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Issues Running Topcons Membrane Prediction

Dear Forum members,

I have been struggling to run TOPCONS on unix, as standalone. It requires ti be run in:

./TOPCONS.sh ./names_of_all_files_sequences_to_run.txt /predictions/topcons_out /predictions/scampi-msa /predictions/scampi-seq /predictions/octopus /predictions/prodiv-tmhmm /predictions/pro-tmhmm


Installing it gives files for: scampi-msa, prodiv-tmhmm, scampi-msa

All these individual have either shell script or .pl script. To get output of each tools, is a 3 step process:

I am stuck at that, run_blast.sh is the file that has to be run to do the first step for each tool prediction listed above.
Pardon me if I this seems confusing. I am having hard time to get this done. The server one takes one protein sequence at one time. I need to predict for 5 files, each having atleast 35+protein sequences in that.

Please guide and help me.
Thanks

prediction
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written by Bioinformatics_NewComer Bioinformatics_NewComer

After complete installation, in local bin ~/bin. bin has folder for var, share, www and other which are created in usr/local by default. When I try to runt he script, I get the following error.

Directory /home/punky/bin/../var/www/topcons.cbr.su.se/docroot/topcons/ does not exist. Aborting /home/punky/bin/run_topcons.sh

I have these folder in my PATH too.

Please help me to solve this issue.

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written by Bioinformatics_NewComer Bioinformatics_NewComer

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