index the 88_otus.fasta file on installation if possible

[amnona]

otherwise user needs to supply/compile the 88_otus.fasta

[wasade]

One concern here is that the user is still required to specify the database at runtime, right? So they'll still need to know the path. They may not realize what the path is, so may end up just reindexing anyway. If we push forward on this, I think it is important that deblur know how to test whether the index exists and is available, and set the default values for the relevant params to the appropriate files. But, this also isn't that bad of a thing to ask users to do especially since it has a direct analog to formatdb which many people are familiar with.

[mortonjt]

One way to make this happen is to have python variables declared within
init.py pointing to the databases at runtime, if no paths are otherwise
specified

On Tue, Aug 23, 2016 at 1:35 PM, Daniel McDonald [email protected]
wrote:

One concern here is that the user is still required to specify the
database at runtime, right? So they'll still need to know the path. They
may not realize what the path is, so may end up just reindexing anyway. If
we push forward on this, I think it is important that deblur know how to
test whether the index exists and is available, and set the default values
for the relevant params to the appropriate files. But, this also isn't that
bad of a thing to ask users to do especially since it has a direct analog
to formatdb which many people are familiar with.

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[wasade]

👍

On Tue, Aug 23, 2016 at 2:17 PM, Jamie Morton [email protected]
wrote:

One way to make this happen is to have python variables declared within
init.py pointing to the databases at runtime, if no paths are otherwise
specified

On Tue, Aug 23, 2016 at 1:35 PM, Daniel McDonald <[email protected]

wrote:

One concern here is that the user is still required to specify the
database at runtime, right? So they'll still need to know the path. They
may not realize what the path is, so may end up just reindexing anyway.
If
we push forward on this, I think it is important that deblur know how to
test whether the index exists and is available, and set the default
values
for the relevant params to the appropriate files. But, this also isn't
that
bad of a thing to ask users to do especially since it has a direct analog
to formatdb which many people are familiar with.

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[mortonjt]

The paths have been created, but after talking to @amnona , we decided that it would be best to leave this feature out of the version 1.0 milestone.

[wasade]

Sounds good