hyperoplus commented 3 years ago

Hi,

I have a contig-based genome assembly that I want to scaffold using LD information from a set of pool sequencing data. I have been thinking of experimenting with LDscaff, but so far have not been able to install it. After git cloning the program to my system, I've tried runnin "make" in the folder /home/user/LDscaff/src, but the compiler retrieves an error with the lemon installation:


Makefile:14: warning: overriding recipe for target 'tools.o'
Makefile:11: warning: ignoring old recipe for target 'tools.o'
g++ -c graph.cc -O3 -g -lemon -std=c++0x
graph.cc:13:10: fatal error: lemon/matching.h: No such file or directory
 #include <lemon/matching.h>
          ^~~~~~~~~~~~~~~~~~
compilation terminated.
make: *** [Makefile:8: graph.o] Error 1

This is despite having lemon installed system-wide. I've tried this using two different machines, one with CentOS and the other with Ubuntu. Do you have any idea what could be the issue?

YingXiaoZhou commented 3 years ago

I think you can modify the makefile, adding the library path, the error shows that it can not locate the matching.h in your system. ---- Replied Message @.>Date07/07/2021 19:49 @.> @.***>Subject[YingXiaoZhou/LDscaff] Problem installation - lemon (#1) Hi, I have a contig-based genome assembly that I want to scaffold using LD information from a set of pool sequencing data. I have been thinking of experimenting with LDscaff, but so far have not been able to install it. After git cloning the program to my system, I've tried runnin "make" in the folder /home/user/LDscaff/src, but the compiler retrieves an error with the lemon installation:

Makefile:14: warning: overriding recipe for target 'tools.o' Makefile:11: warning: ignoring old recipe for target 'tools.o' g++ -c graph.cc -O3 -g -lemon -std=c++0x graph.cc:13:10: fatal error: lemon/matching.h: No such file or directory

include <lemon/matching.h>

      ^~~~~~~~~~~~~~~~~~

compilation terminated. make: *** [Makefile:8: graph.o] Error 1

This is despite having lemon installed system-wide. I've tried this using two different machines, one with CentOS and the other with Ubuntu. Do you have any idea what could be the issue?

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hyperoplus commented 3 years ago

Hi @YingXiaoZhou thanks for the help. Actually I think installing lemon with "yum install" does not provide the correct installation, so I went to: http://lemon.cs.elte.hu/trac/lemon and installed manually from the tar.gz file on this website, the compilation now ran to the end.

I will try to run LDscaff, will let you know if I run into any issues.

Johnsonzcode commented 2 years ago

@hyperoplus Do yuo know how to get .snp1 and snp2 in the manual?

YingXiaoZhou / LDscaff

Problem installation - lemon #1

include <lemon/matching.h>