InstallationΒΆ
Installation should be pretty painless (we hope). We have provided all the softwares in a singularity image which provides continuity across different computing platforms (see HPCNG Singluarity and Sylabs io for more information on singularity images). The only thing to note before you download this image is that the image is ~6.5Gb so, depending on the internet speed, it will take ~15-30 min to download. The good news is that you should only need to do this once unless updates are made to the scripts or image.
Just download the singluarity image with:
wget https://www.dropbox.com/s/6p64z451qobi070/Demuxafy.sif wget https://www.dropbox.com/s/0hpzm04oqbqg4ra/Demuxafy.sif.md5
Then you should check to make sure that the image downloaded completely by comparing the image md5sum to the original md5sum. You can do that by running the following commands:
md5sum Demuxafy.sif > downloaded_Demuxafy.sif.md5 diff -s Demuxafy.sif.md5 downloaded_Demuxafy.sif.md5
If everything was downloaded correctly, that command should report:
Files Demuxafy.sif.md5 and downloaded_Demuxafy.sif.md5 are identical
Note
Please note that the singularity image and this documentation is updated with each release. This means that the most recent documentation may not be 100% compatible with the singularity image that you have. For example, additional parameters and functionality were implemented in v1.0.2 that was not available in v0.0.4.
You can check the version of your singularity image to match with documentation with:
singularity inspect Demuxafy.sif
If you run into any issues with downloading the image or any issue with running anything from this image, you can reach out to us by submitting an issue at Github
Demuxafy software versions - for the curious
Image build date: 18 February, 2022
Software Group
Software
Version
Demultiplexing
popscle
demuxlet
freemuxletv0.1-beta
scSplitv1.0.8.2
Souporcellv2.0
Vireov0.5.6
Doublet Detecting
DoubletDeconv1.1.6
DoubletDetectionv3.0
DoubletFinderv2.0.3
scDblFinderv1.8.0
scdsv1.9.1
scrubletv0.2.3
solov1.2
Supporting Softwares
minimap2v2.7-r654
bedtools2v2.28.0
vartrixv1.1.3
htslibv1.7 & v1.13 & v1.14
samtoolsv1.7
bcftoolsv1.13
freebayesv1.3.5
cellSNP-litev1.2.2
R Supporting Packages (R v4.1.2)
argparsev2.1.3
ComplexHeatmapv2.10.0
ComplexUpsetv1.3.3
vcfRv1.12.0
Seurat4.1.0
SingleCellExperimentv1.16.0
Python Supporting Packages (Python v3.7.2)
argparsev1.4.0
numpyv1.2.2
matplotlibv3.2.2
pandasv1.3.5
PyVCFv0.6.8
scipyv1.7.3
scvi-toolsv0.14.6
umap-learnv0.5.2