search

ntanmayee / decoden

🌊 Analyse experimental conditions and replicates jointly to remove cell-type specific bias in multi-condition ChIP-Seq
GNU General Public License v3.0
8 stars 1 forks source link

Installation fails without some tweaks... #23

Open jamesabbott opened 6 months ago

jamesabbott commented 6 months ago

Hello,

I've successfully installed decoden, but following the instructions directly did not work and needed a couple of modifications.

1) Our cluster environment is very minimalist, so C compilers are not available by default. The necessary build tools can be installed with conda install c-compiler. I also needed to install git, so maybe simply stating in the installation instructions that git and a modern C compiler are required should be enough to address this - many systems will have these available by default.

2) pysam requires htslib/samtools and zlib in order to compile successfully, so a conda install samtools zlib is also required

3) MACS2 fails to install with python 3.12. MACS2.2.9.1 has been released which says it handle some cython updates, but this still fails in the same way. I've had to downgrade to python 3.11 to get the installation to complete which is not ideal if you are stuck needing a particular python version. I don't know that the MACS developers will care about MACS2 being still installable since MACS3 is now out.

James

gvisona commented 5 months ago

The installation section of the readme was updated to include the missing packages. I will examine the version needs for MACS and finish updating the procedure afterwards.