Seqlogo and Homer

Question

[fire_water]

Hello,

Our lab would like to use Homer and install it under the following environment:

• Mac OS X 10.8.5
• Xcode Version 5.0.1 (5A2053)
• Xcode command line tools
• Homebrew
• Python 2.7.2 @ /usr/bin/python

It looks like Homer was successfully installed except for one package, seqlogo. The results of our troubleshooting is listed below. We attempted to contact technical support at Homer and Seqlogo but unfortunately never heard back.

How can we get Homer to see seqlogo? Thanks!

Troubleshooting:

perl configureHomer.pl -check

    Current base directory for HOMER is /Users/Shared/homer/./

    Checking for standard utilities and 3rd party software:

    Checking for wget... /usr/local/bin/wget
    Checking for cut... /usr/bin/cut
    Checking for gcc... /usr/bin/gcc
    Checking for zip... /usr/bin/zip
    Checking for unzip... /usr/bin/unzip
    Checking for make... /usr/bin/make
    Checking for tar... /usr/bin/tar
    Checking for gunzip... /usr/bin/gunzip
    Checking for gzip... /usr/bin/gzip
    Checking for gs... /usr/local/bin/gs
    **Checking for seqlogo..The program seqlogo was not found but is required for making motif logos**
    Checking for blat... /usr/local/bin/blat

    All auxilary programs found.

$ seqlogo
 Command not found
$ which weblogo
 /usr/local/bin/weblogo
 weblogo 3.4

webLogo installed like so

sudo pip install numpy
brew install pdf2svg
sudo pip install weblogo

findMotifs.pl returns help page (good sign, right?)

echo $PATH
/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/Users/administrator/Downloads/software/ngsplot/bin:/Users/Shared/homer/bin:/opt/X11/bin

Edit 2014.09.24

As suggested by Ying W, weblogo 2.8.2 must be used in order for seqlogo to be recognized by HOMER.

Answer 1

[Ying W]

Follow the weblogo install directions found here you will need a specific version that might not be the right one installed by pip

[fire_water]

Thanks for the suggestion. However, seqlogo is still not recognized by homer. Please see the latest edit in my post.

[Ying W]

If you follow the link I gave, this is the file that it will tell you to download. Within that archive, you will find the seqlogo executable

[fire_water]

Thank you. For anyone else following along, weblogo 2.8.2 must be used in order for seqlogo to be recognized by HOMER.