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Non root install #6

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Non root install #6

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2bb35a8
Added non root install instructions
themangoemoji Oct 28, 2014
cd21e3f
EC2 non root install instructions
themangoemoji Oct 31, 2014
becd6f3
pipeline notes and prokka install update
themangoemoji Oct 31, 2014
4a87f7f
pipline note update
themangoemoji Nov 4, 2014
5e8fbd9
changed ~ to /Users/narrows
themangoemoji Nov 4, 2014
dc86e93
rename
themangoemoji Nov 4, 2014
caaa0bb
no mo .profile
themangoemoji Nov 4, 2014
a966b79
no mo .profile
themangoemoji Nov 4, 2014
92bda18
Merge branch 'non-root-install' of github.com:ged-lab/2012-paper-digi…
themangoemoji Nov 4, 2014
3d15fcf
Add RackSpace install instructions
themangoemoji Jan 23, 2015
74bf7d9
Add RackSpace install instructions
themangoemoji Jan 23, 2015
b66eae0
Shake installs out of install-prokka script
themangoemoji Jan 27, 2015
31e9b73
Change install location to ~/src
themangoemoji Jan 30, 2015
9d08ddd
Check out the correct branch, curl correct file
themangoemoji Jan 30, 2015
bfce3b7
Check out the correct branch, curl correct file
themangoemoji Jan 30, 2015
c78f9ba
Merge branch 'non-root-install' of https://github.com/ged-lab/2012-pa…
themangoemoji Jan 30, 2015
55a61f3
Add rackspace instructions and prokka install updates
themangoemoji Feb 10, 2015
4b29611
Merge branch 'non-root-install' of github.com:ged-lab/2012-paper-digi…
themangoemoji Feb 10, 2015
2568739
Upgrade numpy
themangoemoji Feb 10, 2015
fcaf3d0
Seperate EC2 and RackSpace instructions
themangoemoji Feb 17, 2015
353bacb
Expand arguments for Makefile commands
themangoemoji Feb 17, 2015
88e9fa3
Add additional targets for missing files and download data
themangoemoji Feb 17, 2015
a3c77a4
Rerout /mnt/bin to ${HOME}/bin
themangoemoji Feb 18, 2015
6438276
Resolve merge
themangoemoji Feb 18, 2015
727aa85
Merge branch 'non-root-install' of https://github.com/ged-lab/2012-pa…
themangoemoji Feb 18, 2015
8d3b137
Rerout /mnt/bin to ${HOME}/bin
themangoemoji Feb 18, 2015
763a608
Update prokka-11 install
themangoemoji Feb 24, 2015
99eac72
Merge with athyra
themangoemoji Feb 24, 2015
c21b7ba
Merging athyra/local differences
themangoemoji Feb 24, 2015
e8e8a0a
Update notes with proper root/non-root distinctions
themangoemoji Feb 24, 2015
ff79fd1
Merge branch 'non-root-install' of github.com:ged-lab/2012-paper-digi…
themangoemoji Feb 24, 2015
b6fd3f0
Fix install-prokka script
themangoemoji Feb 24, 2015
28a9afe
Fix install-prokka script
themangoemoji Feb 24, 2015
83eade1
Merge branch 'non-root-install' of github.com:ged-lab/2012-paper-digi…
themangoemoji Feb 24, 2015
188a66f
Merge branch 'non-root-install' of github.com:ged-lab/2012-paper-digi…
themangoemoji Feb 24, 2015
e240d39
Merge branch 'non-root-install' of github.com:ged-lab/2012-paper-digi…
themangoemoji Feb 25, 2015
17d9f17
Fixup pipeline notes
themangoemoji Feb 25, 2015
29db18f
Move numpy install to root installs
themangoemoji Mar 17, 2015
a3328ba
Point root to install in user directory
themangoemoji Mar 17, 2015
f525527
Switch home to usert
themangoemoji Mar 17, 2015
1bf737d
Add prodigal to root installs, change path variable ordering
themangoemoji Apr 21, 2015
51e8670
Allow non-root to own their directory
themangoemoji Apr 21, 2015
83267f2
Add screed install
themangoemoji Apr 21, 2015
a890134
Move screed install to non-root
themangoemoji Apr 28, 2015
90cfefd
Correct thread variable syntax
themangoemoji Apr 28, 2015
081d1e7
Use `prokka` directly in makefile, Update pipeline-notes
themangoemoji May 3, 2015
d5dcf9e
Fix user-land installs to use sudo
themangoemoji May 21, 2015
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Fix install-prokka script
  • Loading branch information
@themangoemoji
themangoemoji committed Feb 24, 2015
commit 28a9afe1afc9b114d7028c224124303176d5c191
6 changes: 4 additions & 2 deletions pipeline/install-prokka.sh
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Expand Up @@ -9,6 +9,8 @@ make
mkdir -p ${HOME}/src/prokka
cd ${HOME}/src/prokka
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need to do a mkdir -p first here as well

curl -OL https://github.com/Victorian-Bioinformatics-Consortium/prokka/archive/v1.11.tar.gz
tar xzf prokka-*.tar.gz
export PATH=${PATH}:${HOME}/src/prokka/prokka-*/bin
tar xzf v*.tar.gz
ln -s prokka-* prokka
echo 'export PATH=${PATH}:${HOME}/src/prokka/prokka/bin' >> ~/.bashrc
export PATH=${PATH}:${HOME}/src/prokka/prokka/bin
prokka --setupdb
16 changes: 9 additions & 7 deletions pipeline/pipeline-notes.rst
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Expand Up @@ -43,7 +43,7 @@ Additionally, if you are on RackSpace, you will need to disable the firewall so

If you need to create a new user, you can do so with::

useradd -m -d /home/user <your_user_name>
adduser <your_user_name>
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Inconsistent use of sudo in this section.



Depending on the instance you chose, we may need to add extra space for data by formating and mounting a drive.
Expand All @@ -69,7 +69,12 @@ packages we will need. You will need root permissions to install these::
ncbi-tools-bin prodigal infernal aragorn parallel


Now, with root privledges, you'll need to install the version of 'khmer' that the

All Non-Root
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'User land installs'

--------------------------------------------
Once you have completed all of the previous commands that require root permissions,
go ahead and login as you normally would.
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Drop this paragraph above

Now you'll need to install the version of 'khmer' that the
paper is currently using.::

cd ${HOME}
Expand All @@ -81,11 +86,7 @@ paper is currently using.::
pip install --upgrade numpy
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@mr-c Added this line to fix:

(venv)non-root@cloud-server-02:/mnt/data/2012-paper-diginorm/pipeline$ make
python calc-r2.py > calc-r2.txt
Traceback (most recent call last):
File "calc-r2.py", line 1, in <module>
import numpy, math, itertools
ImportError: No module named numpy
make: *** [calc-r2.txt] Error 1

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Is the python-numpy Debian package new enough to work?
http://packages.ubuntu.com/utopic/python-numpy

On Tue, Feb 10, 2015, 23:40 Michael Wright notifications@github.com wrote:

In pipeline/pipeline-notes.rst
#6 (comment)
:

easy_install -U setuptools
pip install khmer==1.1

  • pip install --upgrade numpy

Added this line due to:

(venv)non-root@cloud-server-02:/mnt/data/2012-paper-diginorm/pipeline$
make
python calc-r2.py > calc-r2.txt
Traceback (most recent call last):
File "calc-r2.py", line 1, in
import numpy, math, itertools
ImportError: No module named numpy
make: *** [calc-r2.txt] Error 1

—
Reply to this email directly or view it on GitHub
https://github.com/ged-lab/2012-paper-diginorm/pull/6/files#r24453165.

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Wrong URL, we're running Ubuntu Trusty:
http://packages.ubuntu.com/trusty/python-numpy

On Wed, Feb 11, 2015, 10:47 Michael Crusoe michael.crusoe@gmail.com wrote:

Is the python-numpy Debian package new enough to work?
http://packages.ubuntu.com/utopic/python-numpy

On Tue, Feb 10, 2015, 23:40 Michael Wright notifications@github.com
wrote:

In pipeline/pipeline-notes.rst
#6 (comment)
:

easy_install -U setuptools
pip install khmer==1.1

  • pip install --upgrade numpy

Added this line due to:

(venv)non-root@cloud-server-02:/mnt/data/2012-paper-diginorm/pipeline$
make
python calc-r2.py > calc-r2.txt
Traceback (most recent call last):
File "calc-r2.py", line 1, in
import numpy, math, itertools
ImportError: No module named numpy
make: *** [calc-r2.txt] Error 1

—
Reply to this email directly or view it on GitHub
https://github.com/ged-lab/2012-paper-diginorm/pull/6/files#r24453165.



All Non-Root
--------------------------------------------
Once you have completed all of the previous commands that require root permissions,
go ahead and login as you normally would.
Now we can go ahead and add the ``~/bin`` to our path::
Now we can go ahead and add ``~/bin`` to our path::

echo 'export PATH=${PATH}:${HOME}/bin' >> ${HOME}/.bashrc
source ${HOME}/.bashrc
Expand All @@ -95,6 +96,7 @@ We need to install Velvet. (We need to do this the old fashioned way to enable l
sizes)::

mkdir -p ${HOME}/src/velvet
mkdir -p ${HOME}/bin
cd ${HOME}/src/velvet
curl -O http://www.ebi.ac.uk/~zerbino/velvet/velvet_1.2.10.tgz
tar xzf velvet_1.2.10.tgz
Expand Down