#5 slight changes to docker image / species classification question

[elizabeth henaff]

Hi all,

First of all, thanks for supplying a docker image to run this!

A couple of modifications I had to do to make it work:

• in MyCC.py, change:
  prodigal='prodigal'
  to
  prodigal='prodigal.linux'

to reflect its name in /opt

• add /opt/cd-hit to $PATH

Secondly, how does one assign species to the clusters? Not sure where the .spe.txt files in the examples come from.

Cheers,

Elizabeth

[OliverLin]

Thank you for using MyCC's docker and figuring out how to run.
For those data we provide in sourceforge, we blasted contigs against their reference genomes to prodcuce the .spe.txt. We did not assign secies to clusters, but assign speces to contigs. Only species names of the exemplars (i.e., cluster's centroid) were shown in the pdf.

[elizabeth henaff]

Great, thanks for the info!

Cheers,

Elizabeth

--

Elizabeth Hénaff, PhD | elizabeth-henaff.net

Postdoctoral Associate
Institute for Computational Biomedicine,
Weill Cornell Medical College

+1 512 299 3051

On Sun, Jul 2, 2017 at 9:36 PM, OliverLin oliverlinnhri@users.sf.net
wrote:

Thank you for using MyCC's docker and figuring out how to run.
For those data we provide in sourceforge, we blasted contigs against their
reference genomes to prodcuce the .spe.txt. We did not assign secies to
clusters, but assign speces to contigs. Only species names of the exemplars
(i.e., cluster's centroid) were shown in the pdf.

---

• [tickets:#5] https://sourceforge.net/p/sb2nhri/tickets/5/ slight
  changes to docker image / species classification question*

Status: open
Milestone: 1.0
Created: Sat Jul 01, 2017 03:21 AM UTC by elizabeth henaff
Last Updated: Sat Jul 01, 2017 03:21 AM UTC
Owner: nobody

Hi all,

First of all, thanks for supplying a docker image to run this!

A couple of modifications I had to do to make it work:

• in MyCC.py, change:
  prodigal='prodigal'
  to
  prodigal='prodigal.linux'

to reflect its name in /opt

• add /opt/cd-hit to $PATH

Secondly, how does one assign species to the clusters? Not sure where the
.spe.txt files in the examples come from.

Cheers,

Elizabeth

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