bigWigToBedGraph installation

[Seb]

dear UCSC community

I tried to install the scripts using the instructions here

http://genome-source.cse.ucsc.edu/gitweb/?p=kent.git;a=blob;f=src/userApps/README

I got the libraries etc...

however, when I try to install the bigWigToBedGraph utility (from the userApps/kent/src/utils/bigWigToBedGraph folder) i get the following error

gcc -O -g -o /appUCSC/userApps/bin/bigWigToBedGraph bigWigToBedGraph.o    ../../lib/local/jkweb.a /usr/local/mysql/lib/libmysqlclient.a -lstdc++ -lm  -pthread -lssl -lcrypto -lpng /appUCSC/userApps/samtabix/libsamtabix.a -lz  -lm -lz -lm

clang: warning: argument unused during compilation: '-pthread'

ld: can't open output file for writing: /appUCSC/userApps/bin/bigWigToBedGraph, errno=2 for architecture x86_64

clang: error: linker command failed with exit code 1 (use -v to see invocation)

make: *** [/appUCSC/userApps/bin/bigWigToBedGraph] Error 1

any help?

I'm running macOSX 10.9 and i do have ssl, mySQL, libpng, make and gcc installed

thanks

[Hiram Clawson]

Good Evening:

Please note the error message:

> ld: can't open output file for writing:
> /appUCSC/userApps/bin/bigWigToBedGraph, errno=2 for architecture x86_64

That means that either this directory: /appUCSC/userApps/bin/
does not exist, or it does not have write permissions.
The build procedure should have created this directory.
Check that it exists and you can write files into it.
To check:
$ ls -l /appUCSC/userApps/bin/

The warning about '-pthread' is not important.

Try running the 'make' from the directory /appUCSC/userApps/
if that is where your 'Makefile' exists from the userApps directory.
The top of that 'Makefile' says:
# Makefile for userApps project
# performs the operations of fetching selected directories from
# the kent source tree using 'git' and then building the utilities
# in the kent source tree. All build results will be kept locally
# in this directory.

Check to see if this file looks correct:
/appUCSC/userApps/kent/src/inc/localEnvironment.mk
for your local build environment. That is also created by
the top-level Makefile during the 'make' procedure.

--Hiram