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  • Summary: Troubleshooting for installing samtools in cygwin on Windows 07042014

    Hi, All,

    I am new user to samtools and Linux and in my short experience I found some people are asking same questions as I do, but answers are bits and pieces everywhere. So i think i could sum up some information here and hopefully they are helpful. This is done in 07042014.

    Please ignore this if you are advanced users.

    I tried to install SAMtools in cygwin which is a linux enviornment in Windows 7 . There are a few things you need to consider when you are doing it. The code is as simple as "3" steps as follows, but it is not that simple in cygwins:

    1. "tar xjvf samtools-0.1.19.tar.bz2" (extract it from the package)

    2. "cd samtools-0.1.19" (change directory to the file where the package was unpacked)

    3. "make" (install it)

    There are a few pains in the A word you need to sort out before you can really "make" it.

    1. Pains in A word in extraction:
    a. The bz2 file is usually not in the directory that you are at, and thats why your 1 code is not working. solution: move your downloaded bz2 file into the directory (in windows) or change your own directory to the location where is bz file is (in cygwin).). If you dont know how to change directory in linux, please google that.....
    b. there are different versions of 'xjvf' according to what types of bz file you downloaded, they are not some random names or part of the file name! You might need to search the 'tar' command.

    2. You should be fine here when you made it through the pains in the first steps by knowing basic commands of 'cd'.

    3. Pains in A word in installation:
    a. This is the best part because you think you r almost done by typing in 'make', but we are just getting started. It usually does not work i you have no idea what is going on.
    Solution: try to calm down and look for these lines where said error. usually it is about the system could not find the command/directory and it is interesting that the 'make' package itself is not even installed in cygwin.
    what to do: when packages are told to be missing (system says it can not be found etc.), go the the cygwin install exe in windows, repeat the installation and when the process tells you to choose package (after choosing mirro webpages), choose whatever the cygwin system said not found.
    This includes, in my experiece, make, gcc, lib, zlib, etc, depending on your luck that day. You might have to come back to install more packages again and again because the system will not tell you what is missing until it finds that during process of installing. So whenever got problems just install the missing package.

    b. There was a step this is that you need to modify the make file (Makefile) in the windows where the cygwin was installed. this is needed when the system tells you that: "bam_tview.c:5:20: fatal error: curses.h: No such file or directory".
    Thanks to Richard Finney's post at so go find Makefile, double click and find CFLAGS and DFLAG and modify them like following:

    CFLAGS= -g -Wall -O2 -I/usr/include/ncurses


    ALSO !!!! run "make clean" or remove all the .o (object) files before re-making

    (Richard Finney saved my day that day, thanks a lot).

    After all this my samtools worked and I am sure I will have more problems while using it but I can get started. i hope those above are helpful and we can start sharing samtools in cygwin troubleshooting here so that more people know this.



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