Hi Andreas, hi Charles,

On 11.10.18 14:12, Charles Plessy wrote:
> Le Wed, Oct 10, 2018 at 11:45:38AM +0200, Andreas Tille a écrit :
>> I'm about to update the epcr package but its homepage[1] says:
>>
>>    The e-PCR suite of tools has been retired. Please consider using
>>    PrimerBLAST[2] as an alternative if you are interested in designing
>>    PCR primers or identifying target sequences for your primers.
>>
>>    For more information, see "Electronic-PCR (e-PCR) is retiring, use
>>    Primer-BLAST instead"[3] at the NCBI Insights blog.
>>
>> Please excuse my ignorance but I know nothing about primer design at
>> all.  I somehow suspect that the command line tool e-PCR should now be
>> replaced by a web tool (or am I missing something?  I can not find
>> something inside the blast package which looks like a command line
>> replacement).  Currently epcr has a popcon which is somehow "medium" in
>> our Debian Med package set - so there is some relevant user base that
>> is using a discontinued / replaced tool.
>
> a search for "primer-blast" in GitHub's repository for the NCBI C++
> toolkit only returns a page containing the URL of the web service,
> confirming that there does not seem to be an offline version.
>
> In my experience, people doing large-scale primer design (where
> command-line or off-line versions are definitely needed) tend to use
> Primer3 directly or (more often?) through a wrapper.  Nevertheless, I
> would suggest to keep the ncbi-epcr package as long as it does not have
> a RC bug (which I expect to eventually as GCC continues to evolve).

I am with Charles. Let us keep it for as long as we can afford it.

Older versions have a scientific merit for benchmarking. And for workflows
the local installation (if not depending on external data) is to be
preferred.

This is especially true when staying in Hotel with an unreliable WLAN
(grrr!!!)
or when running on a cluster that may not allow to access external sites.

Best,

Steffen

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