haotu : an open lab notebook

2012/10/15

Install Osiris: Phylogenetic tools for Galaxy

Filed under: Genomics, phylogeny, Uncategorized — S @ 03:36

Assuming that you have access to a galaxy server, if not it is easy to install: http://wiki.g2.bx.psu.edu/Admin/Get%20Galaxy

1. I first cloned/copied this Osiris tools into the tools directory in the galaxy-dist folder on my computer (Ubuntu)

hg clone http://toolshed.g2.bx.psu.edu/repos/ucsb-phylogenetics/ucsb_phylogenetics

2. OK that was the easy part, now you will need to install all the dependencies and also edit the tool_conf.xml file that is in the galaxy-dist folder such that the Osiris tools are can be seen in the galaxy browser window.

Here is an example:
1. Install Bioperl, I did this through Ubuntu software center.

2. Open tool_conf.xml in a text editor. You can see that the text structure mirrors the left-hand side, tools menu, of the Galaxy browser window.

3. To this file, I then added an Osiris section and the Osiris tool addstring2fashead:

<section name="Osiris" id="osiris" >
    <tool file="ucsb_phylogenetics/ucsb_phylogenetics/addstring2fashead/addstring2fashead.xml" / >
  </section >

I put this at the bottom of the tools under VCF Tools… but I do not think it matters where you put it…

4. Start, or restart Galaxy and see if the Osiris section is in the tools menu along with addstring2fashead.

5. Give the function a try and make sure that it works. Problems occur if you do not put a string in the text box or if you have not installed Bioperl properly.

OK now what I did was add each function I wanted to the tools config file checking for dependencies along the way. Todd Oakley listed most of the dependences on the depository toolshed website
Osiris_toolshed

Good Luck!

2012/10/10

install PHLAWD on 32bit Ubuntu Dell

Filed under: Uncategorized — S @ 06:02

http://phlawd.net/manual/installation

 

  • inux

1. Download the source (or clone the repo). If you have git installed you can just run

git clone git://github.com/blackrim/phlawd.git

2. Then you will need to compile and install the prerequisites. At this point that includes MAFFTMUSCLEquicktreesqlitewrapped library, and the sqlite3library.

For UBUNTU users, you can add almost all of these by entering (though compiling MAFFT from source will allow you to use threads)

sudo apt-get install muscle libsqlite3-dev

3. For quicktree, the source is in the deps directory and you can unarchive that and just do

make && sudo cp bin/quicktree /usr/bin/

the deps directory is in the phlawd directory and git made.

4. For mafft, the source is in the deps directory and you can unarchive that and just do

cd core

edit line 8 of the Makefile removing “#” from

ENABLE_MULTITHREAD = -Denablemultithread

then

make && sudo make install

Next from this thread https://groups.google.com/forum/?fromgroups=#!searchin/phlawd/error$201/phlawd/OLtKngZJDSY/cKbYGmZhbJEJ

5. in the deps directory
tar -xzf sqlitewrapped-1.3.1.tar.gz
cd sqlitewrapped-1.3.1/
make
cp libsqlitewrapped.a ../linux/

6.Once prerequisites are installed, you can go into the src PHLAWD directory and type
./configure
make
sudo make install

7. If this fails in the src PHLAWD directory do:

make clean
make




2012/10/03

Use R to shut down programs like adobe acrobat OpenPDF ClosePDF

Filed under: Uncategorized — S @ 02:38
 
library(Biobase)
openPDF("figure_1.pdf")
cmd<-"TSKILL Acrobat"
shell(cmd)

OpenPDF

See http://127.0.0.1:15885/library/Biobase/html/openPDF.html

ClosePDF

USE TaskKill for exe killing_

2012/10/02

open pdf from R

Filed under: Uncategorized — S @ 02:12

http://rss.acs.unt.edu/Rdoc/library/Biobase/html/openPDF.html

2012/10/01

cannot turn off mail notifications when using thunderbird with gmail

Filed under: Uncategorized — S @ 23:41

I think that google makes sure that the notifications you receive about their emails are difficult to silence. Just take the advise of an old post: http://ilias.ca/blog/2006/05/getting-rid-of-the-new-mail-alert-in-the-windows-system-tray/

 

Customize your system tray!

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