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Re: https://salsa.debian.org/med-team/community/2020-covid19-hackathon/-/wikis/2nd-Covid-19-Hackathon



On 23/05/2020 01:57, Steffen Möller wrote:
Hello,

We had a nice and friendly Debian Med Covid-19 fireside this, well, "evening" my time. Quite some of us felt prepared to invest their time into a revisited Covid-19 Sprint. On https://salsa.debian.org/med-team/community/2020-covid19-hackathon/-/wikis/2nd-Covid-19-Hackathon I put my recollection what we had discussed/thought about. Please give it a spin.

Hi, Steffen.

Sorry I been quiet lately, but I am still lurking on the list :-)

I read your musings on the Wiki...

Re: Installing using your "conda" package - I've been struggling a bit recently to install the previous QIIME 1.9.1 under bioconda and get a strange warning about the CUDA driver, so I'll have a try using your "conda" instead and let you know how I get on. I've managed to install QIIME 1.9.1 manually, using a combination of "conda" and "pip" under "bioconda2", but the Bioconda receipe doesn't work (reports the CUDA error). My colleague at the IAEA in Vienna wants to analyse new data using QIIME 1.9.1 for comparision with previous analyses. We've been using a Bio-Linux 8.0.7 VM, but it will be faster if we can go native!

I think I've told you about my "bioconda" wrapper before, which I use to isolate the bioconda environment from the APT-managed system (attached). This avoids the conflicts between "pip/pip3" and APT-managed packages.

Bye,

  Tony.

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#!/bin/bash
#@(#)bioconda3.sh  2019-09-20  A.J.Travis

#
# Wrapper for Bioconda Python environment
#

exec /bin/bash --rcfile /usr/local/bin/bioconda2.rc

Attachment: bioconda2.rc
Description: application/vnd.kde.kxmlguirc

#!/bin/bash
#@(#)bioconda3.sh  2019-02-23  A.J.Travis

#
# Wrapper for Bioconda Python environment
#

exec /bin/bash --rcfile /usr/local/bin/bioconda3.rc

Attachment: bioconda3.rc
Description: application/vnd.kde.kxmlguirc


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