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Re: ePCR fetch

Hi Saira,

On Wed, Jun 26, 2019 at 04:30:54PM +0100, Saira Hussain wrote:
> > 
> > Now you have two data files.  Anything else that stops you from using
> > these in epcr as test cases?

I've commited some changes to possibly help you.  I've changed the script
to fetch the primer to move it into the data/ dir next to the fasta file.
I've also added a run-unit-test script.

> Now I am manipulating those files using the internal tools from epcr. My
> question is the following though. To test manually (and sucesfully) the
> package, some of the steps involved are:
> ../../re-PCR -S ginko.hash -n 5 -g 0 -d 100-300 -o rbcL5.rePCR
> rbcL-primer.txt
> now by following the script template when I add this line of code (without
> the relative parent directory dots ../../) I do get an error.

That's strange.  The test environment assumes the package ncbi-epcr is
installed and thus re-PCR should be in the PATH.

> I think the
> unclear part of me is the:
> cp -a /usr/share/doc/${pkg}/examples/* "${AUTOPKGTEST_TMP}"
> Do I need to change the {pkg}/examples to {pkg}/data or something else?

That's just an example.  I've moved your data files now (see changes
in debian/ncbi-epcr.docs.  This installs the data files into


Its a matter of taste whether you consider it examples or data - I do
not really mind but finally the run-unit-test script needs to find the
data it needs so it must match the install path.

> It's
> not clear for me what is this copying and where my data files are or what
> the AUTOPKGTEST_TMP has during the build time!

AUTOPKGTEST_TMP does NOT exist at build time.  It exists in the debci
environment (or since we decided by design that it should be serve as a
simple user example it will be set otherwise).  So the workflow is to
build the package first, install the package and than run run-unit-test
(or use debci).
With my run-unit-test script I get:

+ re-PCR -S ginko.hash -n 5 -g 0 -d 100-300 -o rbcL5.rePCR rbcL-primer.txt
! Fatal: ginko.hash: No such file or directory
+ rm -rf /tmp/ncbi-epcr-test.UxeEI8

Seems another data file ginko.hash is needed.  Any idea how to get this?

Kind regards



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