Installation issues

[bobems1215]

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

[sharpton]

Hi Bob,

Thanks for your message. Can you please confirm the following:

1. 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

1. 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

1. 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 notifications@github.com
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
#3.

Thomas J. Sharpton

Assistant Professor
Department of Microbiology
Department of Statistics
Oregon State University

(541) 737-8623
thomas.sharpton@gmail.com
@tjsharpton
lab.sharpton.org

[bobems1215]

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

[sharpton]

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 notifications@github.com
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
#3 (comment).

Thomas J. Sharpton

Assistant Professor
Department of Microbiology
Department of Statistics
Oregon State University

(541) 737-8623
thomas.sharpton@gmail.com
@tjsharpton
lab.sharpton.org