problem with installation

[TerezaClarence]

Dear developers,

I am having trouble installing the tool, can you please advise me?

> library(devtools)
> install_github('wangjr03/FLAMINGO/FLAMINGOr',ref='HEAD')

Loading required package: usethis
Warning message:
package ‘usethis’ was built under R version 4.1.3 
Downloading GitHub repo wangjr03/FLAMINGO@HEAD
Error in utils::download.file(url, path, method = method, quiet = quiet,  : 
  download from 'https://api.github.com/repos/wangjr03/FLAMINGO/tarball/HEAD' failed

Thank you, Tereza

[Fillot]

I have been having the same problem. Downloading through a browser instead works, so I highly suspect that devtools rejects the download because the tarball is so large. I think the github should remove any hic/bed file other than maybe a demonstration file to let users insure the library is working as intended.

[SarahBeecroft]

I also had the same issue. My colleague and I made a container you could use here https://quay.io/repository/sarahbeecroft9/flamingo (just because we needed one). The recipe is there if you wanted to see the install instructions and not actually use the container, up to you.

Otherwise this method seemed to get around the issue for us

options(download.file.method = "wget"); devtools::install_github("wangjr03/FLAMINGO/FLAMINGOr")

[SarahBeecroft]

For future users: a conda/mamba installation that worked for us

mamba create -n flamingo
mamba activate flamingo
mamba install -y -c cyclus -c bioconda -c anaconda -c conda-forge -c r java-jre java-jdk r-matrix r-prodlim r-strawr r-data.table bioconductor-biocgenerics bioconductor-genomicfeatures bioconductor-s4vectors bioconductor-IRanges bioconductor-genomeinfodb bioconductor-genomicranges bioconductor-annotationdbi cairo mysql-devel freetype r-matrix r-rmysql zlib unixodbc libxml2 libssh2 libsqlite sasl libpq r-rcurl r-biocmanager r-devtools  r-r.utils r-mgcv

R -e 'options(download.file.method = "wget"); devtools::install_github("wangjr03/FLAMINGO/FLAMINGOr")'

[JiaxinYangJX]

Thanks for using our software and raising the issue. We will further move the data to Google Drive and only maintain the scripts in the repository.

In addition, we are currently collecting all the feedback and reorganizing our tools. We will release a more user-friendly version by next month.

[JiaxinYangJX]

Hi @SarahBeecroft @Fillot @TerezaClarence Thanks for using our tools! We just released a lite version of FLAMINGO, which is faster, more memory-efficient, and more user-friendly. We fixed the majority of bugs and hope the new version could help. Below is the link. https://github.com/JiaxinYangJX/FLAMINGOrLite