In connorhknight/IBRAP: Integrated Benchmarking scRNA-seq Analytical Pipeline (IBRAP)

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

klippy::klippy(tooltip_message = 'Click to copy', tooltip_success = 'Done', position = c('bottom', 'right'))

Incorrect gcc version

In some instances old versions are automatically stored in your user bin. If you recieve the following error you may have an older version of gcc loaded.

g++: error: unrecognized command line option ‘-fno-plt’
g++: error: unrecognized command line option ‘-fno-semantic-interposition’

If you see this you can use the following to see which version you have loaded:

find gcc 
{paste previous output here} -- version

If you are in a HPC environemnt then you must load the correct version >=7 using the HPC infastructure or compile the correct version yourself.

ImageMagick for celda

ImageMagick version inside a HPC is commonly known to create issues. For IBRAP this affects the installation of celda. A known way to fix this is to compile a specific version of ImageMagick and to supply the pathways.

step 1: Get ImageMagick from the following link by doing:

curl -L -O https://download.imagemagick.org/ImageMagick/download/releases/ImageMagick-6.9.10-86.tar.xz

step 2: cd into the downloaded directory containing ImageMagick. Then execute the following command:

tar -xf ImageMagick-6.9.10-86.tar.xz 
cd ImageMagick-6.9.10-86
./configure
make
make install

step 3: now we must export the LD_LIBRARY_PATH and pkgconfig path to the library location of ImageMagick package. For example:

export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/path/to/magick/ImageMagick-6.9.10-86/lib
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/path/to/magick/ImageMagick-6.9.10-86/Magick++/lib
export PKG_CONFIG_PATH=$PKG_CONFIG_PATH:/path/to/magick/ImageMagick-6.9.10-86/lib/pkgconfig

This should allow R tofind the correct imagemagick librarys and allow celda to install. However, take now that every HPC environment is different and different troubleshooting may be required on a case-by-case basis.

If you have any more isses/solutions please post them on our issues section in our github.

connorhknight/IBRAP documentation built on March 9, 2023, 7:01 p.m.