Commits

olgert denas committed 5ec00b5 Draft

added howtoinstall link

Comments (0)

Files changed (1)

 This page describes how to use bnMapper for mapping genomic features.
 
 === Setup ===
-If you haven't done so, install numpy and bx-python (instructions on ??). Upon successful  installation you should find, among other scripts, bnMapper.py and out_to_chain.py in the scripts directory. You can run both scripts without arguments or with the -h option to get a usage message. 
+If you haven't done so, install numpy and bx-python (instructions on how to install bx-python are here [[HowToInstall]]). Upon successful  installation you should find, among other scripts, bnMapper.py and out_to_chain.py in the scripts directory. You can run both scripts without arguments or with the -h option to get a usage message. 
 
 === Out to Chain coversion ===
 The out_to_chain.py script is a simple format converter that expects in input an EPO alignment file and converts it into the UCSC chain format (http://genome.ucsc.edu/goldenPath/help/chain.html). 
Tip: Filter by directory path e.g. /media app.js to search for public/media/app.js.
Tip: Use camelCasing e.g. ProjME to search for ProjectModifiedEvent.java.
Tip: Filter by extension type e.g. /repo .js to search for all .js files in the /repo directory.
Tip: Separate your search with spaces e.g. /ssh pom.xml to search for src/ssh/pom.xml.
Tip: Use ↑ and ↓ arrow keys to navigate and return to view the file.
Tip: You can also navigate files with Ctrl+j (next) and Ctrl+k (previous) and view the file with Ctrl+o.
Tip: You can also navigate files with Alt+j (next) and Alt+k (previous) and view the file with Alt+o.