Suggestions to improve the installation

[cgirardot]

Hi,

I just installed your package. I wanted to have it installed centrally so colleagues could also use the tool. But I have encountered different issues:

1. sklearn & psutil have been found missing (for GenomeDISCO) after the install
2. The --rlib option did not work for me. The R packages where installed in a default location (that is specific to the user doing the install) and the tool could not be shared.
3. ${pythondir}conda install -c anaconda mpi4py failed

To solve these issues and successfully share the package, I encapsulated the install into a conda environment.

conda create --prefix /path/to/condaenv/3DChromatin_ReplicateQC python=2.7
conda activate /path/to/condaenv/3DChromatin_ReplicateQC

Then:

1. was solved by simply

   pip install sklearn
   pip install psutil

2. was a little more tricky. The way I could solve this was :

   • bypass your R lib installation altogether i.e. comment the line 108-109 :

     #cmd="${PATHTOR}script ${dir_of_script}/install_R_packages.R"
     #eval "${cmd}"

   • pre-install the needed packages and R using conda :

     conda install -c r r=3.5.1 r-reshape2 r-rmarkdown r-testthat
     conda install -c bioconda bioconductor-rhdf5 r-pheatmap

   • Note that hicrep could also be easily conda installed (v 1.2 as of today) but it turned out that the v1.2 did not work with your code (would be great to fix this) so I had to stick with the 1.0.1 version. But to get it installed in the right place (ie in the conda env), I had to do it manually and give the right lib=/path/to/condaenv/3DChromatin_ReplicateQC/lib/R/library/ :

     # launch R (the one from the conda env)
     $ R
     > source("https://bioconductor.org/biocLite.R")
     > install.packages("Supplemental_hicrep_1.0.1.tar.gz", lib="/path/to/condaenv/3DChromatin_ReplicateQC/lib/R/library/")

3. ${pythondir}conda install -c anaconda mpi4py was replaced with ${pythondir}conda install mpi4py

I hope this feedback will help.

[oursu]

Hi @cgirardot,

Thank you immensely for this extremely useful feedback.

I will incorporate the changes to the install scripts and modify the code to be compatible with the newest version of hicrep. Will confirm here when these changes are done.

Thank you again for your help! This is one of the most useful and nicely written github issues I have encountered.

Best, Oana

[rachelzhu123]

Hi @cgirardot, Thank you for your suggestion! I successfully installed this software according to your suggestion.