Manually install dependent tools to run pipeline without iMARGI-Docker

[frankyan]

We don't recommend to run iMARGI data processing pipeline without iMARGI-Docker. Because it needs a bundle of dependencies and many system configurations.

If you really need to run pipeline without Docker and you have much experience of system configuration, you can try to follow the instructions in the documentation. Please keep in mind, you might need to do more configurations to make it work.

• Ubuntu:

  • If your operating system is Ubuntu, the instructions could work perfectly, because the iMARGI-Docker is built on Ubuntu 18.04.

• CentOS or other Linux distributions

  • You might encounter system "locale" setting problems, which caused by python3 package pairtools. You need to use UTF-8 locale settings (such as en_US.UTF-8 and C.UTF-8). We succesfully solve the problem in CentOS with commands export LC_ALL=C.UTF-8 and export LANG=C.UTF-8.

• MacOS

  • You have to do more coonfiguration work on MacOS. First of all, please use Homebrew to install all required tools. Besides, you need to install one more tool, coreutils using Homebrew. Because some basic shell utilities, such as sort and zcat on MacOS are different to GNU Linux version. Then you need to edit the source files of python3 package pairtools, which located in directory /usr/local/lib/python3.7/site-packages/pairtools/. You need to open the source file pairtools_sort.py to edit line 110, replace 'sort' with 'gsort'. Besides, the reads fastq files must be renamed with .Z extension name, such as sample_R1.fastq.gz.Z and sample_R2.fastq.gz.Z.

Although we can succesffuly run the pipeline without Docker on different operating system, we cannot guarantee sucess for any user. Because every user might has some customized system settings, which might be caused some special problems. We cannot forecast those situations. It needs expert experience to figure out those problems. If you encounter special problems related to your own system settings, please reply to this issue providing more information about your system settings. We will try to help you solve them.