That's pretty much what I had to do. Thanks for the full explanation so
others will know!
National Microbiology Laboratory
Public Health Agency of Canada
On Wed, Aug 29, 2012 at 10:31 AM, Assaf Gordon <gor...@cshl.edu> wrote:
> Hello Philip,
> Philip Mabon wrote, On 08/29/2012 10:08 AM:
> > Looks like I forgot to reset that value. So making progress... I can
> install freebayes successfully (the front end timeout but it worked)
> > However, samtools fails with the following message in web worker log:
> > [localhost] local: sed -i .bak -e 's/-lcurses/-lncurses/g' Makefile
> > Warning: local() encountered an error (return code 2) while executing
> 'sed -i .bak -e 's/-lcurses/-lncurses/g' Makefile'
> > Front end error: "sed: can't read .bak: No such file or directory"
> > So for some reason the sed did not work...
> I haven't followed the full thread, but the direct reason for this error
> (with 'sed') is that the command-line uses a Mac/BSD syntax which is not
> standard and not compatible with the most common linux version of sed.
> The parameter "-i" instructs sed to work in-place, and create a backup
> with with the given extension.
> Mac/BSD sed accepts "-i<SPACE>.bak" and "-i.bak" (without space), but the
> GNU sed does not accept a space, and so assumes that ".bak" is the input
> file name you want to work on (which obviously doesn't exist, hence the
> error "no such file").
> So the following are identical on Mac:
> sed -i .bak -e 's/-lcurses/-lncurses/g' Makefile
> sed -i.bak -e 's/-lcurses/-lncurses/g' Makefile
> But with GNU sed, the first one will not work as expected.
> To fix it, simply remove the space after the "-i" parameter (I'm not sure
> where the command is - is it part of freebayes or part of the tool-shed).
Please keep all replies on the list by using "reply all"
in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at: