Problem Installing Velvet Assembler On Mac Os X 10.5.8

Question

[Anjan]

Hello all, The Velvet "make" returns an error when I try to install it on my Mac. There were some instructions to change the Makefile to allow for a smooth install on Macs- they do not help. Have any of you had any success? Will appreciate any pointers. Thanks. Anjan Tail of the installation report:

Undefined symbols:
  "_egzseek", referenced from:
      _readBAMFile in readSet.o
  "_egzgetc", referenced from:
      _readFastQGZFile in readSet.o
      _readFastAGZFile in readSet.o
  "_egzgets", referenced from:
      _readRawGZFile in readSet.o
      _readFastQGZFile in readSet.o
      _readFastQGZFile in readSet.o
      _readFastQGZFile in readSet.o
      _readFastQGZFile in readSet.o
      _readFastQGZFile in readSet.o
      _readFastAGZFile in readSet.o
      _readFastAGZFile in readSet.o
      _parseDataAndReadFiles in readSet.o
  "_egzungetc", referenced from:
      _readFastQGZFile in readSet.o
      _readFastAGZFile in readSet.o
  "_egzclose", referenced from:
      _readBAMFile in readSet.o
      _readRawGZFile in readSet.o
      _readFastQGZFile in readSet.o
      _readFastAGZFile in readSet.o
      _parseDataAndReadFiles in readSet.o
  "_egzopen", referenced from:
      _readBAMFile in readSet.o
      _readRawGZFile in readSet.o
      _readFastQGZFile in readSet.o
      _readFastAGZFile in readSet.o
      _parseDataAndReadFiles in readSet.o
  "_egzread", referenced from:
      _readBAMFile in readSet.o
      _readBAMFile in readSet.o
      _readBAMFile in readSet.o
      _readBAMFile in readSet.o
      _readBAMFile in readSet.o
      _readBAMFile in readSet.o
      _readBAMFile in readSet.o
      _readBAMFile in readSet.o
  "_egzdopen", referenced from:
      _readBAMFile in readSet.o
      _readRawGZFile in readSet.o
      _readFastQGZFile in readSet.o
      _readFastAGZFile in readSet.o
      _parseDataAndReadFiles in readSet.o
ld: symbol(s) not found
collect2: ld returned 1 exit status
make: *** [velveth] Error 1

Answer 1

[Pierre Lindenbaum]

The libraries for the gzip library are missing from your path. Find it or install it. Then, in the Makefile change:

LDFLAGS = -lm

to

LDFLAGS = -L /path/to/the/zlib/libary/folder -lm