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Skip screed install #65

Closed mr-c closed 10 years ago

ctb commented 10 years ago

Please wait for auto extracted tests to merge.

C. Titus Brown, ctb@msu.edu

On Feb 15, 2014, at 20:37, "Michael R. Crusoe" notifications@github.com wrote:

You can merge this Pull Request by running

git pull https://github.com/ged-lab/khmer-protocols skip-screed Or view, comment on, or merge it at:

https://github.com/ged-lab/khmer-protocols/pull/65

Commit Summary

no need to explicitly install screed don't install screed explicitly nor use pip at least we can simplify the khmer install File Changes

M metagenomics/1-quality.txt (12) M mrnaseq/1-quality.txt (15) Patch Links:

https://github.com/ged-lab/khmer-protocols/pull/65.patch https://github.com/ged-lab/khmer-protocols/pull/65.diff — Reply to this email directly or view it on GitHub.

mr-c commented 10 years ago

I came across this while assisting a lab member. Just documenting things as I find them.

No rush here :-)

ctb commented 10 years ago

On Sat, Feb 15, 2014 at 05:48:15PM -0800, Michael R. Crusoe wrote:

I came across this while assisting a lab member. Just documenting things as I find them.

No rush here :-)

OK. As I think I said before, I know this particular command breaks several things downstream, so am skeptical about the pull request.

--t

C. Titus Brown, ctb@msu.edu

LSheneman commented 10 years ago

I am running the test on the scan.sh on an instance and getting caught in the downstreamŠ. I have it working through step 6Š. Want me to push it in so we can start hammering out the issues?

mr-c commented 10 years ago

@LSheneman Hmm.. I don't understand your request. It is in relation to #65 (this issue) or #30 ?

You own #30 now, so feel free to delete that branch or push your changes to it. I am happy to provide review upon request.

LSheneman commented 10 years ago

This issue #65 directly correlates with #30. I have auto extracted tests done, trying to do a run through on the pages, but fixing minor issues as I go.

I now scan.sh seems to be ok through script 7. Question was: would you like me to merge so test can see if this fixes issues, or continue to run completely through with manual fixes then merge?

I think #60 and #30 are both intertwined enough that we can help each issue. Does that make more sense?

ctb commented 10 years ago

Please push to this whenever you feel like it!

LSheneman commented 10 years ago

@mr-c and @ctb The comments suggest that pip installs need to wait a bit... am I correct that #56 also needs to be put on hold?

ctb commented 10 years ago

On Tue, Feb 18, 2014 at 06:26:11PM -0800, LSheneman wrote:

@mr-c and @ctb The comments suggest that pip installs need to wait a bit... am I correct that #56 also needs to be put on hold?

Actually, if you have the literate test extraction script working, then switchin to pip installs is fine! They just need to be tested.

tnx,

--t

C. Titus Brown, ctb@msu.edu

ctb commented 10 years ago

On Tue, Feb 18, 2014 at 06:26:11PM -0800, LSheneman wrote:

@mr-c and @ctb The comments suggest that pip installs need to wait a bit... am I correct that #56 also needs to be put on hold?

Note that I think there are still some reasons to install a protocols- specific branch of khmer; until we get a few of the sandbox scripts sorted out, I don't want to have to increment khmer's version number if

we need to patch khmer-protocols.

C. Titus Brown, ctb@msu.edu