Plz optimize details such as directories

[PhrenoVermouth]

Honestly speaking, I'm very pretty interested in your new algorithm. But at now your scripts are not robust enough for use. Since I cloned the scripts and added the PATH to .bashrc, I'd been tortured by directory issues. I need to fix them one by one, then finally when I did QC for lambda, I gave up. Look at the code below as an example, it really drives me crazy:

align_cmd = 'python bs3-align.py -i ' + options.input  + '  -o lamdba_unconversion -g ' +   options.genome
call_methyl_cmd = 'python bs3-call_methylation.py -i lamdba_unconversion -o lamda_unconversion  --db bs_align/reference_genomes/lamdba.fa_snap/'
print_graph_cmd =  'python bs3-methyl_display.py -u y -m lamda_unconversion.CGmap.gz'

1. First, I cannot run the script under the installation directory, so it is impossible to find the script bs3-align.py under the current directory. This is a universal problem in bs3;
2. The output temp file uses one fixed name called "lambda_unconversion" to save the aligned result. But what if I running in batches? They would clash others ruthlessly. Isn't it common sense?
3. Even if I bypass these two problems, STILL I can't get my aligned result using align_cmd. It just output: BS-Seeker3 beta And the aligned script, bs3-align.py , is too complicated for me to fix it. I've lost all my patience and here I do wish you could optimize your software and make it more user-friendly!

Thx!!!!

yours, Gran