Tangram Installation Issue

[CodyS5]

Hello,

I have recently tried to install Tangram on both my lab linux box, and a virtual ubuntu machine on my laptop. I ran into the same errors during the compilation on both machines, most of which seem to be stemming from g++. As I am very new to programming, I have posted the commands from start to finish hoping that I have made a simple mistake. Any advice you could offer about what is causing the errors would be greatly appreciated.

Thank you,

Cody

cody@cody-virtual-machine:~$ cd /home/cody/Desktop cody@cody-virtual-machine:~/Desktop$ git clone git://github.com/jiantao/Tangram.git Cloning into 'Tangram'... remote: Counting objects: 1289, done. remote: Total 1289 (delta 0), reused 0 (delta 0) Receiving objects: 100% (1289/1289), 14.63 MiB | 1.72 MiB/s, done. Resolving deltas: 100% (669/669), done. Checking connectivity... done. cody@cody-virtual-machine:~/Desktop$ cd Tangram cody@cody-virtual-machine:~/Desktop/Tangram$ cd src cody@cody-virtual-machine:~/Desktop/Tangram/src$ make

Building Tangram

• Building in OutSources
  • compiling ssw_cpp.cpp
  • compiling ssw.c
  • compiling Fasta.cpp Fasta.cpp: In member function ‘std::string FastaReference::getSequence(std::string)’: Fasta.cpp:256:43: warning: ignoring return value of ‘sizet fread(void, size_t, sizet, FILE)’, declared with attribute warn_unused_result [-Wunused-result] fread(seq, sizeof(char), seqlen, file); ^ Fasta.cpp: In member function ‘std::string FastaReference::getSubSequence(std::string, int, int)’: Fasta.cpp:295:51: warning: ignoring return value of ‘sizet fread(void, size_t, sizet, FILE)’, declared with attribute warn_unused_result [-Wunused-result] fread(seq, sizeof(char), (off_t) seqlen, file); ^
  • compiling split.cpp
  • generating libbamtools.a /bin/sh: 1: cmake: not found make[1]: *\ [/home/cody/Desktop/Tangram/src/lib/libbamtools.a] Error 127
• Building in TangramBam
  • compiling hashes_collection.cpp
  • compiling special_hasher.cpp
  • compiling tangram_bam.cpp In file included from tangram_bam.cpp:1:0: tangram_bam.h:6:30: fatal error: api/BamAlignment.h: No such file or directory

    include "api/BamAlignment.h"

                    ^

    compilation terminated. make[1]: *\ [/home/cody/Desktop/Tangram/obj/tangram_bam.o] Error 1

• Building in TangramScan
  • compiling TGM_ReadPairScan.c TGM_ReadPairScan.c:19:19: fatal error: khash.h: No such file or directory

    include "khash.h"

         ^

    compilation terminated. make[1]: *\ [TGM_ReadPairScan.o] Error 1

• Building in TangramMerge
  • compiling TGM_MergeLibGetOpt.c
  • compiling TGM_MergeLibMain.c In file included from TGM_LibInfo.h:26:0, from TGM_MergeLibMain.c:19: ../OutSources/util/TGM_BamHeader.h:22:17: fatal error: bam.h: No such file or directory

    include "bam.h"

       ^

    compilation terminated. make[1]: *\ [TGM_MergeLibMain.o] Error 1

• Building in TangramDetect
  • compiling TGM_Aligner.cpp In file included from TGM_Aligner.h:24:0, from TGM_Aligner.cpp:33: TGM_BamPair.h:23:30: fatal error: api/BamAlignment.h: No such file or directory

    include "api/BamAlignment.h"

                    ^

    compilation terminated. make[1]: *\ [/home/cody/Desktop/Tangram/obj/TGM_Aligner.o] Error 1

• Building in TangramIndex
  • compiling TGM_IndexRef.cpp
  • compiling TGM_RefParameters.cpp
  • linking /home/cody/Desktop/Tangram/bin/tangram_index g++: error: /home/cody/Desktop/Tangram/obj/TGM_Reference.o: No such file or directory g++: error: /home/cody/Desktop/Tangram/obj/TGM_Error.o: No such file or directory g++: error: /home/cody/Desktop/Tangram/obj/TGM_GetOpt.o: No such file or directory g++: error: /home/cody/Desktop/Tangram/obj/md5.o: No such file or directory make[1]: *\ [/home/cody/Desktop/Tangram/bin/tangram_index] Error 1
• Building in TangramTools
  • copying /home/cody/Desktop/Tangram/bin/tangram_filter.pl /home/cody/Desktop/Tangram/bin/tangram_view_scan_file.py

cody@cody-virtual-machine:~/Desktop/Tangram/src$