[ome-users] Fw: bfconvert command

[Josh Moore]

Hi Mohan,

Thanks for the details. It looks like there is a typo in the command
line you are using in docker:

bfconvert -bigtiff -compression LZW OS-1.vsi sample1-s%.tif

Here "s%" should be "%s".

All the best,
~Josh


---------- Forwarded message ----------
From: Narapareddy, Mohanapriya <mohanapriya.narapareddy at emory.edu>
Date: Wed, Aug 15, 2018 at 8:12 PM
Subject: Re: ome-users mailing list email
To: Josh Moore <j.a.moore at dundee.ac.uk>


Hello Josh Moore,

Thanks for your reply.

i have used java version 7 and bio formats version 5.8.2 .
docker run -it -v ~/Desktop/dir:/home/bf/data test
                                            ]This is my docker run
command. and inside the container i am executing the following
command.
                                                             bfconvert
-bigtiff -compression LZW OS-1.vsi sample1-s%.tif
FROM java:7 MAINTAINER ome-devel at lists.openmicroscopy.org.uk RUN
apt-get install -y curl RUN curl -o bftools.zip $(curl -Ls -o
/dev/null -w %{url_effective}
http://downloads.openmicroscopy.org/latest/bio-formats)/artifacts/bftools.zip
RUN apt-get install -y unzip RUN unzip -d /opt bftools.zip && rm
bftools.zip RUN chmod a+rx /opt/bftools/* RUN useradd -m bf USER bf
RUN echo 'export PATH=/opt/bftools:$PATH' >> /home/bf/.bashrc ENV HOME
/home/bf WORKDIR /home/bf CMD bash



The above is my docker file.


4. I dont see any error messages but i am getting the following out put.


bf at 935e7d25059c:~/data$ bfconvert -bigtiff -compression LZW OS-1.vsi
sample1-s%.tif

OS-1.vsi

CellSensReader initializing OS-1.vsi

Missing expected .ets files in /home/bf/data/_OS-1_

[CellSens VSI] -> sample1-s%.tif [Tagged Image File Format]

Converted 1/1 planes (100%)

[done]

6.95s elapsed (69.0+5815.0ms per plane, 1053ms overhead)




look forward to hear from you.

Thanks,

Mohanapriya

On Tue, Aug 14, 2018 at 10:59 PM, Narapareddy, Mohanapriya
<mohanapriya.narapareddy at emory.edu> wrote:
>
>
> mohanapriya
>
>
>
> ________________________________
> From: Narapareddy, Mohanapriya
> Sent: Tuesday, August 14, 2018 4:39 PM
> To: ome-users-bounces at lists.openmicroscopy.org.uk
> Subject: bfconvert command
>
>
>  I am trying to execute this command
>  bfconvert -bigtiff -compression LZW <input file.vsi> <outfile>-%s.tif
>
> its working fine in centOs , i am getting multiple image planes,
>  but when i am trying to execute in docker container i am getting only a
> single image plane. Please resolve this issue.
>
>
> Thanks,
>
> Mohanapriya