have prepared all input files.

Thanks

[User 59]

The readme is on the page you linked to: http://pseudogene.org/DOWNLOADS/pipeline_codes/readme.txt

[Kumar]

Thanks for reply. However, I have been used these all steps of that file. when I run the pipeline its shows Source not found error. I am trying to run simple its example files. Plz if run at your desk let me know.

Thanks

[alice.tky.0331]

Hi, I think the Source is not found you might manually copy and paste the setenvPipelineVars from plus and minus output file into terminal and run the pseudopipe command again. It worked for me for the sample data.

[pharaohs.son]

Hey, I read this topic bash_source and edited pseudopipe.sh script file. I replaced source setenvPipelineVars; per . ./setenvPipelineVars; inside loop of 'M' and 'P' strands (you can find this line of code above: echo 'Working on '$t' strand').

It's been a log time since this topic came up, but i solved this problem and think that maybe someone else can solve that way.