VBoxManage modifyvm Ubuntu --natpf1 "server,tcp,,8080,,8080"
This is exactly what the docs say to do. The extra twist was to modify
and to modify
/etc/apache2/sites-available/default. I basically duplicated the whole
<VirtualHostentry and changed the second part to read:
And now it works. From the host in Safari or using curl in Terminal:
SERVER_SOFTWARE Apache/2.2.17 (Ubuntu)
Apache/2.2.17 (Ubuntu) Server at localhost Port 8080
HTTP_USER_AGENT Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7) AppleWebKit/534.48.3 (KHTML, like Gecko) Version/5.1 Safari/534.48.3
HTTP_ACCEPT_ENCODING gzip, deflate
The other thing I've done today is to install EMBOSS and PyCogent.
sudo apt-get install emboss
How easy is that! The rebase files are at
We want # 5 and # 31 as described.
chmodfor the EMBOSS directories so we can write there:
sudo chmod 777 -R /usr/share/EMBOSS
tell it where the files are, and it'll do its thing.
head -5 /usr/share/EMBOSS/data/REBASE/embossre.enz > cat
# REBASE enzyme patterns for EMBOSS
pattern len ncuts blunt c1 c2 c3 c4
put a sequence file DA19.txt on the Desktop
remap -sequence DA19.txt
SgeI | SgeI
Cac8I | NspI | | SgeI HindIII
| PcsI Cac8I | SgeI | | | SgeI | Cac8I
\ \ \ \ \ \ \ \ \ \ \
[ UPDATE: Something wrong with the formatting here. The HindIII site, AAGCTT, is at the far right. ]
sudo apt-get install cython
Get Pycogent from
tar -xzvf ~/Downloads/PyCogent-1.5.1.tgz
python setup.py build
sudo python setup.py install
I tested Pocogent by downloading sequences and making a phylogenetic tree as described here (I had to install a MUSCLE binary first). I pasted the source into four scripts.
Not exactly as before, but it looks reasonable.