Hello all, I managed to install CNVnator after much hair-ripping. But now that I have figured everything out, follow the steps to this procedure and hopefully you will have no more issues with installation! Here we go:
1. Install "root" http://root.cern.ch/drupal/content/downloading-root
2. Once you have downloaded the package, unzip it, personally I use this code to untar things...
where you replace [name of tar file] with the actual name of your tar file e.g. "root_v5.32.00.source.tar.gz" (without quotations)
3. now you have a folder called "root" containing everything inside the package you just extracted. Note the path to this "root" folder and save that path somewhere. I will refer to the "root" folder path as "rootpath" from now on
4. Now you want to open up a terminal window and type the commands to install root, which is fairly simple.
wait for it to finish....
wait again....
done!
5. NOW you want to download CNVnator http://sv.gersteinlab.org/cnvnator/
6. To unzip it you can do it conventionally or use terminal
7. You now have a folder called "CNVnator" or whatever you extracted it to. So just do the following commands from terminal:
now if you type "ls" and hi enter you should see the src, license, and readme
now wait for it to finish...
now your back in the "src" directory
EVERYTHING up until this point should just work. BUT the next code you type will not unless you do the following first, so just follow...
*recall that "rootpath" is the file path to your ".../root" folder where root is installed
Now type
and hit enter. No errors should come up.
8. Now for the final step... cd back into your CNVnator/src folder and type "make" and hit enter. You should get no errors and now will be able to use CNVnator! Happy analyzing!
1. Install "root" http://root.cern.ch/drupal/content/downloading-root
2. Once you have downloaded the package, unzip it, personally I use this code to untar things...
Code:
tar -zxvf [name of tar file]
3. now you have a folder called "root" containing everything inside the package you just extracted. Note the path to this "root" folder and save that path somewhere. I will refer to the "root" folder path as "rootpath" from now on
4. Now you want to open up a terminal window and type the commands to install root, which is fairly simple.
Code:
cd root
Code:
./configure
Code:
make
done!
5. NOW you want to download CNVnator http://sv.gersteinlab.org/cnvnator/
6. To unzip it you can do it conventionally or use terminal
Code:
unzip -o [zip file name]
Code:
cd CNVnator
Code:
cd src/samtools
Code:
make
Code:
cd ..
EVERYTHING up until this point should just work. BUT the next code you type will not unless you do the following first, so just follow...
Code:
export ROOTSYS=[rootpath]
Now type
Code:
export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${ROOTSYS}/lib
8. Now for the final step... cd back into your CNVnator/src folder and type "make" and hit enter. You should get no errors and now will be able to use CNVnator! Happy analyzing!
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