misc

Homepages / Entry points https://github.com/ged-lab/khmer (the homepage according to CTB) http://khmer.readthedocs.org/en/latest/ http://ged.msu.edu/papers/2012-diginorm/ & http://github.com/ged-lab/2012-paper-diginorm/ & http://arxiv.org/abs/1203.4802 https://github.com/ged-lab/khmer/tree/2012-paper-diginorm

http://ged.msu.edu/angus/diginorm-2012/tutorial.html

Documentation / Tutorials: http://khmer.readthedocs.org/en/latest/ http://ged.msu.edu/angus/metag-assembly-2011/ http://ged.msu.edu/angus/2012-oslo-metagenomics/ http://ged.msu.edu/angus/diginorm-2012/pipeline-notes.html http://ged.msu.edu/papers/2012-diginorm/notebook/ http://ged.msu.edu/angus/stamps-2012 http://ged.msu.edu/angus/2013-hmp-assembly-webinar

Git repo cleanup of 2014-04-01 through 04

git clone --mirror [email protected]:ged-lab/khmer.git
cd khmer.git
du -hs
# 113M
git config --unset-all remote.origin.fetch
git config --add remote.origin.fetch '+refs/heads/*:refs/heads/*'
git config --add remote.origin.fetch '+refs/tags/*:refs/heads/*'
rm -Rf refs/pull
sed -i '/.*pull.*/d' packed-refs
git-largest-object.sh
# modified to sort based on packed size & to work on bare repo
# examine output to craft the next command
git filter-branch --force --index-filter 'git rm --cached --ignore-unmatch tests/test-data/test-overlap1.ht lib/test-data/stamps-reads.fa.gz.bin lib/test-data/stamps-reads.fa.gz.bin.index data/1m-filtered.fa data/MSB2-surrender.fa data/25k.fq.gz.bin tst-pipeline/part-test.fa' --prune-empty --tag-name-filter cat -- --all
# takes ~1 minute
rm -Rf refs/original
git reflog expire --expire=now --all
git gc --prune=now
git gc --aggressive --prune=now
du -hs
# 25M