Header Leaderboard Ad

Collapse

SAMtools installation

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • #16
    thanks mate i managed to install samtools successfully

    Comment


    • #17
      I'm having many of the same problems as you all in installing samtools with Cygwin. I have added the changes to makefile as suggested by jmarshall and huyvuong, am using samtools 0.1.9, and running make clean before make.

      Still, several lines indicating : undefined reference to '_expl' (or '_logl') are appearing.

      Is there something else I'm missing here?

      Comment


      • #18
        Nevermind, finally got it working. Spacing error on my part in makefile. Thank you all for your previous posts. Very helpfull.

        Comment


        • #19
          After all changes in Make file were done and you run make command, type ./samtools.exe to run the samtools

          Comment


          • #20
            Originally posted by jmarshall View Post
            The Cygwin folks changed the way they install ncurses a while back; see http://www.cygwin.com/ml/cygwin-anno.../msg00002.html.

            Hence you should add -I/usr/include/ncurses to CFLAGS in the samtools Makefile. This will solve the <curses.h> problem you are running into.

            After that, you'll probably find that it fails to link, complaining that expl() and logl() are not defined. You can work around the absence of these C99 functions by adding -Dexpl=exp -Dlogl=log to DFLAGS in the samtools Makefile, though this may have an adverse effect on SNP calling: http://sourceforge.net/mailarchive/m...l.sanger.ac.uk.

            With these additions, samtools 0.1.8 can be compiled on Cygwin.
            I recently found a way may resolve the precision problem:
            First: Install CEPHES library or only install the ldouble library (here install cephes)
            1. Using this package to install cephes.
            http://sage.math.washington.edu/home...ephes-2.8.spkg
            It's just a bzip2 compressed tar archive.
            which still lacks of two code-files: whitebxf.c and whitebx.c under "c9x-complex".
            They can be downloaded from github of cephes' master branch.
            (You even can complie without these two files, they are just for test.)

            2. Before installation, environment var "SAGE_LOCAL" should be specified like the "prefix" var in auto-configure process.

            3. run 'spkg-install' to install cephes.

            After installation of cephes, you will find libml.a in your-installed-lib dir.
            Then, change the makefile of samtools to cover the installed-lib dirs,
            replace " -lm" with " -lml" option in make file.(besides the makefile in bcftools dir)

            Then make


            I haven't made any test of the prog, maybe the correct way should be that include cephes header file (cephes_ldouble.h) to the C code files which include math.h already.

            Though I think it can get through the precision problem, and I just installed samtools 0.1.16 using this method.

            May it help!

            Comment


            • #21
              Hi everbody,

              In http://download.fedora.redhat.com/pub/epel/6/x86_64/ there are several files .rpm for installation in CentOS including Samtools, Bedtools, bwa, bowtie and others.

              Comment


              • #22
                Originally posted by jmarshall View Post
                The Cygwin folks changed the way they install ncurses a while back; see http://www.cygwin.com/ml/cygwin-anno.../msg00002.html.

                Hence you should add -I/usr/include/ncurses to CFLAGS in the samtools Makefile. This will solve the <curses.h> problem you are running into.

                After that, you'll probably find that it fails to link, complaining that expl() and logl() are not defined. You can work around the absence of these C99 functions by adding -Dexpl=exp -Dlogl=log to DFLAGS in the samtools Makefile, though this may have an adverse effect on SNP calling: http://sourceforge.net/mailarchive/m...l.sanger.ac.uk.

                With these additions, samtools 0.1.8 can be compiled on Cygwin.
                I followed these instructions (including beginning with the command 'make clean' before compilation), but still get an error message.

                I added '-I/usr/include/ncurses' to CFLAGS and '-Dexpl=exp -Dlogl=log to DFLAGS' to DFLAGS in both Makefile and Makefile.mingw. However, I still get the message:
                bam_tview.c:5:20: fatal error: curses.h: No such file or directory
                compilation terminated.
                Makefile:21: recipe for target `bam_tview.o' failed
                make: *** [bam_tview.o] Error 1

                Any suggestions?

                Comment


                • #23
                  Originally posted by jmarshall View Post
                  The -Dexpl[etc] flags need to be in action when bam_maqcns.c is compiled. (And in the just-released samtools 0.1.9, also when errmod.c is compiled.) You probably have a faulty bam_maqcns.o lying around from the previous compilation attempts. Remove it.

                  In fact, whenever you change settings like this in a makefile, it's a good idea to use "make clean" before building again. So try again, typing "make clean" and then "make".
                  I added these to Makefile. After "CFLAGS=", I kept one space and one tab (the same as the original line of CFLAGS) and then "-l/usr/include/ncurses".

                  And both ncurse and nurses-dev are installed.

                  My error message is as follows:
                  /usr/include/bits/mathcalls.h:101: error: conflicting types for ‘exp’
                  /usr/include/bits/mathcalls.h:110: error: conflicting types for ‘log’
                  make[2]: *** [bam_md.o] Error 1
                  make[2]: Leaving directory `/usr/local/samtools-0.1.18'
                  make[1]: *** [lib-recur] Error 1
                  make[1]: Leaving directory `/usr/local/samtools-0.1.18'
                  make: *** [all-recur] Error 1

                  Could anyone help me? I have been confused with this problem for a while.

                  Comment


                  • #24
                    Hi All, I'm a newbie in bioinformatics, and am hoping to compile samtools in Cygwin. I could see that most of the posts are shared by senior members, which is way too difficult to understand. Most of the information is also spread out on the net. Can anyone please write a step by step walk through for newbies like me. It would really useful. Thank you.

                    Comment


                    • #25
                      Looking for Cephes-2.8.spkg

                      The link that was posted for Cephes-2.8.spkg is dead. I am trying to find it. Can someone post me a link? I

                      Comment


                      • #26
                        In future start a new thread if you are asking a question that is not related to the parent.

                        A google search found this: http://ftp.riken.jp/sagemath/spkg/up...hes/index.html I am not sure if this is the package you are looking for or if the file is genuine. Use with caution.
                        Last edited by GenoMax; 03-12-2016, 03:04 PM.

                        Comment


                        • #27
                          thanks

                          I though that since I was asking about a file given in the post to fix an issue and the link was dead it still my request still counted as being part of the thread. I will post a new thread then. The link that you gave does not have the spkg part of it and is the original code. Thanks for your help.

                          Comment


                          • #28
                            The spkg file is here: http://old.files.sagemath.org/spkg/a...es-2.8.p1.spkg

                            Edit: My apologies. I re-merged your question back into the original thread where you had originally asked it for benefit of future users. The new thread you had started has this answer as well.
                            Last edited by GenoMax; 03-12-2016, 02:53 PM.

                            Comment

                            Working...
                            X