Tangram Installation Issue

Question

Tangram Installation Issue

Closed this issue 10 years ago · 0 comments

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 ‘size_t fread(void_, size_t, size_t, 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 ‘size_t fread(void_, size_t, size_t, 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$