Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • cufflinks 2.0.0 source missing a header?

    Has anyone had success installing the latest cufflinks (2.0.0 beta) from source? It seems like a required local header file "rounding.h" is not included in the source distribution. I have emailed their support email about this, but I just wanted to double check that I am not the only one having this issue. Thanks!

    Code:
    g++44 -DHAVE_CONFIG_H -I. -I..  -I../src  -I/usr/include  -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -m64 -march=nocona -O3  -DNDEBUG  -pthread -I/hive/groups/genomeAssem/include -I/hive/groups/genomeAssem/src/samtools_svn/include -I/hive/groups/genomeAssem/include -MT abundances.o -MD -MP -MF .deps/abundances.Tpo -c -o abundances.o abundances.cpp
    abundances.cpp:38:22: error: rounding.h: No such file or directory
    The reason I think that it is a local file rather than something my system is missing is that it is included right in the middle of a block of other locally included header files, and the include statement uses the double quote syntax rather than the <> syntax. Thanks!

  • #2
    Er..I didn't know there was a 2.0. I thought they were working on 1.4 still.
    /* Shawn Driscoll, Gene Expression Laboratory, Pfaff
    Salk Institute for Biological Studies, La Jolla, CA, USA */

    Comment


    • #3
      There is a 2.0 version as of yesterday.

      Comment


      • #4
        Hi Kopi-o,
        Did you figure out the installation problem yet? I am having another problem with the Eigen libray. I downloaded and copied the eigen-eigen-b23437e61a07/Eigen to a directory in my PATH and gave --with-eigen arguments while configuring. But the configure log still says could not find eigen libraries. Any idea?

        Thanks

        Comment


        • #5
          Hi segmagician,
          Thanks for the tip. If possible, can you please provide the round.h? I am also having problem with that.
          Thanks.

          Comment


          • #6
            I corresponded with Cole earlier today about problems with the original tar file.

            He has kindly provided a new source tar ball that fixed problems we were noticing. Get the latest source from the download link.

            Comment


            • #7
              Yes... I just noticed that... the source file has been updated.

              Comment


              • #8
                Hi,
                I stills can not install Cufflinks. My make is successful but when I try to execute the cufflinks executable it gives me the following error:

                error while loading shared libraries: libboost_thread.so.1.48.0: cannot open shared object file: No such file or directory

                I tried installing with boost 1.49 but got the same error. Any idea?

                Thanks.

                Comment


                • #9
                  Try appending the LD_LIBRARY_PATH as described here.

                  Discussion of next-gen sequencing related bioinformatics: resources, algorithms, open source efforts, etc



                  Originally posted by vinay052003 View Post
                  Hi,
                  I stills can not install Cufflinks. My make is successful but when I try to execute the cufflinks executable it gives me the following error:

                  error while loading shared libraries: libboost_thread.so.1.48.0: cannot open shared object file: No such file or directory

                  I tried installing with boost 1.49 but got the same error. Any idea?

                  Thanks.

                  Comment


                  • #10
                    Thank GenoMax..
                    for some reason I can't find libboost_thread.so.1.48.0 on my system. My boost installation was successful though. I noticed that /my_boost_install_dir/lib is empty. Is this the place where libboost_thread.so.1.48.0 supposed to be?

                    Comment


                    • #11
                      The file (libboost_thread.so.1.*) should be in the "lib" directory. Perhaps your boost installation did not work right.

                      Originally posted by vinay052003 View Post
                      Thank GenoMax..
                      for some reason I can't find libboost_thread.so.1.48.0 on my system. My boost installation was successful though. I noticed that /my_boost_install_dir/lib is empty. Is this the place where libboost_thread.so.1.48.0 supposed to be?

                      Comment

                      Latest Articles

                      Collapse

                      • seqadmin
                        Strategies for Sequencing Challenging Samples
                        by seqadmin


                        Despite advancements in sequencing platforms and related sample preparation technologies, certain sample types continue to present significant challenges that can compromise sequencing results. Pedro Echave, Senior Manager of the Global Business Segment at Revvity, explained that the success of a sequencing experiment ultimately depends on the amount and integrity of the nucleic acid template (RNA or DNA) obtained from a sample. “The better the quality of the nucleic acid isolated...
                        03-22-2024, 06:39 AM
                      • seqadmin
                        Techniques and Challenges in Conservation Genomics
                        by seqadmin



                        The field of conservation genomics centers on applying genomics technologies in support of conservation efforts and the preservation of biodiversity. This article features interviews with two researchers who showcase their innovative work and highlight the current state and future of conservation genomics.

                        Avian Conservation
                        Matthew DeSaix, a recent doctoral graduate from Kristen Ruegg’s lab at The University of Colorado, shared that most of his research...
                        03-08-2024, 10:41 AM

                      ad_right_rmr

                      Collapse

                      News

                      Collapse

                      Topics Statistics Last Post
                      Started by seqadmin, 03-27-2024, 06:37 PM
                      0 responses
                      12 views
                      0 likes
                      Last Post seqadmin  
                      Started by seqadmin, 03-27-2024, 06:07 PM
                      0 responses
                      11 views
                      0 likes
                      Last Post seqadmin  
                      Started by seqadmin, 03-22-2024, 10:03 AM
                      0 responses
                      52 views
                      0 likes
                      Last Post seqadmin  
                      Started by seqadmin, 03-21-2024, 07:32 AM
                      0 responses
                      68 views
                      0 likes
                      Last Post seqadmin  
                      Working...
                      X