[HESmith]

Try 'make clean' to replace old objects and dependencies that were generated by the prior makes.

[jlelias]

Thank you! Unfortunately, this did not work. . .Is there something else I should try?

[dpryan]

From what you originally wrote, there's no reason for it to try to go to a non-existent /home/lab/Desktop/JL directory. There's also no reason I've ever seen to edit the Makefile for samtools aside from changing the LIBCURSES value (if needed). I'm guessing that there's something weird with your Makefile. You might try just deleting the samtools directory and redownloading it (from the samtools page on sourceforge and no where else) so you know nothing is screwy. Then, (1) extract the files, (2) cd into the resulting directory and (3) type make without editing any files. You mentioned using Ubuntu earlier and I can confirm that this works correctly under Ubuntu.

[jlelias]

So, I've tried re-downloading both samtools and ubuntu several times. The simple directions to just go into the folder and command "make" is simply not working. And when I get tricky (changing the makefile, downloading my own c++, nsurses, or zlib, trying it as a different user ect.) but it still won't work. I feel as if I've exhausted my google search results. I even contacted the samtools people, who told me to download and try again. This I have done many many times. What could I be missing?
Thank you for your continuing comments. I can't tell you how much I appreciate your efforts on my behalf.

[Alex Renwick]

Here's what I did to download and compile a new version of samtools:

wget -O samtools-0.1.18.tar.bz2 http://sourceforge.net/projects/samtools/files/samtools/0.1.18/samtools-0.1.18.tar.bz2/download
tar xjf samtools-0.1.18.tar.bz2
cd samtools-0.1.18
make
make razip

The wget command goes through a few redirects before downloading. The make process takes about 10 seconds. After that I can use the samtools mpileup command:

[server samtools-0.1.18]$ ./samtools mpileup

Usage: samtools mpileup [options] in1.bam [in2.bam [...]]

Input options:

       -6           assume the quality is in the Illumina-1.3+ encoding
       -A           count anomalous read pairs
       -B           disable BAQ computation
       -b FILE      list of input BAM files [null]
       -C INT       parameter for adjusting mapQ; 0 to disable [0]
       -d INT       max per-BAM depth to avoid excessive memory usage [250]
       -E           extended BAQ for higher sensitivity but lower specificity
       -f FILE      faidx indexed reference sequence file [null]
       -G FILE      exclude read groups listed in FILE [null]
       -l FILE      list of positions (chr pos) or regions (BED) [null]
       [...etc...]

At what point does this process fail for you?

[jlelias]

THANK YOU everyone for your help!! I did get this to work. In case some poor student is struggling with the same thing I was, here's what finally worked:
1) I deleted the samtools folders I had.
2) used command:
sudo apt-get install samtools
3) Now, I need to figure out where it went, so I did
dpkg -s samtools
It showed-- samtools: /usr/bin/samtools /usr/lib/samtools /usr/share/samtools /usr/share/man/man1/samtools.1.gz
4) In usr/bin, the executable is locked. To unlock I did
cd ../
cd usr
cd bin
sudo chmod a+rwx samtools
5) manually move the files I'm working with (the reference.fasta and the output.sorted.bam) to the usr>bin folder
6) try command in usr>bin folder
sudo samtools mpileup -f reference.fasta output.sorted.bam >output.mpileup