CODEWITHSUNDEEP
unixbuildcondazlib
Wesley Hanson
Wesley Hanson

Reputation: 43

Kallisto build keeps failing when attempting to link CXX executable

I'm super new to coding in general so apologies for any lack of clarity or conciseness. I'm attempting to make a build for Kallisto to use in RNA sequence alignment and I'm getting stuck at the "make" stage. The cmake was successful after a little fiddling and downloading a CXX compiler, but the make keep exiting with an error status:

[ 27%] Built target htslib
[ 93%] Built target kallisto_core
[ 96%] Linking CXX executable kallisto
/home/wahanson/miniconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: cannot find -lz
collect2: error: ld returned 1 exit status
make[2]: *** [src/CMakeFiles/kallisto.dir/build.make:88: src/kallisto] Error 1
make[1]: *** [CMakeFiles/Makefile2:130: src/CMakeFiles/kallisto.dir/all] Error 2

the main error appears to be "cannot find -lz" causing the subsequent errors. From what I understand, this is referencing zlib1g-dev and/or an inability to find it within the path. I have installed zlib1g-dev through conda and made sure to update to no avail. If anyone could let me know what I'm missing or a next place to look it'd be much appreciated. Thanks!

Upvotes: 3

Views: 374

Answers (1)

merv
merv

Reputation: 77098

The error looks like the zlib package was not installed in the env. Fortunately, I've recently built kallisto and can share the Conda environment I have been using, which I've tested on both osx-64 and linux-64 platforms:

kallisto-build.yaml

name: kallisto-build
channels:
  - bioconda
  - r
  - conda-forge
  - defaults
dependencies:
  - autoconf
  - automake
  - hdf5
  - cmake
  - cxx-compiler
  - zlib

Create and then activate this environment:

conda env create -f kallisto-build.yaml
conda activate kallisto-build

then follow the kallisto instructions for building from source.

Upvotes: 1

Related Questions