Hi Hiram, my PATH environment is set properly,
/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/usr/texbin:/usr/X11/bin:/usr/ebiotools/bin I took Jennifer's advice onboard and downloaded the chromSizes directly. Just reformatting my wig tracks to not have the track line at the moment and my laptop is struggling! :-) Nick On 12/08/2010, at 9:33 AM, Hiram Clawson wrote: > Good Afternoon Nick: > > The program *is* using your ftp command from /usr/bin/ftp > > What the error says is that the ftp attempt did not work correctly. > > This script is having difficulty locating any commands on your system. > Do you have any PATH set at all in your login terminal ? Try this > at your command line prompt: > > echo $PATH > > Does it indicate /bin:/usr/bin or anything like that ? > > --Hiram > > ----- Original Message ----- > From: "Nicholas Wong" <[email protected]> > To: "Jennifer Jackson" <[email protected]> > Cc: [email protected] > Sent: Wednesday, August 11, 2010 2:44:00 PM GMT -08:00 US/Canada Pacific > Subject: Re: [Genome] Running the wigToBigWig program > > Hi again, > > I tried to run the fetchChromSizes script, it executes but now there is a new > error (see below): > > INFO: trying FTP /usr/bin/ftp for database hg19 > ERROR: ftp command failed > ERROR: sorry, attempt to fetch chrom.sizes has failed ? > > ftp on my computer resides in /usr/bin I don't have a /usr/bin/ftp folder > > executing ftp from terminal works, but the script doesn't, I have had a look > at the script to see if I could point it in the right directory, but I am not > soooo comupter savvy sorry. > > Thanks for your time and help > > Nick > > > On 12/08/2010, at 4:03 AM, Jennifer Jackson wrote: > >> Hi Nick, >> >> Your shell is having trouble finding the program(s). They do need to be made >> executable (so that was good to do) and the location added your path. If not >> already, add the path to your shell file then be sure to source it. Most >> likely this is the problem. >> >> There are many online resources for Mac OS if you need unix/shell syntax >> help. >> >> Best wishes, >> >> Jen >> UCSC Genome Browser Support >> >> On 8/10/10 8:24 PM, Nicholas Wong wrote: >>> I am sorry for probably a very simple question, I have tried to download >>> wigToBigWig and fetchChromSizes programs from the website and tried to >>> execute them in terminal. >>> >>> I just get bash: command not found. >>> >>> I did try a chmod to make these files executable and get the same error >>> result. >>> >>> I am running MacOSX 10.6.4, Terminal version 2.1.1 >>> >>> Cheers >>> >>> Nick >>> >>> >>> Dr Nick Wong BSc(Hons), Ph.D >>> Postdoctoral Fellow >>> Developmental Epigenetics, Early Development and Disease >>> >>> Murdoch Childrens Research Institute >>> The Royal Children’s Hospital >>> Flemington Road Parkville Victoria 3052 Australia >>> T 8341 6205 T 9345 6603 F 9348 1391 >>> M 0421 030 482 >>> E [email protected] >>> www.mcri.edu.au >>> >>> >>> >>> This e-mail and any attachments to it (the "Communication") are, unless >>> otherwise stated, confidential, may contain copyright material and is for >>> the use only of the intended recipient. If you receive the Communication in >>> error, please notify the sender immediately by return e-mail, delete the >>> Communication and the return e-mail, and do not read, copy, retransmit or >>> otherwise deal with it. Any views expressed in the Communication are those >>> of the individual sender only, unless expressly stated to be those of >>> Murdoch Childrens Research Institute (MCRI) ABN 21 006 566 972 or any of >>> its related entities. MCRI does not accept liability in connection with the >>> integrity of or errors in the Communication, computer virus, data >>> corruption, interference or delay arising from or in respect of the >>> Communication. >>> >>> Please consider the environment before printing this email >>> >>> >>> >>> >>> >>> _______________________________________________ >>> 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
