sharpton
Installation issues
Hello I just installed Shotmap and I am just running some tests with a few metagenomic fasta files that I have and I can't seem to create the configuration file. I keep getting this error: Can't locate Shotmap.pm in @INC (you may need to install the Shotmap module). I put everything on my bash profile that the installer told me to, I am just curious what else needs to be installed to run this program. Thanks Bob
Hi Bob,
Thanks for your message. Can you please confirm the following:
- You have added SHOTMAP_LOCAL to your ~/.bash_profile. Can you please type the following at the command line and send me the output?
echo $SHOTMAP_LOCAL
- You have updated your PERL5LIB in your ~/.bash_profile. Can you please type the following at the command line and send me the output?
echo $PERL5LIB
- After adding the above items to your ~/.bash_profile, did you source your ~/.bash_profile thusly:
source ~/.bash_profile
This is needed to load the variables you added to your ~/.bash_profile into your active bash environment. Note that if you log out and log back in, you'll automatically source this file and those variables will be loaded. So, if steps 1 and 2 look good (e.g., the shotmap perl libraries are in the PERL5LIB), then you might try to rerun shotmap again.
Finally, note that you do not have to set up a configuration file to run shotmap. If you're looking to just give it a whirl, you might try the following:
Build your search database:
perl $SHOTMAP_LOCAL/scripts/build_shotmap_searchdb.pl -r=</directory/path/to/reference/database> -d=</directory/path/to/search/database>
Execute shotmap:
perl $SHOTMAP_LOCAL/scripts/shotmap.pl -i=</directory/path/to/metagenomes> -d=</directory/path/to/search/database>
Please do let me know if you have further questions.
Best, Tom
On Mon, Jun 1, 2015 at 10:25 AM, bobems1215 [email protected] wrote:
Hello I just installed Shotmap and I am just running some tests with a few metagenomic fasta files that I have and I can't seem to create the configuration file. I keep getting this error: Can't locate Shotmap.pm in @INC https://github.com/INC (you may need to install the Shotmap module). I put everything on my bash profile that the installer told me to, I am just curious what else needs to be installed to run this program. Thanks Bob
— Reply to this email directly or view it on GitHub https://github.com/sharpton/shotmap/issues/3.
Thomas J. Sharpton
Assistant Professor Department of Microbiology Department of Statistics Oregon State University
(541) 737-8623 [email protected] @tjsharpton lab.sharpton.org
Hi Tom, I think I figured it out for now. I just had to tweek the code that I put into my blast profile. It is working for now but I will let you know of any more issues that I come across. Thanks again for all the help, Bob
Not a problem. I'm glad to hear that it seems to be working for you. Please do let us know if you have any additional challenges with the software, or specific feedback for us.
Best, Tom
On Mon, Jun 1, 2015 at 11:23 AM, bobems1215 [email protected] wrote:
Hi Tom, I think I figured it out for now. I just had to tweek the code that I put into my blast profile. It is working for now but I will let you know of any more issues that I come across. Thanks again for all the help, Bob
— Reply to this email directly or view it on GitHub https://github.com/sharpton/shotmap/issues/3#issuecomment-107663103.
Thomas J. Sharpton
Assistant Professor Department of Microbiology Department of Statistics Oregon State University
(541) 737-8623 [email protected] @tjsharpton lab.sharpton.org