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ECDP integration with Clarity LIMS #818

Closed GoogleCodeExporter closed 8 years ago

GoogleCodeExporter commented 8 years ago 
We are back down to one computer only (mine) being able to recognize the old 
GENEUS.  We need to get integration of Clarity happening ASAP

Original issue reported on code.google.com by cmnico...@gmail.com on 29 Sep 2014 at 9:00

GoogleCodeExporter commented 8 years ago 
unless the VM was updated, that should not happen.

Original comment by zack...@gmail.com on 1 Oct 2014 at 2:40

GoogleCodeExporter commented 8 years ago 
Need consistency in entering lane numbers in workflowparams file to recognize 
the one lane NextSeq flowcells. Right now analysis dirs for three new flowcells 
H11FGBGXX,H11FKBGXX,H11FUBGXX are named inconsistently, in some lane "0" is 
used, in some  - lane "1". See below
H11FGBGXX_0_MCM4A1
H11FKBGXX_0_MCM413 
H11FUBGXX_1_CAP2A21

I suggest to use lane 1 in  workflowparam file since this is how its entered in 
Clarity.

Original comment by natalia....@gmail.com on 15 Oct 2014 at 8:46

GoogleCodeExporter commented 8 years ago 
in theory, no one should have to enter something by hand in the workflowparams.
ideally, this file is generated automatically, using the data from the LIMS, 
not the other way around. such is the case for hiseq, nextseq/miseq should 
follow.

Original comment by zack...@gmail.com on 15 Oct 2014 at 8:50

GoogleCodeExporter commented 8 years ago 
Hi Natalia
was there any perl code to read from claritylims? all i see in SVN and on the 
filesystem reads exclusively from the old lims. 

I understand this is no longer your responsibility, so thanks in advance for 
insight you can provide.

-zack

Original comment by zack...@gmail.com on 26 Nov 2014 at 6:26

GoogleCodeExporter commented 8 years ago

Original comment by zack...@gmail.com on 12 Mar 2015 at 7:28