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  • #16
    Last time I successfully installed Cufflinks using the option --with-boost=/PATH/TO/BOOST/ROOT when configuring. I give my solution here.

    1. get the path to boost root, in which there are at least two dirs: include and lib
    2. cd into the dir cufflinks-0.8.1
    * type ./configure --with-boost=/PATH/TO/BOOST/ROOT
    * type make
    * type make install

    Let me know if this trial fails.
    Xi Wang

    Comment


    • #17
      Yes I downloaded boost library and try to add path to it with the command path=<home/path to the boost folder...>.

      I do not know if there is anything else I need to do!

      Thank you

      Comment


      • #18
        Originally posted by Xi Wang View Post
        Last time I successfully installed Cufflinks using the option --with-boost=/PATH/TO/BOOST/ROOT when configuring. I give my solution here.

        1. get the path to boost root, in which there are at least two dirs: include and lib
        2. cd into the dir cufflinks-0.8.1
        * type ./configure --with-boost=/PATH/TO/BOOST/ROOT
        * type make
        * type make install

        Let me know if this trial fails.
        Thank you for your prompt reply.

        I did not understand how 1st step works? i.e How to get a path to boost root. Also I searched boost folder, I found Lib Directory but can not see include directory in it. PLease let me know how this works.

        Thank you.

        Comment


        • #19
          Thank you everyone for the help.

          Comment


          • #20
            Originally posted by BioTalk View Post
            Thank you everyone for the help.
            Have you solved this problem? I didn't hear from you any more:-)
            Xi Wang

            Comment


            • #21
              I seem to be having the same problem. I am trying to install Cufflinks on a 32 bit Linux system, for which there are no pre-compiled binaries available (only 64 bit). I successfully built the Boost package using bjam, as instructed on the Getting Started page of Cufflinks.
              Then I ran ./configure in the cufflinks directory, which gave no obvious errors (the Boost package was found, too). However, when I run 'make' there are several error messages that I don't understand (see below). Specially the '-m64' argument is suspicious, does this mean that it is trying to compile in 64 bit mode? I don't have enough experience with Linux to know how to proceed.
              How did other people do this? Or is everyone using a 64 bit system? I have none available, as far as I know.
              Any help would be greatly appreciated! Thanks..

              Output after running 'make':
              Code:
              rob@robin:~/cufflinks-0.8.2$ make
              make  all-recursive
              make[1]: Entering directory `/home/robin/cufflinks-0.8.2'
              Making all in src
              make[2]: Entering directory `/home/robin/cufflinks-0.8.2/src'
              if g++ -DHAVE_CONFIG_H -I. -I. -I..  -I../src    -Wall -Wno-strict-aliasing -g -gdwarf-2 -m64 -O3  -DNDEBUG  -pthread -I/usr/local/include -MT clustering.o -MD -MP -MF ".deps/clustering.Tpo" -c -o clustering.o clustering.cpp; \
              	then mv -f ".deps/clustering.Tpo" ".deps/clustering.Po"; else rm -f ".deps/clustering.Tpo"; exit 1; fi
              In file included from /usr/include/features.h:354,
                               from /usr/include/assert.h:37,
                               from /usr/include/c++/4.2/cassert:49,
                               from /usr/local/include/boost/graph/vector_as_graph.hpp:17,
                               from clustering.h:17,
                               from clustering.cpp:10:
              /usr/include/gnu/stubs.h:9:27: error: gnu/stubs-64.h: No such file or directory
              In file included from clustering.cpp:10:
              clustering.h:29:41: error: boost/vector_property_map.hpp: No such file or directory
              clustering.h:142:7: warning: no newline at end of file
              make[2]: *** [clustering.o] Error 1
              make[2]: Leaving directory `/home/robin/cufflinks-0.8.2/src'
              make[1]: *** [all-recursive] Error 1
              make[1]: Leaving directory `/home/robin/cufflinks-0.8.2'
              make: *** [all] Error 2

              Comment


              • #22
                I too experienced the same kind of problem with Cufflinks in 32 bit system. It was a problem because of 32 bit OS, as the binary available for 32 bit is getting compiled into 64bit and therefore it is of no use. I would suggest you to install cufflinks in 64 bit machine.

                Thanks!

                Comment


                • #23
                  Thanks BioTalk, unfortunately I don't have a 64 bit system available right now, so I'll have to think of something else...

                  Comment


                  • #24
                    finding boost package in cufflinks

                    Hi all

                    The discussion is ended abruptly with out any answer
                    I was installed boost and bjam and built them on usr\local and after that ran ./configure but it is not detecting boost libraries.
                    i have added boost libraries to path also.

                    Then I ran ./configure in the cufflinks directory, which gave errors (the Boost package was not found).

                    PS:I'm using 32 bit computer and downloaded 32 bit boost packages

                    Code:
                    [bogugk@Trivia ~]$ [B]cd /usr/local/boost_1_41_0/[/B]
                    [bogugk@Trivia boost_1_41_0]$ [B]ls -l[/B]
                    total 320
                    drwxr-xr-x  3 root   root   4096 Jan  8 15:18 bin.v2
                    -rwxr-xr-x  1 root   root 171424 Jan  8 15:17 bjam
                    drwxr-xr-x 74    400  401  12288 Nov 18  2009 boost
                    -rw-r--r--  1    400  401    849 Nov 13  2009 boost-build.jam
                    -rw-r--r--  1    400  401    989 Nov 13  2009 boost.css
                    -rw-r--r--  1    400  401   6308 Nov 13  2009 boost.png
                    -rw-r--r--  1    400  401   1958 Nov 13  2009 bootstrap.bat
                    -rw-r--r--  1 root   root    852 Jan  8 15:17 bootstrap.log
                    -rwxr-xr-x  1    400  401  10211 Nov 13  2009 bootstrap.sh
                    -rw-r--r--  1    400  401    427 Nov 13  2009 CMakeLists.txt
                    drwxr-xr-x  7    400  401   4096 Nov 18  2009 doc
                    -rw-r--r--  1    400  401    770 Nov 13  2009 index.htm
                    -rw-r--r--  1    400  401   5485 Nov 13  2009 index.html
                    -rw-r--r--  1    400  401    291 Nov 13  2009 INSTALL
                    -rw-r--r--  1    400  401  23355 Nov 13  2009 Jamroot
                    drwxr-xr-x 85    400  401   4096 Nov 18  2009 libs
                    -rw-r--r--  1    400  401   1338 Nov 13  2009 LICENSE_1_0.txt
                    drwxr-xr-x  4    400  401   4096 Nov 18  2009 more
                    drwxr-xr-x  2    400  401   4096 Nov 18  2009 people
                    -rw-r--r--  1 root   root    822 Jan  8 15:17 project-config.jam
                    -rwxrwxrwx  1 gisv12  401   6009 Nov 18  2009 README.txt
                    -rw-r--r--  1    400  401   2610 Nov 13  2009 rst.css
                    drwxr-xr-x  3 root   root   4096 Jan  8 15:18 stage
                    drwxr-xr-x  2    400  401   4096 Nov 18  2009 status
                    drwxr-xr-x 13    400  401   4096 Nov 18  2009 tools
                    drwxr-xr-x  2    400  401   4096 Nov 18  2009 wiki
                    Code:
                    [B]./configure --with-boost=/usr/local/boost_1_41_0/boost/[/B]
                    checking for a BSD-compatible install... /usr/bin/install -c
                    checking whether build environment is sane... yes
                    checking for gawk... gawk
                    checking whether make sets $(MAKE)... yes
                    checking for gawk... (cached) gawk
                    checking for g++... g++
                    checking for C++ compiler default output file name... a.out
                    checking whether the C++ compiler works... yes
                    checking whether we are cross compiling... no
                    checking for suffix of executables... 
                    checking for suffix of object files... o
                    checking whether we are using the GNU C++ compiler... yes
                    checking whether g++ accepts -g... yes
                    checking for style of include used by make... GNU
                    checking dependency style of g++... gcc3
                    checking for gcc... gcc
                    checking whether we are using the GNU C compiler... yes
                    checking whether gcc accepts -g... yes
                    checking for gcc option to accept ISO C89... none needed
                    checking dependency style of gcc... gcc3
                    checking whether make sets $(MAKE)... (cached) yes
                    checking for ranlib... ranlib
                    checking for a BSD-compatible install... /usr/bin/install -c
                    checking for boostlib >= 1.38.0... configure: error: We could not detect the boost libraries (version 1.38 or higher). If you have a staged boost library (still not installed) please specify $BOOST_ROOT in your environment and do not give a PATH to --with-boost option.  If you are sure you have boost installed, then check your version number looking in <boost/version.hpp>. See http://randspringer.de/boost for more documentation.

                    Comment


                    • #25
                      Did you use bjam to build Boost? You can find instructions here: http://cufflinks.cbcb.umd.edu/tutorial.html

                      But anyway, this didn't work for me in the end. It would seem that cufflinks doesn't compile properly on a 32 bit system, so I used a MacBook (to run a few tests) and a 64 bit system (to do the actual analysis) instead.

                      Comment


                      • #26
                        yes 32 bit is not working

                        yes i used bjam.
                        yes i agree some thing wrong with 32 bit
                        seems 64 bit doesnt have any configure file so no need to run the commands??????????

                        Code:
                        ./configure --prefix=/path/to/cufflinks/install --with-boost=/path/to/boost
                        make
                        make install
                        but ./command (ex: ./cufflinks) are working fine

                        [bogugk@Trivia cufflinks-0.8.2.Linux_x86_64]$ ./cufflinks ./test_data.sam
                        Counting hits in map
                        Total map density: 104.000000
                        Processing bundle [ test_chromosome:52-550 ] with 99 non-redundant alignments
                        Last edited by repinementer; 06-15-2010, 12:44 AM. Reason: adding commands

                        Comment


                        • #27
                          That's right, there are pre-compiled binaries for 64 bit systems and/or Macs. Much easier, eh? :-)

                          Comment


                          • #28
                            FluxCapacitor and FluxStimulator

                            Have you installed these?
                            Seems pretty google code RNASEQ tools.

                            Comment


                            • #29
                              Gonna bump this thread again. I was able to get through all the boost and sam/bam issues for this installation (I've successfully installed bowtie and tophat as well), but now with Cufflinks I'm having a 'make' error (it is a 64 bit system).

                              GList.hh(413): remark #981: operands are evaluated in unspecified order
                              if (Found(item, result)) return true;
                              ^

                              compilation aborted for clustering.cpp (code 2)
                              make[2]: *** [clustering.o] Error 1
                              make[2]: Leaving directory `/work/emucaki/goblin/Cufflinks/cufflinks-0.9.1/src'
                              make[1]: *** [all-recursive] Error 1
                              make[1]: Leaving directory `/work/emucaki/goblin/Cufflinks/cufflinks-0.9.1'
                              make: *** [all] Error 2
                              Any ideas?

                              Comment


                              • #30
                                Originally posted by emucaki View Post
                                GList.hh(413): remark #981: operands are evaluated in unspecified order
                                You are using Intel's compiler and you have configured cufflinks so as to compile with -Werror.

                                This is a relatively useless warning, and it's hard to see why it's being triggered by this code. It seems that the usual advice is to switch the warning off: http://software.intel.com/en-us/foru...ad.php?t=62309.

                                Comment

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