Wednesday, December 9, 2009

elementary $PATH stuff

As I mentioned the other day, it seems like PyCogent likes to use the $PATH variable rather than Python's sys.path to look for executables like clustalw and muscle. While I was updating my clustalw (actually clustalw2) installation at work to version 2.0.12, I worked on this quite elementary BASH shell issue. (I got clustalw from EMBL-EBI, see FTP download link here).

There is a directory in my home directory ~/bin where my bioinformatics binaries live. I copied the new folder clustalw-2.0.12-macosx from the download into there, as usual. Then, I just made a symbolic link to the executable like so:

ln -s ~/bin/clustalw-2.0.12-macosx/clustalw2 ~/bin/clustalw

I used clustalw for the link since that's what Py-Cogent expects. I tested it by doing ~/bin/clustalw from the Desktop. Now I needed to put ~/bin on my PATH. You can look at the $PATH variable as follows:

echo $PATH

output before the modification:

/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/usr/X11/bin

To modify it, I made a text file called on my Desktop containing this line:

PATH=$PATH:$HOME/bin/ ;export PATH

I put it in the right place by doing:

cp ~/Desktop/x.txt ~/.bash_profile

and tested by first doing

echo $PATH

which gives /Users/te/bin/ appended to the previous output. The final test (for now, anyway) is to do clustalw from the Desktop.

$ clustalw



**************************************************************
******** CLUSTAL 2.0.12 Multiple Sequence Alignments ********
**************************************************************


1. Sequence Input From Disc
2. Multiple Alignments
3. Profile / Structure Alignments
4. Phylogenetic trees

S. Execute a system command
H. HELP
X. EXIT (leave program)

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