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fix #780 - Update do.sh #781

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merged 15 commits into from
Feb 23, 2015
Merged

fix #780 - Update do.sh #781

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83797c9
Update do.sh
drtamermansour Feb 19, 2015
a039d49
automate checking of do.sh script
drtamermansour Feb 19, 2015
3a0636e
add -c to the bash command
drtamermansour Feb 19, 2015
43a7086
Merge branch 'master' of https://github.com/ged-lab/khmer into fix/#780
drtamermansour Feb 20, 2015
b6c37d6
edit the ChangeLog
drtamermansour Feb 20, 2015
cdc608b
correct ChangeLog
drtamermansour Feb 20, 2015
681513e
add error message
drtamermansour Feb 21, 2015
71a7bcd
Update ChangeLog
drtamermansour Feb 22, 2015
2044d88
Update ChangeLog
drtamermansour Feb 22, 2015
9137df5
correct conflict
drtamermansour Feb 23, 2015
87b4544
remove embty line
drtamermansour Feb 23, 2015
afe03ad
adding empty line at the top of Changelog
drtamermansour Feb 23, 2015
b66a2b0
fix jenkins script line
drtamermansour Feb 23, 2015
a55a987
resolve Changelog conflict
drtamermansour Feb 23, 2015
f0baea1
better jenkins syntex
drtamermansour Feb 23, 2015
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5 changes: 5 additions & 0 deletions ChangeLog
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Original file line number Diff line number Diff line change
@@ -1,3 +1,8 @@
2015-02-20 Tamer A. Mansour <drtamermansour@gmail.com>

* In the do.sh script, the old argument --savehash has been updated to
--savetable
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Wrapped lines should be indented to match the line above. In this instance you need three space before --savetable


2015-02-20 Titus Brown <titus@idyll.org>

* doc/dev/scripts-and-sandbox.txt: policies for sandbox/ and scripts/
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4 changes: 2 additions & 2 deletions examples/stamps/do.sh
100644 → 100755
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Expand Up @@ -10,7 +10,7 @@ load-into-counting.py -x 1e8 -k 20 stamps-reads.ct \
abundance-dist.py stamps-reads.ct ../../data/stamps-reads.fa.gz \
stamps-reads.hist
normalize-by-median.py -k 20 -C 10 -x 1e8 ../../data/stamps-reads.fa.gz \
--savehash stamps-dn.ct
--savetable stamps-dn.ct
abundance-dist.py stamps-dn.ct stamps-reads.fa.gz.keep stamps-dn.hist
do-partition.py -k 32 -x 1e8 -s 1e4 -T 8 stamps-part \
../../data/stamps-reads.fa.gz
Expand All @@ -27,7 +27,7 @@ abundance-dist.py stamps-part.g1.ct stamps-part.group0001.fa stamps-part.g1.hist

filter-abund.py stamps-dn.ct stamps-reads.fa.gz.keep
normalize-by-median.py -x 1e8 -k 20 -C 10 stamps-reads.fa.gz.keep.abundfilt \
--savehash stamps-dn3.ct
--savetable stamps-dn3.ct

abundance-dist.py stamps-dn3.ct stamps-reads.fa.gz.keep.abundfilt.keep \
stamps-dn3.hist
3 changes: 3 additions & 0 deletions jenkins-build.sh
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Expand Up @@ -64,3 +64,6 @@ if type sloccount >/dev/null 2>&1
then
make sloccount.sc
fi

bash -ex -c 'cd examples/stamps/; ./do.sh' || { echo examples/stamps/do.sh no longer runs; /bin/false }