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install applications using debian packages when available #48

Open mr-c opened 10 years ago

mr-c commented 10 years ago

For example: GNU Parallel is available in both Ubuntu Precise & Quantel

http://packages.ubuntu.com/search?keywords=parallel

Bonus: work with the Debian bioinformatics team (with whom @mr-c has worked with in the past) to get non-packages programs in to mainline Debian (and therefore Ubuntu and derivatives)

ctb commented 10 years ago

On Fri, Jan 03, 2014 at 02:35:19PM -0800, Michael R. Crusoe wrote:

For example: GNU Parallel is available in both Ubuntu Precise & Quantel

http://packages.ubuntu.com/search?keywords=parallel

Bonus: work with the Debian bioinformatics team (with whom @mr-c has worked with in the past) to get non-packages programs in to mainline Debian (and therefore Ubuntu and derivatives)

Happy to use apt-get instead!

Any thoughts on how hard it is to translate the apt-get instructions, to, say, RHEL?

-titus

C. Titus Brown, ctb@msu.edu

mr-c commented 10 years ago

Users on RHEL systems tend not to have root privileges.

If they have root and suitable packages exist then the commands to install a RHEL package are straightforward.

On Sun, Jan 12, 2014 at 11:16 AM, C. Titus Brown notifications@github.comwrote:

On Fri, Jan 03, 2014 at 02:35:19PM -0800, Michael R. Crusoe wrote:

For example: GNU Parallel is available in both Ubuntu Precise & Quantel

http://packages.ubuntu.com/search?keywords=parallel

Bonus: work with the Debian bioinformatics team (with whom @mr-c has worked with in the past) to get non-packages programs in to mainline Debian (and therefore Ubuntu and derivatives)

Happy to use apt-get instead!

Any thoughts on how hard it is to translate the apt-get instructions, to, say, RHEL?

-titus

C. Titus Brown, ctb@msu.edu

— Reply to this email directly or view it on GitHubhttps://github.com/ged-lab/khmer-protocols/issues/48#issuecomment-32126031 .

mr-c commented 10 years ago

Programs used by khmer-protocols:

Eel-pond:

Kalamazoo

mr-c commented 10 years ago

IDBA is now packaged for Debian

http://blends.debian.org/med/tasks/bio#ibda

https://lists.debian.org/debian-med/2014/02/msg00171.html

ctb commented 10 years ago

For things that are likely to change frequently, I believe our policy should be to not use packages. Obviously judgement calls are involved here ;).

(This applies specifically to IDBA, Velvet, etc; but also maybe many of the packages above.)

mr-c commented 10 years ago

To clarify: you'd prefer only to use packaged software if it is stable thus lessoning the need to retest?

Sounds like another vote for shell-literate ReST :-)

LSheneman commented 10 years ago

Yes and it is being coded/tested this weekend. Just not sure a shell parser is the way to go... but that is a whole different thread =0

luizirber commented 10 years ago

As a MVP I think the shell parser is good. Once it is working we can think about how to integrate it better with Sphinx.

On Sat, Feb 15, 2014 at 2:53 PM, LSheneman notifications@github.com wrote:

Yes and it is being coded/tested this weekend. Just not sure a shell parser is the way to go... but that is a whole different thread =0

Reply to this email directly or view it on GitHubhttps://github.com/ged-lab/khmer-protocols/issues/48#issuecomment-35165950 .

LSheneman commented 10 years ago

For the latest on the parser please go to #30 and check out my test links. Input based on that would be appreciated.

mr-c commented 9 years ago

blockers:

mr-c commented 9 years ago

transdecoder was accepted into Debian unstable! https://tracker.debian.org/pkg/transdecoder

mr-c commented 9 years ago

Parafly was also accepted into Debian unstable https://tracker.debian.org/pkg/parafly

mr-c commented 9 years ago

r-cran-blockmodeling was just accepted into Debian unstable: http://tracker.debian.org/pkg/r-cran-blockmodeling