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Add literate resting to kalamazoo metagenome protocol #108

Closed SherineAwad closed 10 years ago

ctb commented 10 years ago

Sherine, this looks good, thanks! You may need to merge in from the ged-lab repository and then push those changes into this pull request -- just do

git pull master git push -u origin Metagenome

in your repository.

ctb commented 10 years ago

OK! Make sure you keep the pull request updated, please -- just do a 'git push' whenever you make a set of changes.

cheers, --titus

On Thu, Jun 05, 2014 at 06:23:56AM -0700, Sherine Mahmoud wrote:

Thanks I did that. Please note that I still will do some refinement, like hiding some commands from the user to make things better/change some text. And I will fix the re-inflate and modify mapping to the new subset now.

On Thu, Jun 5, 2014 at 9:03 AM, C. Titus Brown notifications@github.com wrote:

Sherine, this looks good, thanks! You may need to merge in from the ged-lab repository and then push those changes into this pull request -- just do

git pull master git push -u origin Metagenome

in your repository.

??? Reply to this email directly or view it on GitHub https://github.com/ged-lab/khmer-protocols/pull/108#issuecomment-45216066 .

Regards Sherine

Reply to this email directly or view it on GitHub:

https://github.com/ged-lab/khmer-protocols/pull/108#issuecomment-45218110

C. Titus Brown, ctb@msu.edu

ctb commented 10 years ago

@SherineAwad, this PR still can't be automatically merged. Could you fix, please?

ctb commented 10 years ago

(Which is probably as simple as pushing whatever your local changes are.)

ctb commented 10 years ago

Note that you can remove '/usr/local/share/khmer/scripts/' from the commands wherever it appears -- the new install of khmer (1.0) puts anything in scripts/ into the PATH, so they can be run without specifying their full directory. Not urgent, thought I'd note.

ctb commented 10 years ago

The :: at the end of https://github.com/SherineAwad/khmer-protocols/blob/Metagenome/metagenomics/2-diginorm.txt#L25 needs to be changed to a : for proper formatting.

ctb commented 10 years ago

'rm .pe.fq.gz' on line https://github.com/SherineAwad/khmer-protocols/blob/Metagenome/metagenomics/1-quality.txt#L139 should be 'rm .pe.qc.fq.gz'.

ctb commented 10 years ago

The :: at the end of https://github.com/SherineAwad/khmer-protocols/blob/Metagenome/metagenomics/2-diginorm.txt#L67 needs to be changed to a : for proper formatting.

ctb commented 10 years ago

I think the '::' at https://github.com/SherineAwad/khmer-protocols/blob/Metagenome/metagenomics/2-diginorm.txt#L98 should be at the end of 'various files' as this is a command that should not be put into the shell script.

ctb commented 10 years ago

Please also run 'git pull https://github.com/ged-lab/khmer-protocols.git master' in your Metagenome branch, and then push.

ctb commented 10 years ago

@SherineAwad, I ran through 1-, 2-, and 3- with both manual copy/paste and literate-resting, and it all worked -- nice job. Note, I put kalamazoo instructions here:

https://github.com/ged-lab/literate-resting/blob/master/kp/kalamazoo.txt