Re: ePCR fetch

[Saira Hussain]

On 6/26/19 5:37 PM, Andreas Tille wrote:
Hi Saira,
Hey Andreas,

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

    /usr/share/doc/ncbi-epcr/data

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.
Oh thanks! Now I understand. I though examples, is a predefined folder, 
so I couldn't realise what I was copying into it. Thanks for clearing 
this up :)

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?

Yes, definitely I've written this part of the test. I am updating now. 
Also I changed my Python script to output both files: the fasta and the 
primer inside the data directory (and renamed it to make this clear).

I pushed this onto master and I am going to do the same for the rest of 
the test! Thank you so much for the support!
Kind regards

       Andreas.