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You need to add "execute" permissions to the downloaded compiled files before they can be run. Do the following in a terminal:
Code:$ cd /to_directory_where_the_downloaded_files_are_located $ chmod u+x * (if you only downloaded axtchain then chmod u+x axtchain)
If you are trying to do this from a "regular" account you may need to use "sudo" before the chmod command.
While running the program you can either use (./axtchain ,if you are in the directory where the program is located) or provide the full directory path to "axtchain" program ($/full_path_to/axtchain)Last edited by GenoMax; 09-24-2013, 07:53 AM.
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How do I unpack the files
Im sorry this may be a stupid question but once I download the pre compiled binaries how do I run them. I tried many different things running them in my command line
I tried just running the file
155-99-216-224:~ rebeccabruders$ /Users/rebeccabruders/Downloads/axtChain
-bash: /Users/rebeccabruders/Downloads/axtChain: Permission denied
I tried using sudo and entered my password
155-99-216-224:hg rebeccabruders$ sudo /Users/rebeccabruders/Downloads/axtChain sudo: /Users/rebeccabruders/Downloads/axtChain: command not found
I tried adding make
155-99-216-224:hg rebeccabruders$ sudo make /Users/rebeccabruders/Downloads/axtChain
make: Nothing to be done for `/Users/rebeccabruders/Downloads/axtChain'.
I tried to just type axtChain
155-99-216-224:~ rebeccabruders$ axtChain
-bash: axtChain: command not found
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You can download pre-compiled binaries (which includes axtchain) for Mac (kent utilities) here: http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/
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Real Time extension Library
From what I can see this RT library is not available for Mac OS systems....
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Your system appears to be missing "real time extensions" library (librt). You should be able to locate and install that library.
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UCSC AXTCHAIN installation error
I am trying to install axtchain on my computer through the UCSC genome brower and I have MYSQL installed but I keep getting a error involving MYSQL library.
Here is what I have done.
##edited .bashrc to include
MACHTYPE=x86_64
export MACHTYPE
export MYSQLINC="/usr/local/mysql/include"
export MYSQLLIBS="/usr/local/mysql/lib -mysqlclient -pthread "
I got these directories using the command:
mysql_config --libs
will display the appropriate libraries to link with
for your system configuration. And:
mysql_config --include
will display the appropriate MYSQLINC directory.
MY GOAL was to install the hg folder and then the mousestuff folder so i can get axtchain
I was able to get part of it set up but then ran into the following error.
Last login: Mon Sep 23 10:57:18 on ttys000
155-99-166-194:~ rebeccabruders$ cd /Users/rebeccabruders/scripts/kent
155-99-166-194:kent rebeccabruders$ cd src
155-99-166-194:src rebeccabruders$ cd hg
155-99-166-194:hg rebeccabruders$ make
cd lib && make
make[1]: `../../lib/x86_64/jkhgap.a' is up to date.
cd cartReset && echo cartReset && make
cartReset
gcc cartReset.o ../../lib/x86_64/jkhgap.a ../../lib/x86_64/jkweb.a -pthread -L/lib -lssl -lcrypto -lpng -lm -L/usr/local/mysql/lib -mysqlclient -pthread -lstdc++ -lrt
ld: library not found for -lrt
collect2: ld returned 1 exit status
make[1]: *** [compile] Error 1
make: *** [cartReset.bins] Error 2
155-99-166-194:hg rebeccabruders$
I dont get where the -LRT is coming from since it isnt in my directory. Any help would be much appreciated.
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