running the tool

[amerello]

According to the README file, it's necessary to "Download the 80% non-redundant blast database (big_80 * ) combining SWISS-PROT, TrEMBL and PDB from https://rostlab.org/rost-db-data/big/" is there way to run it without these files? The big_80* files sum together more than 18Gb.

[juanmirocks]

Did you contact @goldbergtatyana already?

I saw another email. Please keep all communication of this matter within github issues.

[juanmirocks]

I just copy the content of the email I found for cross-reference:

Hi there,

I did not really understand what files exactly you need.

If you are interested in the example .fasta and .profile files, then you can find these in the wiki entry of the loctree2 method: https://rostlab.org/owiki/index.php/Loctree2

The wiki of loctere3 describes only the web server, but not the programs that it is made of.

Best wishes,
Tatyana

On Nov 10, 2015, at 1:25 PM, Alejandro Merello wrote:

> Hi Tatyana,
>  as part of Protein Prediction 2 we're trying to migrate the program
> loctree3 to git and add some documentation files to the repository.
> We're currently trying to run the application, but are having some
> difficulties with the input parameters. In the README file on the
> original repo it is suggested that we download some big_80* files, but
> unfortunately we don't have so much space available (~18GB).
> Additionally there is a reference to another tool (blastpgp) which we
> weren't able to find in the repository.
>
> Is there a way to test the functionality of the program with some other
> smaller files  that you may have available? We understand that we need a
> .fasta file and a .profile file. We found on this website [1] some
> .fasta files, but no accompanying .profile file.
>
> Thank you very much for your help.
> Here is the link to the new git repository of loctree3 [2]
>
> Kind regards,
> Sonja Vogl, Alejandro Merello.
>
> [1] https://rostlab.org/services/loctree3/downloads
> [2] https://github.com/Rostlab/LocTree

Hi Tatyana,
  thank you for this information. Trying to run the tool with the provided data I still encounter the following error:
Can't exec "blastpgp": No such file or directory
...
Error running PSI-BLAST command: No such file or directory

I tried locating this program which lead me to this link [1], but there is no "blastpgp" on that package. Do you know where could we find this tool? Google didn't provide much help.

Thanks.
Kind regards,
Alejandro Merello

[1] ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/

[amerello]

This problem has been solved. Relevant information has been added to README.md

[WJH58]

@amerello Hi I had exactly the same problem running this tool (Docker version):
Can't exec "blastpgp": No such file or directory
...
Error running PSI-BLAST command: No such file or directory

I wonder what information on README.md could help to solve this problem?

RUN wget -q https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.26/ncbi-blast-2.2.26+-x64-linux.tar.gz && tar xf ncbi-blast-2.2.26+-x64-linux.tar.gz
RUN /bin/echo -e "[NCBI]\nData=/ncbi-blast-2.2.26+/data/" > ~/.ncbirc && /bin/echo -e "export PATH=$PATH:/ncbi-blast-2.2.26+/bin" >> ~/.bashrc

I think the above codes in Dockerfile performed downloading blast database, but why I still had this error?