Installation¶
Singularity Image Download¶
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 singlularity image with:
wget -O Demuxafy.sif https://www.dropbox.com/scl/fi/g0cuyjwomdavom6u6kb2v/Demuxafy.sif?rlkey=xfey1agg371jo4lubsljfavkh& wget -O Demuxafy.sif.md5 https://www.dropbox.com/scl/fi/bk3p2k2440un6sb6psijn/Demuxafy.sif.md5?rlkey=x3vl8ejpfhjsrvmjanwzkxty9
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 version: 2.0.1 Image build date: 20 January, 2023
Software Group
Software
Version
Demultiplexing
Demuxalotv0.2.0
popscle
demuxlet
freemuxletv0.1-beta
Dropulationv2.5.4
scSplitv1.0.8.2
Souporcellv2.0
Vireov0.5.7
Doublet Detecting
DoubletDeconv1.1.6
DoubletDetectionv4.2
DoubletFinderv2.0.3
scDblFinderv1.12.0
scdsv1.13.1
scrubletv0.2.3
solov1.2
Supporting Softwares
minimap2v2.7-r654
bedtools2v2.30.0
vartrixv1.1.22
htslibv1.16
samtoolsv1.16
bcftoolsv1.16
freebayesv1.3.5
cellSNP-litev1.2.1
R Supporting Packages (R v4.2.2)
argparsev2.2.1
ComplexHeatmapv2.14.0
ComplexUpsetv1.3.3
vcfRv1.13.0.9999
Seuratv4.3.0
SingleCellExperimentv1.20.0
Python Supporting Packages (Python v3.7.2)
argparsev1.4.0
numpyv1.21.5
matplotlibv3.5.3
pandasv1.3.5
PyVCFv0.6.8
scipyv1.7.3
scvi-toolsv0.14.6
umap-learnv0.5.3
Notes About Singularity Images¶
Singularity images effectively store an operating system with files, softwares etc. that can be easily transported across different operating systems - ensuring reproducibility. Most HPCs have singularity installed making it easy to implement. There are some tips and tricks we have identified through using singularity images that we thought might help new users.
Tips and Tricks¶
1. Error: File Not Found¶
Reason
Singularity only loads the directories directly downstream from where you execute the singularity command. If any of the files that need to be accessed by the command are not downstream of the that location, you will receive an error similar to this one:
Failed to open file "/path/to/readfile.tsv" : No such file or directoryIf you then check for that file:
ll /path/to/readfile.tsvWe can see that the file does truly exist:
-rw-rw-r-- 1 user group 70636291 Dec 21 2020 /path/to/readfile.tsvSolution
The easiest solution to this problem is to “bind” a path upstream of all the files that will need to be accessed by your command:
singularity exec --bind /path Demuxafy.sif ...
If you don’t have access to Singularity on your HPC, you can ask your HPC administrators to install it (see the Singularity page)