mcveanlab/mccortex

Build without sudo apt install

ShawnCone opened this issue · 2 comments

ShawnCone commented

Apologies in advance if this is not the right place to ask this question.

During the build process, it is stated that on linux:
sudo apt install liblzma-dev libbz2-dev
should be done for htslib dependency purposes.

However, in our local system, only the admin has the ability to use this command. Is there any alternative to this?

What has been done:

  • Manually downloading both liblzma-dev and libbz2-dev using wget
  • Installing both liblzma-dev and libbz2-dev
  • Add both paths to $LD_LIBRARY_PATH variable

After these, running make all within cloned mccortex folder still results in error. Attached is the stderr/stdout of the make all command.

McCortex Stdout and Stderr.txt

Thank you very much

winni2k commented

You can try compiling mccortex in a conda environment. Try installing miniconda from here. Then activate the environment and install libz with conda install zlib.

noporpoise commented

Sorry I'm not sure how best to install the dependencies without admin. If @winni2k's suggestion doesn't work for you, could you ask your administrator to install the dependencies?