Comments (4)
Did you contact @goldbergtatyana already?
I saw another email. Please keep all communication of this matter within github issues.
from loctree3.
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/
from loctree3.
This problem has been solved. Relevant information has been added to README.md
from loctree3.
@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?
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Related Issues (10)
- [Protein Prediction 2] SVN Repo HOT 1
- cannot configure HOT 7
- Register in Elixir **LocTree 2** (not 3) (since 3 is already there) HOT 4
- FYI
- Put Dockerfile image onto Docker hub (Rostlab organization) HOT 7
- Move older wiki content to this repo's wiki
- loctree2-data unavailable HOT 4
- Change the pass of NCBI BLAST
- How to install pp-popularity-contest in centos
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