In addition to needing the right permissions on a downloaded executable, linux by default does not include "." (the current directory) on the path for security reasons.
This means you may have to type ./executable to run something in the current directory. The reason that this security issue exists is because if some program you download happens to be have the same name as some important system-level utility, it might get executed when you were not intending it and it would then be potentially running without your permission or knowledge. Although we like to help people, there are many tutorials on basic unix questions. Just do a google search. Good luck. -Galt 3/11/2011 9:57 AM, Katrina Learned: > Hi, > > To find out what type of machine you have, you can follow the > instructions on the instructions in the directory containing the > liftover executables: > > "...\To determine your machine type, at the command line type: > > uname -a > > When you type "liftOver" on the command line, make sure the letter "O" > in the command is capitalized. Also, make sure you have permission to > execute the file. Type "ls -l" to see the permissions of the liftOver > file. To add permission to execute type "chmod u+x liftOver". > > I hope this information is helpful. Please don't hesitate to contact the > mail list again if you have any further questions. > > Katrina Learned > UCSC Genome Bioinformatics Group > > [email protected] wrote, On 03/10/11 23:29: >> Hi, >> I am a PhD candidate, and want to use your too liftOve to convert a >> coordinate file of mouse transcript(based on mm5) to based on mm9 assembly. >> I downloaded the liftOver bin file from >> http://hgdownload.cse.ucsc.edu/admin/exe/ >> >> Then I put the binary file "liftOver" on my Linux Server >> Next I go to the directory where the "liftOver" was, and type liftOver >> on the cammand line, the message "-bash: liftOver: command not found" >> but I type "ls", the output show the file "liftOver" exist. >> Because I am not sure of my linux (64 linux or 32 linux), so both of >> liftOver for 64 or 32 were downloaded and tested, but the message above was >> output always. >> Would you be kind to tell me why? And how I should do? >> >> >> >> _______________________________________________ >> Genome maillist - [email protected] >> https://lists.soe.ucsc.edu/mailman/listinfo/genome >> > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
