As you may guess by the title, I am not very experienced with Linux. I have been trying to follow the advice on these websites:
Basically, I downloaded bedtools2 (from this site -https://github.com/arq5x/bedtools2/releases/tag/v2.19.1) so that I could generate a count table using the command (as seen on the first referenced biostars site):
bedtools multicov –bams run1.bam run2.bam run3.bam -bed genes.bed
I do not have XCode (and my MacOSX App Store has an installation problem), so I cannot use the "make" command to make this easy.
So, this is what I have tried so far:
1) I used "echo$PATH", which looks like this:
/usr/local/bin:/Users/MacOwner/anaconda/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/usr/local/git/bin:/usr/texbin:/usr/X11/bin:/opt/local/bin:~/bin
2) I know I have to copy "executables of interest" to /usr/local/bin (I chose that from one output of echo$PATH).
However, my question is: What are the executables of interest? I keep seeing this on forums, and am still stuck after hours. What exactly should I copy to /usr/local/bin for me to run a command like:
bedtools multicov –bams run1.bam run2.bam run3.bam -bed genes.bed
from anywhere? (And yes, I am guessing I will change the first word to "bedtools2").
Do I copy an entire directory? There are numerous subdirectories in bedtools (/bin /data /docs /genomes /obj /scripts /src/ test).
I don't see any files in /bin. I don't see a "multicov" directory in /src (although I see a "multiBamCov" directory there). I see a "multicov" directory in /test.
If you have an idea of what exactly I should copy to /usr/local/bin, and anything else I need to do to run such a command, I would greatly appreciate. I have spent a while on this, and feel like if I needed to start a thread (even if it seems simple).
Thank you!
Basically, I downloaded bedtools2 (from this site -https://github.com/arq5x/bedtools2/releases/tag/v2.19.1) so that I could generate a count table using the command (as seen on the first referenced biostars site):
bedtools multicov –bams run1.bam run2.bam run3.bam -bed genes.bed
I do not have XCode (and my MacOSX App Store has an installation problem), so I cannot use the "make" command to make this easy.
So, this is what I have tried so far:
1) I used "echo$PATH", which looks like this:
/usr/local/bin:/Users/MacOwner/anaconda/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/usr/local/git/bin:/usr/texbin:/usr/X11/bin:/opt/local/bin:~/bin
2) I know I have to copy "executables of interest" to /usr/local/bin (I chose that from one output of echo$PATH).
However, my question is: What are the executables of interest? I keep seeing this on forums, and am still stuck after hours. What exactly should I copy to /usr/local/bin for me to run a command like:
bedtools multicov –bams run1.bam run2.bam run3.bam -bed genes.bed
from anywhere? (And yes, I am guessing I will change the first word to "bedtools2").
Do I copy an entire directory? There are numerous subdirectories in bedtools (/bin /data /docs /genomes /obj /scripts /src/ test).
I don't see any files in /bin. I don't see a "multicov" directory in /src (although I see a "multiBamCov" directory there). I see a "multicov" directory in /test.
If you have an idea of what exactly I should copy to /usr/local/bin, and anything else I need to do to run such a command, I would greatly appreciate. I have spent a while on this, and feel like if I needed to start a thread (even if it seems simple).
Thank you!
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