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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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pipeline notes and prokka install update
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@themangoemoji
themangoemoji committed Oct 31, 2014
commit becd6f318da99107157d718e58dbc4f103622ed1
12 changes: 6 additions & 6 deletions pipeline/install-prokka.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -6,41 +6,41 @@ cd /mnt
curl -O ftp://selab.janelia.org/pub/software/hmmer3/3.1b1/hmmer-3.1b1.tar.gz
tar xzf hmmer-3.1b1.tar.gz
cd hmmer-3.1b1/
./configure --prefix=/usr && make && make install
./configure --prefix=${HOME} && make && make install
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http://packages.ubuntu.com/search?keywords=hmmer :-)


cd /mnt
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These lines could be the problem; depends on the permissions of the 'mnt' folder. Lets download source code and build inside ${HOME}/src

curl -O http://mbio-serv2.mbioekol.lu.se/ARAGORN/Downloads/aragorn1.2.36.tgz
tar -xvzf aragorn1.2.36.tgz
cd aragorn1.2.36/
gcc -O3 -ffast-math -finline-functions -o aragorn aragorn1.2.36.c
cp aragorn /usr/local/bin
cp aragorn ~/bin
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When copying to a directory I usually use a trailing slash for clarity


cd /mnt
curl -O http://prodigal.googlecode.com/files/prodigal.v2_60.tar.gz
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Use https://github.com/hyattpd/Prodigal/archive/v2.6.1.tar.gz

tar xzf prodigal.v2_60.tar.gz
cd prodigal.v2_60/
make
cp prodigal /usr/local/bin
cp prodigal ~/bin

cd /mnt
curl -O ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools/converters/by_program/tbl2asn/linux64.tbl2asn.gz
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http://packages.ubuntu.com/trusty/ncbi-tools-bin

gunzip linux64.tbl2asn.gz
mv linux64.tbl2asn tbl2asn
chmod +x tbl2asn
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@mr-c this and several other actions in this file require root.
Maybe I can extract these to the beginning?

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Which lines require root? I don't see any.

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The chmod, no? Its halting on this install anyways
in particular
prokka-1.7/db/hmm: Cannot utime: Operation not permitted
tar: prokka-1.7/db/hmm: Cannot change mode to rwxr-xr-x: Operation not permitted
and many like this. I figured this was throw from this line

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Did you try it? How does it halt? Anyone is allowed to chmod files that they own.

cp tbl2asn /usr/local/bin
cp tbl2asn ~/bin

cd /mnt
curl -O http://ftp.gnu.org/gnu/parallel/parallel-20130822.tar.bz2
tar xjvf parallel-20130822.tar.bz2
cd parallel-20130822/
ls
./configure && make && make install
./configure --prefix=${HOME} && make && make install

cd /mnt
curl -O http://selab.janelia.org/software/infernal/infernal-1.1rc4.tar.gz
tar xzf infernal-1.1rc4.tar.gz
cd infernal-1.1rc4/
ls
./configure && make && make install
./configure --prefix=${HOME} && make && make install


10 changes: 8 additions & 2 deletions pipeline/pipeline-notes.rst
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Expand Up @@ -58,12 +58,17 @@ OK, now we have installed almost all of the software we need, hurrah!

Running the pipeline
--------------------
If running on EC2::
mkdir /mnt/bin
ln -s /mnt/bin ~/

First, check out the source repository and grab the (...large) initial data
sets::

echo "export PATH=${PATH}:~/bin" >> ~/.bashrc
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and run it right here as well
export PATH=${PATH}:~/bin


cd /mnt
git clone https://github.com/ged-lab/2012-paper-diginorm.git
git clone https://github.com/ged-lab/2012-paper-diginorm.git --branch ubuntu14.04/v1.1
cd 2012-paper-diginorm

curl -O https://s3.amazonaws.com/public.ged.msu.edu/2012-paper-diginorm/pipeline-data-new.tar.gz
Expand All @@ -73,9 +78,10 @@ Now go into the pipeline directory and install Prokka & run the pipeline. This
will take 24-36 hours, so you might want to do it in 'screen' (see
http://ged.msu.edu/angus/tutorials-2011/unix_long_jobs.html). ::


cd pipeline
bash install-prokka.sh
make /usr/local/share/khmer
make
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@mr-c I don't understand why this line is not working. Before I added lines 90 and 91, I had the problem no module screed. Are lines 90 and 91 incorrect ways to install screed? If not, I now have this error after make:

miguel@cloud-server-02:~/2012-paper-diginorm/pipeline$ make
load-into-counting.py -k 20 -N 4 -x 1e8 genome-reads.fa.ct genome-reads.fa
make: load-into-counting.py: Command not found
make: *** [genome-reads.fa.ct] Error 127

This makes me think this is a screed problem still.

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See my above comment about root vs. non-root.


Once it successfully completes, copy the data over to the ../data/ directory::

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